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File:GACRC Teaching Cluster Training-Python.pdf

2026-09-02T13:56:27Z

Chelsea: Chelsea uploaded a new version of File:GACRC Teaching Cluster Training-Python.pdf

File:GACRC Teaching Cluster Training-Amber.pdf

2026-09-02T13:55:55Z

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File:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf

2026-09-02T13:54:01Z

Chelsea: Chelsea uploaded a new version of File:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf

Policies

2026-09-01T14:08:56Z

Chelsea: /* Research Data Compliance */

==Introduction to GACRC Policies==

The following policies are subject to revision, especially as the GACRC grows in scope and services. Your comments and questions will be useful to our policy formulation and refinement and are actively solicited by the GACRC Advisory Committee.

The GACRC computational infrastructure, including its servers, clusters, data stores, and other related devices are for the exclusive use of authorized users only.

Anyone using these systems expressly consents to abide by the policies of the University of Georgia and the Georgia Advanced Computing Resource Center and, accordingly, is subject to account termination and/or immediate disconnection from GACRC resources.

==GACRC Resource Usage==

The computational resources of the Georgia Advanced Computing Resource Center are to be used in direct support of research programs at the University of Georgia. Support is also provided for classes that teach computational methods, and provide training for high performance computing. The GACRC reserves the right to restrict access to its resources for course work if such work is deemed to present a negative impact to authorized research activities.

GACRC policies supplement UGA’s Policies on the Use of Computers, found at: [https://policy.uga.edu/policies#/programs/BJWfhwRra?group=Information%20Technology%20&bc=true&bcCurrent=Information%20Technology%20&bcItemType=programs&bc=true&bcCurrent=Acceptable%20Use%20Policy&bcGroup=Information%20Technology%20&bcItemType=programs UGA’s Policies on the Use of Computers]

==GACRC Eligibility and Access ==

Access to and use of the computing facilities managed by the Georgia Advanced Computing Resource Center are limited to persons affiliated with the University of Georgia or associated with research projects sponsored by UGA.

Affiliation in this context means faculty, research staff and supervised students of the University of Georgia. Faculty includes persons holding permanent or temporary appointments as well as adjunct faculty, instructors and visiting faculty while in residence at the University. It also includes those persons with faculty status such as research associates, research scientists, post-doctoral researchers and academic and service professionals. Staff includes all those non-faculty persons employed directly by the University in a research-support role. Graduate and undergraduate students who are members of faculty research labs are eligible for accounts as well. For directly affiliated users, accounts on the GACRC computers will remain active as long as the individuals hold the above status.

Access by non-UGA researchers and their students, affiliated to higher-education institutions or non-profit research organizations, for work on research projects conducted in collaboration with UGA Faculty is possible under the guidelines established by the Office of the Vice President for Research and the Office of International Education. A request for access can be forwarded to the GACRC by the UGA Faculty, providing details of the collaboration on a joint research project. Such Affiliate users will be considered part of the UGA Faculty’s group and will be under the Faculty’s responsibility. Affiliate users’ access will be granted for a fixed period of time, according to the expected length of the collaborative project. Renewal of affiliate accounts will be required annually.

All accounts will remain active no more than 30 days following a status change (i.e., leaving the university). Graduate instructional accounts will only remain active for the duration of the semester in which they are actually needed. HOME and PROJECT directories will be archived for at least 90 days, but no longer than 180 days after an account becomes inactive.

Requests for access by individuals other than those listed above should be directed to the Director of the Center for consideration with the GACRC Advisory Committee.

Access will be granted to a specific GACRC resource after appropriate training is undertaken with GACRC staff. Existing access to other GACRC resources is not a sufficient criteria for access to a new resource. No exceptions will be given to the training requirement.

==GACRC Identity Management==

Below are described the procedures for validating the identity of account users.

===UGA Users and Faculty Lab Groups===

*A UGA Faculty must first establish a GACRC group account using the instructions provided on the GACRC website (http://gacrc.uga.edu/accounts). The UGA Faculty can choose or not to obtain a GACRC user account affiliated with his/her group account.

*User accounts will only be created at the request of a UGA Faculty member, using the instructions provided on the GACRC website (http://gacrc.uga.edu/accounts).

*Upon acceptance of the application, the user will be notified via e-mail. The applicant’s UGA MyID and password will be used to log into the requested GACRC resources.

===Affiliate Users===

*A recognized Affiliate user must be sponsored by a UGA Faculty member through an established GACRC group account. The UGA Faculty involved in an established collaboration with the Affiliate user, must apply on behalf of the applicant by contacting the GACRC staff.

*A request will be made by the GACRC to EITS to allocate to the Affiliate a UGA MyID.

*Upon acceptance of the Affiliate user application, the Affiliate will be notified via e-mail. The Affiliate’s UGA MyID and password will be used to log into the requested GACRC resources.

===Protection of Passwords===

As described in UGA’s Password Policy, an account holder must never divulge their MyID and password to a third party. Only authorized account holders may access the resources of the GACRC. If a third party is found to be using an account holder’s login with or without the permission of the account holder, the account holder’s access privileges may be revoked at the sole discretion of the GACRC Manager or Director. Enforcement of this policy is under the responsibility of the Office of the Vice President for Information Technology’s Division of Information Security.

More information is found at the following EITS website:

[https://policy.uga.edu/policies#/programs/HJe8T3sH6?group=Information%20Technology%20&bc=true&bcCurrent=Information%20Technology%20&bcItemType=programs&bc=true&bcCurrent=Password%20Policy&bcGroup=Information%20Technology%20&bcItemType=programs UGA Policy Website]

==GACRC Storage Usage ==

===Some working definitions===

'''Snapshot''' - Copies of files that are stored on the same storage system as the original files. Snapshots are primarily used to recover files that have been accidentally deleted or corrupted within the recent past. Users are able to manage the file recovery tasks. Snapshots are not maintained beyond a defined rotation schedule, i.e., some number of hourly, daily, weekly, and monthly snapshots are kept on the storage system.

'''Backup''' - Copies of files and/or snapshots kept on a storage system (disk/tape) other than the one that the original files reside on. Backups are primarily used to recover files following a catastrophic failure of the original file or storage system. Backups require administrators to perform file system recovery tasks. Like snapshots, backups have a defined rotation schedule.

'''Archive''' - Copies of files that are not currently being accessed, on a resilient storage system dedicated to reliable long-term storage. Archives can be tape-based or disk-based, and typically part of a disaster recovery plan. The files may be copies of original data which is stored elsewhere (individual groups having their own copies), or the archive storage system may be fed by a dedicated "backup" storage system.

'''Active Projects''' – Projects that have on-going computational work being performed with files that are regularly created, accessed or modified.

===Policy Statement for SCRATCH File System===

The SCRATCH file system resides on a high-performance storage device and is to be used uniquely for temporary storage of files in use by actively running compute jobs. Files are to be removed from SCRATCH when a job completes, e.g. can be copied to the PROJECT file system. The SCRATCH file system is not backed up in any way and no snapshots are taken. The SCRATCH filesystem is mounted under /scratch on all the compute nodes, login nodes and data transfer nodes.

Any file that is not accessed or modified by a compute job in a time period of at least 30 days will be automatically deleted off the SCRATCH file system. Measures circumventing this policy will be monitored and actively discouraged.

There is no storage size quota for SCRATCH usage. Space is only limited by the physical size of the scratch space being used. If usage across the entire file system is more than 80% of total capacity, the GACRC will take additional measures to reduce usage to a more suitable level. Amongst possible actions, the GACRC may request/force users to clean up their SCRATCH directories or reduce temporarily the 30 day limit to a lower limit.

===Policy Statement for WORK File System===

The WORK file system resides on a high-performance storage device and is to be used for storing files that are frequently used by the group for computation. The WORK file system is '''NOT''' subject to the 30-day purge policy. The filesystem usage is controlled using a quota on the size and number of files that can be stored in a lab group's WORK area. Initially each group is given a 500GB and 100,000-file quota. The WORK file system is not backed up in any way and no snapshots are taken. The WORK filesystem is mounted under /work on all the compute nodes, login nodes and data transfer nodes. Each lab group has a directory under the /work directory.

The WORK file system is '''NOT''' subject to the 30-day purge policy. But if there is sufficient space consumption on the storage appliance, we reserve the right to ask users to clean up their WORK area. If the users do not respond in a timely fashion we will purge files beginning with the oldest ones. Please do not use the WORK area to store files long term.

===Policy Statement for HOME File System===

The HOME file system resides on a high-performance storage device and is used for long-term storage of files, typically programs and scripts, needed for analysis on the GACRC computing cluster.

All users have 200GB allocated for their HOME usage.

HOME directories will have daily, weekly and up to 3 monthly snapshots kept on the same storage unit to protect against accidental file deletion. HOME directories will also be backed-up on a different storage unit to protect against filesystem or hardware issues.

Users are strongly encouraged to make their own copies of critical files, while accepting any risks associated with HOME usage.

Snapshot retention, data purge and quota allocation policies are subject to change based on available storage capacity, users’ demand, equipment condition and availability, as well as any other conditions that might affect the provision of the HOME service.

===Policy Statement for PROJECT File System===

The PROJECT filesystem resides on lower-performance/higher-capacity storage devices.

This filesystem is accessible only from the GACRC’s transfer (xfer) nodes. PROJECT will not be accessible on Sapelo2's compute nodes.

This filesystem is to be used by groups for storage of active projects using Sapelo2. PROJECT should not be seen as a long-term repository, as it is not designed as such. Once a project is completed, data should be moved from the PROJECT space to user-managed storage, freeing up capacity for the next active project.

This filesystem is not for backing-up non-GACRC-related material, such as personal files (music, photos), office documents, and the like. If found, this material is subject to immediate deletion.

Access to the PROJECT filesystem is not supported through NFS to a destination outside of the Boyd Data Center, or through the use of the Samba or CIFS protocols. Transfer protocols available through the data transfer nodes are secure ftp, scp, rsync, GridFTP, amongst others.

Each group can request a PROJECT volume with an initial 1TB allocation, accessible by all users ascribed to the group, where the sharing of files will be enabled. Users are encouraged to consider their PROJECT space as the primary area to transfer compute job outputs. Additional space can be requested by a Faculty on behalf of his/her group.

The GACRC reserves the right to establish a cost-recovery rate for PROJECT storage beyond the initial 1TB allocation. Appropriate communications will take place in such an event.

PROJECT directories will have daily, weekly and monthly snapshots kept on the same storage unit to protect against accidental file deletion. PROJECT directories will also be backed-up on a different storage unit to protect against filesystem or hardware issues.

Users are strongly encouraged to make their own copies of critical files, while accepting any risks associated with PROJECT usage.

Snapshot retention, data purge and quota allocation policies are subject to change based on available storage capacity, users’ demand, equipment condition and availability, as well as any other conditions that might affect the provision of the PROJECT service.

==GACRC Software Policy==

The GACRC maintains a collection of program libraries and software packages to support research computing activities across diverse research domains. While a user can install a software package in their own environment, for the sake of general access across groups, and an appropriate deployment with current libraries, compilers and other dependencies, we strongly recommend that GACRC staff be asked to perform the installation or upgrade.

Any software that requires a signed license or contract, even if it is a click-through agreement, must absolutely be reviewed and handled by the Office of Legal Affairs before being signed by an appropriate signature authority. After the license or contract is accepted and the software is made available, GACRC users must fully comply and use the software in a way that does not violate any terms of the license or contract. Further information on licensing issues can be found at the following EITS website:


As a matter of policy, the GACRC will not purchase any commercial software for the use of a single group or a small number of groups. Commercial software currently purchased and maintained by the GACRC are of general interest and applicability to the whole UGA research community. The GACRC will however install and maintain a group-purchased commercial software, which complies with the above comments on licenses and contracts.

== AI Workflows and GPU Usage Expectations ==
GACRC is seeing a significant increase in the use of AI-assisted tools and workflows, including code assistants, automated job generation, and model-serving frameworks. These patterns are placing increasing pressure on shared resources, particularly high-end GPUs and interactive systems. As a result, GACRC is issuing a policy update to clarify and reinforce expectations for shared GPU usage, interactive workflows, and AI-driven activity.

'''1. Monitoring and Enforcement'''

The GACRC actively monitors system usage to ensure fair access, system stability, and compliance with institutional policies. Patterns of concern include:

* Long-running interactive GPU sessions with low or intermittent utilization
* Persistent or service-like workloads running on shared compute nodes
* Running of software on the login/head node, including remote development environments
* Excessive or automated job submission that impacts scheduler performance
* Large-scale filesystem activity that degrades shared storage performance

If these patterns persist, the GACRC will take additional action, including applying stricter limits, modifying scheduling policies, terminating compute jobs, or temporarily or permanently removing user access to GACRC resources.

'''2. GPU Usage and Interactive Work'''

High-end GPUs (e.g., A100, H100) are scarce shared resources and are intended for scheduled batch workloads. '''Long-running or persistent interactive use of these GPUs is not permitted.''' Holding GPUs for extended periods—especially when usage is intermittent or low—reduces availability for other researchers and undermines the scheduling system. Interactive GPU sessions must be limited to short-duration development and debugging. Production workloads must be submitted through the batch scheduler. This policy statement does not apply if the GPU resources are buy-in compute nodes.

'''3. Persistent and Service-Like Workloads'''

Shared compute nodes are not designed to support persistent or service-like workloads. This includes model-serving endpoints, long-lived notebooks, AI assistants, and agent-based systems. '''Running such workloads on shared GPU resources is not permitted.''' Groups requiring persistent or always-on GPU-backed services should work with GACRC to identify appropriate alternatives. This policy statement does not apply if the GPU resources are buy-in compute nodes.

'''4. Login Node Usage and Development Environments'''

Login nodes are reserved for lightweight activities such as code editing, and job submission. '''Running persistent or resource-intensive processes on login nodes—including remote IDE backends such as VSCode, Cursor, or similar tools—is not permitted.''' Users who require interactive development environments should use [[OnDemand|'''Open OnDemand''']] '''or other approved interactive compute options''', which provide a supported way to run these tools without impacting the shared login infrastructure.

'''5. Automated and AI-Driven Workflows'''

AI-assisted and automated workflows must be used in a controlled manner. Users are responsible for all activity executed under their accounts. Workflows that generate excessive job submissions, recursive execution patterns, or unintended system load are not acceptable.

'''6. Data, Software, and Filesystem Use'''

Users are responsible for ensuring that models and software are obtained from trusted sources and do not introduce security risks. Sensitive or restricted data must not be transmitted to external AI services in violation of institutional or sponsor requirements. AI tools that scan or index files must be limited to appropriate project directories. Large-scale scanning of shared filesystems may be restricted.

'''Finally, a reminder of the Archnews memo of March 26, 2025 from USG Chancellor Perdue in which the following software restrictions were announced:'''

“As part of this continued effort, Governor Kemp’s administration has updated the list of prohibited apps and websites. In addition to TikTok, WeChat, and Telegram, the following apps are now also disallowed from use on any state-owned and/or -issued devices, including mobile phones, laptops, and tablets:

# RedNote (social media app)
# DeepSeek (AI chatbot)
# Webull (online stock trading)
# Tiger Brokers (online stock trading)
# Moomoo (investing app)
# Lemon8 (social media app)

'''Please work with the GACRC to find the most appropriate way to accomplish your research goals.'''

We recognize that AI workflows are evolving rapidly. If your research requires capabilities that do not fit within these expectations, please contact the GACRC. We are committed to working with researchers to support these use cases in a sustainable way.

==Security==

To minimize disruption of service, protect data integrity, conserve facility resources and maximize the effectiveness of staff support, the GACRC maintains strict security requirements for access to GACRC resources. Over time, the enforcement of these requirements will become increasingly strict, with the goal of preventing any access to the GACRC resources by any person or any device that is not in strict compliance with these requirements.

===Operating Systems===

Any computer accessing the GACRC for any purpose must run a currently supported operating system, updated to the latest version and update (patch) levels.

===Anti-Virus Software===

Any computer accessing the GACRC for any purpose must meet minimum levels of anti-virus protection. Any computer used by an account holder must have anti-virus software from a source approved by UGA’s Office of Information Security must have that virus protection activated, and must have automatic updates activated.

More information can be found at the following EITS website:

[https://policy.uga.edu/policies#/programs/BySr6vy8a?q=%20Minimum%20Security%20Standards%20Policy&&limit=20&skip=0&bc=true&bcCurrent=Minimum%20Security%20Standards%20Policy&bcItemType=programs Minimum Security Standards Policy]

===Suspiciously Behaving Software===

Any software that behaves in a suspicious manner may at any time be terminated and/or deleted from GACRC resources at the sole discretion of the GACRC’s systems administrator(s), manager, Director, or EITS information security staff.

===Suspiciously Behaving Networks and Devices===

Any connection from any device to the GACRC may be terminated at any time, if the device or the connection or a network to which the device is attached appears to be not in compliance with UGA’s security requirements, is behaving suspiciously, or if a threat emerges requiring termination for intrusion prevention at the sole discretion of the GACRC’s systems administrator(s), manager, Director, or EITS information security staff.

===Account Holder Responsibility===

The account holder is responsible for diligently monitoring their account and compliance with the GACRC’s operating system, intrusion and virus protection standards. The account holder will be duly notified if GACRC personnel determine that minimum security requirements are not met. Specific actions will be requested of the account holder and compliance to these will be expected in a timely fashion. An account holder’s privileges to use GACRC facilities may be terminated by the GACRC Manager or Director at any time, without notice if, in the opinion of either, the account holder is reluctant or averse to practicing diligence in meeting the GACRC’s minimum requirements for intrusion and/or anti-viral protection.

==Resolving Disagreements about Revocation of Privileges or Provisioning Resources==

The Director of the Georgia Advanced Computing Resource Center has full authority to revoke a user's privileges or deny the request of a new resource allocation. The decision to revoke a user's privileges will be based on, but not limited to, abuses of the UGA Policies on the Use of Computers and/or abuses of the UGA Password Policy.

If an account holder is denied a request for provisioning of GACRC resources or resource privileges are revoked, the account holder’s Department Head may appeal to the Vice President for Research and the Vice President for Information Technology. Their decision will be informed by the Director of the GACRC, the Chief Technology Officer as well as the Associate Chief Information Officer for Information Security. The decision of the Vice President for Research and Vice President for Information Technology is final.

==System Maintenance and Downtime==

===Planned Maintenance===

The GACRC instituted monthly maintenance windows in order to perform maintenance operations requiring system operations to be reduced or interrupted.

The schedule will be as follows:

*The last Wednesday of each month from 10AM to 4PM will be reserved for partial cluster maintenance.

*Twice a year, a two-day shut-down of GACRC services will be scheduled for more complex maintenance operations. These will occur on the last Tuesday and Wednesday of the months of January and July.

These maintenance windows represent periods when the GACRC may choose to drain the queues of running jobs and suspend access to the Sapelo2 cluster, as well as storage devices for maintenance purposes. Interruptions will be kept as brief as possible.

The GACRC will notify all users at least 10 days in advance that a maintenance window will be in effect. The notification will describe the nature and extent (partial or full) of the interruptions of cluster and or storage services. In case a maintenance window has to be extended due to unavoidable technical reasons, adequate communications will be made to all users.

The impact of the outages will vary, and the GACRC will do its best to preserve pending and running jobs, which is often very doable. Nevertheless, users will need to plan their job submissions around the maintenance windows.

===Unplanned Maintenance and System Outage===

From time to time, hardware, software, and/or environmental factors may cause a system or subsystem to malfunction, causing disruption to service. Also, there may be circumstances or events related to possible security issues or intrusions which will cause GACRC staff to take systems offline while the nature of the apparent breach is analyzed and appropriate action is taken.

Whenever possible, account holders will be notified by e-mail of these outages in advance, but that may not always be possible. Account holders will be notified by e-mail if the disruption should last more than 30 minutes.

GACRC staff will strive to preserve the work and/or prevent disruption of jobs in process during such outages. However, there may be circumstances which cause disruption of jobs and loss of data. Users are encouraged to implement methods in their code which minimize the effect of unplanned interruption of a job’s execution, such as checkpoints. Users are also strongly encouraged to maintain copies of files of importance.

==Regulatory Compliance==

The GACRC as an infrastructure and service provider does NOT currently warrant that its practices or facilities meet government-mandated requirements for the storage and protection of sensitive, private or classified information. Users may not store such information on GACRC facilities. In other words, data that falls under HIPAA, FERPA, FISMA or similar regulatory requirements, may not be stored, computed against or otherwise transacted through, or with, GACRC infrastructure.

The GACRC and its users must comply with all existing Federal export control regulations for services and infrastructure. Research groups must agree to NOT install or use any software or data that falls under Export Control regulations. More information on the subject of Export Control is available at the following OVPR website:

http://research.uga.edu/export-control/

Copyrighted materials are prohibited without proper authorization. Additionally, illegal content is prohibited.

Non-compliance with any such Federal requirements might impact GACRC operations or delivery of services and could place the GACRC and UGA at risk. If a research group is found to be in non-compliance, then account access will be immediately suspended, while an investigation by EITS’s Information Security division is instigated.

===Disclosure===

Research groups that are involved in activities that store protected data on GACRC infrastructure must contact immediately the GACRC Director in order to address the issue. Depending on circumstances, accommodations might be possible for such activities.

===Research Data Compliance===

Research Data Management is a critical factor in both obtaining federal funding from the NSF, NIH, DoD and other federal agencies, and in the conduct of funded research. Responsibility in maintaining and preserving research data, as detailed in data management plans submitted to Federal funding agencies, is entirely placed upon the research faculty, post docs, and graduate students conducting the research. The GACRC will help by providing information and assistance, but will not be responsible to ensure compliance with a project’s data management plan.

During the phase of proposal writing, arrangements can be discussed and agreed upon as to the GACRC playing an active role, and ensuring the provision of specific services towards the compliance of a data management plan. Depending on the complexity or the nature of the proposed services, the GACRC might require the purchase of specific hardware/software and/or the availability of a %FTE salary and benefits.

More information on data management plans can be found at the UGA Library's [https://guides.libs.uga.edu/data-services/data-management Data Management page].

Policies

2026-09-01T14:04:53Z

Chelsea: /* Research Data Compliance */

==Introduction to GACRC Policies==

The following policies are subject to revision, especially as the GACRC grows in scope and services. Your comments and questions will be useful to our policy formulation and refinement and are actively solicited by the GACRC Advisory Committee.

The GACRC computational infrastructure, including its servers, clusters, data stores, and other related devices are for the exclusive use of authorized users only.

Anyone using these systems expressly consents to abide by the policies of the University of Georgia and the Georgia Advanced Computing Resource Center and, accordingly, is subject to account termination and/or immediate disconnection from GACRC resources.

==GACRC Resource Usage==

The computational resources of the Georgia Advanced Computing Resource Center are to be used in direct support of research programs at the University of Georgia. Support is also provided for classes that teach computational methods, and provide training for high performance computing. The GACRC reserves the right to restrict access to its resources for course work if such work is deemed to present a negative impact to authorized research activities.

GACRC policies supplement UGA’s Policies on the Use of Computers, found at: [https://policy.uga.edu/policies#/programs/BJWfhwRra?group=Information%20Technology%20&bc=true&bcCurrent=Information%20Technology%20&bcItemType=programs&bc=true&bcCurrent=Acceptable%20Use%20Policy&bcGroup=Information%20Technology%20&bcItemType=programs UGA’s Policies on the Use of Computers]

==GACRC Eligibility and Access ==

Access to and use of the computing facilities managed by the Georgia Advanced Computing Resource Center are limited to persons affiliated with the University of Georgia or associated with research projects sponsored by UGA.

Affiliation in this context means faculty, research staff and supervised students of the University of Georgia. Faculty includes persons holding permanent or temporary appointments as well as adjunct faculty, instructors and visiting faculty while in residence at the University. It also includes those persons with faculty status such as research associates, research scientists, post-doctoral researchers and academic and service professionals. Staff includes all those non-faculty persons employed directly by the University in a research-support role. Graduate and undergraduate students who are members of faculty research labs are eligible for accounts as well. For directly affiliated users, accounts on the GACRC computers will remain active as long as the individuals hold the above status.

Access by non-UGA researchers and their students, affiliated to higher-education institutions or non-profit research organizations, for work on research projects conducted in collaboration with UGA Faculty is possible under the guidelines established by the Office of the Vice President for Research and the Office of International Education. A request for access can be forwarded to the GACRC by the UGA Faculty, providing details of the collaboration on a joint research project. Such Affiliate users will be considered part of the UGA Faculty’s group and will be under the Faculty’s responsibility. Affiliate users’ access will be granted for a fixed period of time, according to the expected length of the collaborative project. Renewal of affiliate accounts will be required annually.

All accounts will remain active no more than 30 days following a status change (i.e., leaving the university). Graduate instructional accounts will only remain active for the duration of the semester in which they are actually needed. HOME and PROJECT directories will be archived for at least 90 days, but no longer than 180 days after an account becomes inactive.

Requests for access by individuals other than those listed above should be directed to the Director of the Center for consideration with the GACRC Advisory Committee.

Access will be granted to a specific GACRC resource after appropriate training is undertaken with GACRC staff. Existing access to other GACRC resources is not a sufficient criteria for access to a new resource. No exceptions will be given to the training requirement.

==GACRC Identity Management==

Below are described the procedures for validating the identity of account users.

===UGA Users and Faculty Lab Groups===

*A UGA Faculty must first establish a GACRC group account using the instructions provided on the GACRC website (http://gacrc.uga.edu/accounts). The UGA Faculty can choose or not to obtain a GACRC user account affiliated with his/her group account.

*User accounts will only be created at the request of a UGA Faculty member, using the instructions provided on the GACRC website (http://gacrc.uga.edu/accounts).

*Upon acceptance of the application, the user will be notified via e-mail. The applicant’s UGA MyID and password will be used to log into the requested GACRC resources.

===Affiliate Users===

*A recognized Affiliate user must be sponsored by a UGA Faculty member through an established GACRC group account. The UGA Faculty involved in an established collaboration with the Affiliate user, must apply on behalf of the applicant by contacting the GACRC staff.

*A request will be made by the GACRC to EITS to allocate to the Affiliate a UGA MyID.

*Upon acceptance of the Affiliate user application, the Affiliate will be notified via e-mail. The Affiliate’s UGA MyID and password will be used to log into the requested GACRC resources.

===Protection of Passwords===

As described in UGA’s Password Policy, an account holder must never divulge their MyID and password to a third party. Only authorized account holders may access the resources of the GACRC. If a third party is found to be using an account holder’s login with or without the permission of the account holder, the account holder’s access privileges may be revoked at the sole discretion of the GACRC Manager or Director. Enforcement of this policy is under the responsibility of the Office of the Vice President for Information Technology’s Division of Information Security.

More information is found at the following EITS website:

[https://policy.uga.edu/policies#/programs/HJe8T3sH6?group=Information%20Technology%20&bc=true&bcCurrent=Information%20Technology%20&bcItemType=programs&bc=true&bcCurrent=Password%20Policy&bcGroup=Information%20Technology%20&bcItemType=programs UGA Policy Website]

==GACRC Storage Usage ==

===Some working definitions===

'''Snapshot''' - Copies of files that are stored on the same storage system as the original files. Snapshots are primarily used to recover files that have been accidentally deleted or corrupted within the recent past. Users are able to manage the file recovery tasks. Snapshots are not maintained beyond a defined rotation schedule, i.e., some number of hourly, daily, weekly, and monthly snapshots are kept on the storage system.

'''Backup''' - Copies of files and/or snapshots kept on a storage system (disk/tape) other than the one that the original files reside on. Backups are primarily used to recover files following a catastrophic failure of the original file or storage system. Backups require administrators to perform file system recovery tasks. Like snapshots, backups have a defined rotation schedule.

'''Archive''' - Copies of files that are not currently being accessed, on a resilient storage system dedicated to reliable long-term storage. Archives can be tape-based or disk-based, and typically part of a disaster recovery plan. The files may be copies of original data which is stored elsewhere (individual groups having their own copies), or the archive storage system may be fed by a dedicated "backup" storage system.

'''Active Projects''' – Projects that have on-going computational work being performed with files that are regularly created, accessed or modified.

===Policy Statement for SCRATCH File System===

The SCRATCH file system resides on a high-performance storage device and is to be used uniquely for temporary storage of files in use by actively running compute jobs. Files are to be removed from SCRATCH when a job completes, e.g. can be copied to the PROJECT file system. The SCRATCH file system is not backed up in any way and no snapshots are taken. The SCRATCH filesystem is mounted under /scratch on all the compute nodes, login nodes and data transfer nodes.

Any file that is not accessed or modified by a compute job in a time period of at least 30 days will be automatically deleted off the SCRATCH file system. Measures circumventing this policy will be monitored and actively discouraged.

There is no storage size quota for SCRATCH usage. Space is only limited by the physical size of the scratch space being used. If usage across the entire file system is more than 80% of total capacity, the GACRC will take additional measures to reduce usage to a more suitable level. Amongst possible actions, the GACRC may request/force users to clean up their SCRATCH directories or reduce temporarily the 30 day limit to a lower limit.

===Policy Statement for WORK File System===

The WORK file system resides on a high-performance storage device and is to be used for storing files that are frequently used by the group for computation. The WORK file system is '''NOT''' subject to the 30-day purge policy. The filesystem usage is controlled using a quota on the size and number of files that can be stored in a lab group's WORK area. Initially each group is given a 500GB and 100,000-file quota. The WORK file system is not backed up in any way and no snapshots are taken. The WORK filesystem is mounted under /work on all the compute nodes, login nodes and data transfer nodes. Each lab group has a directory under the /work directory.

The WORK file system is '''NOT''' subject to the 30-day purge policy. But if there is sufficient space consumption on the storage appliance, we reserve the right to ask users to clean up their WORK area. If the users do not respond in a timely fashion we will purge files beginning with the oldest ones. Please do not use the WORK area to store files long term.

===Policy Statement for HOME File System===

The HOME file system resides on a high-performance storage device and is used for long-term storage of files, typically programs and scripts, needed for analysis on the GACRC computing cluster.

All users have 200GB allocated for their HOME usage.

HOME directories will have daily, weekly and up to 3 monthly snapshots kept on the same storage unit to protect against accidental file deletion. HOME directories will also be backed-up on a different storage unit to protect against filesystem or hardware issues.

Users are strongly encouraged to make their own copies of critical files, while accepting any risks associated with HOME usage.

Snapshot retention, data purge and quota allocation policies are subject to change based on available storage capacity, users’ demand, equipment condition and availability, as well as any other conditions that might affect the provision of the HOME service.

===Policy Statement for PROJECT File System===

The PROJECT filesystem resides on lower-performance/higher-capacity storage devices.

This filesystem is accessible only from the GACRC’s transfer (xfer) nodes. PROJECT will not be accessible on Sapelo2's compute nodes.

This filesystem is to be used by groups for storage of active projects using Sapelo2. PROJECT should not be seen as a long-term repository, as it is not designed as such. Once a project is completed, data should be moved from the PROJECT space to user-managed storage, freeing up capacity for the next active project.

This filesystem is not for backing-up non-GACRC-related material, such as personal files (music, photos), office documents, and the like. If found, this material is subject to immediate deletion.

Access to the PROJECT filesystem is not supported through NFS to a destination outside of the Boyd Data Center, or through the use of the Samba or CIFS protocols. Transfer protocols available through the data transfer nodes are secure ftp, scp, rsync, GridFTP, amongst others.

Each group can request a PROJECT volume with an initial 1TB allocation, accessible by all users ascribed to the group, where the sharing of files will be enabled. Users are encouraged to consider their PROJECT space as the primary area to transfer compute job outputs. Additional space can be requested by a Faculty on behalf of his/her group.

The GACRC reserves the right to establish a cost-recovery rate for PROJECT storage beyond the initial 1TB allocation. Appropriate communications will take place in such an event.

PROJECT directories will have daily, weekly and monthly snapshots kept on the same storage unit to protect against accidental file deletion. PROJECT directories will also be backed-up on a different storage unit to protect against filesystem or hardware issues.

Users are strongly encouraged to make their own copies of critical files, while accepting any risks associated with PROJECT usage.

Snapshot retention, data purge and quota allocation policies are subject to change based on available storage capacity, users’ demand, equipment condition and availability, as well as any other conditions that might affect the provision of the PROJECT service.

==GACRC Software Policy==

The GACRC maintains a collection of program libraries and software packages to support research computing activities across diverse research domains. While a user can install a software package in their own environment, for the sake of general access across groups, and an appropriate deployment with current libraries, compilers and other dependencies, we strongly recommend that GACRC staff be asked to perform the installation or upgrade.

Any software that requires a signed license or contract, even if it is a click-through agreement, must absolutely be reviewed and handled by the Office of Legal Affairs before being signed by an appropriate signature authority. After the license or contract is accepted and the software is made available, GACRC users must fully comply and use the software in a way that does not violate any terms of the license or contract. Further information on licensing issues can be found at the following EITS website:


As a matter of policy, the GACRC will not purchase any commercial software for the use of a single group or a small number of groups. Commercial software currently purchased and maintained by the GACRC are of general interest and applicability to the whole UGA research community. The GACRC will however install and maintain a group-purchased commercial software, which complies with the above comments on licenses and contracts.

== AI Workflows and GPU Usage Expectations ==
GACRC is seeing a significant increase in the use of AI-assisted tools and workflows, including code assistants, automated job generation, and model-serving frameworks. These patterns are placing increasing pressure on shared resources, particularly high-end GPUs and interactive systems. As a result, GACRC is issuing a policy update to clarify and reinforce expectations for shared GPU usage, interactive workflows, and AI-driven activity.

'''1. Monitoring and Enforcement'''

The GACRC actively monitors system usage to ensure fair access, system stability, and compliance with institutional policies. Patterns of concern include:

* Long-running interactive GPU sessions with low or intermittent utilization
* Persistent or service-like workloads running on shared compute nodes
* Running of software on the login/head node, including remote development environments
* Excessive or automated job submission that impacts scheduler performance
* Large-scale filesystem activity that degrades shared storage performance

If these patterns persist, the GACRC will take additional action, including applying stricter limits, modifying scheduling policies, terminating compute jobs, or temporarily or permanently removing user access to GACRC resources.

'''2. GPU Usage and Interactive Work'''

High-end GPUs (e.g., A100, H100) are scarce shared resources and are intended for scheduled batch workloads. '''Long-running or persistent interactive use of these GPUs is not permitted.''' Holding GPUs for extended periods—especially when usage is intermittent or low—reduces availability for other researchers and undermines the scheduling system. Interactive GPU sessions must be limited to short-duration development and debugging. Production workloads must be submitted through the batch scheduler. This policy statement does not apply if the GPU resources are buy-in compute nodes.

'''3. Persistent and Service-Like Workloads'''

Shared compute nodes are not designed to support persistent or service-like workloads. This includes model-serving endpoints, long-lived notebooks, AI assistants, and agent-based systems. '''Running such workloads on shared GPU resources is not permitted.''' Groups requiring persistent or always-on GPU-backed services should work with GACRC to identify appropriate alternatives. This policy statement does not apply if the GPU resources are buy-in compute nodes.

'''4. Login Node Usage and Development Environments'''

Login nodes are reserved for lightweight activities such as code editing, and job submission. '''Running persistent or resource-intensive processes on login nodes—including remote IDE backends such as VSCode, Cursor, or similar tools—is not permitted.''' Users who require interactive development environments should use [[OnDemand|'''Open OnDemand''']] '''or other approved interactive compute options''', which provide a supported way to run these tools without impacting the shared login infrastructure.

'''5. Automated and AI-Driven Workflows'''

AI-assisted and automated workflows must be used in a controlled manner. Users are responsible for all activity executed under their accounts. Workflows that generate excessive job submissions, recursive execution patterns, or unintended system load are not acceptable.

'''6. Data, Software, and Filesystem Use'''

Users are responsible for ensuring that models and software are obtained from trusted sources and do not introduce security risks. Sensitive or restricted data must not be transmitted to external AI services in violation of institutional or sponsor requirements. AI tools that scan or index files must be limited to appropriate project directories. Large-scale scanning of shared filesystems may be restricted.

'''Finally, a reminder of the Archnews memo of March 26, 2025 from USG Chancellor Perdue in which the following software restrictions were announced:'''

“As part of this continued effort, Governor Kemp’s administration has updated the list of prohibited apps and websites. In addition to TikTok, WeChat, and Telegram, the following apps are now also disallowed from use on any state-owned and/or -issued devices, including mobile phones, laptops, and tablets:

# RedNote (social media app)
# DeepSeek (AI chatbot)
# Webull (online stock trading)
# Tiger Brokers (online stock trading)
# Moomoo (investing app)
# Lemon8 (social media app)

'''Please work with the GACRC to find the most appropriate way to accomplish your research goals.'''

We recognize that AI workflows are evolving rapidly. If your research requires capabilities that do not fit within these expectations, please contact the GACRC. We are committed to working with researchers to support these use cases in a sustainable way.

==Security==

To minimize disruption of service, protect data integrity, conserve facility resources and maximize the effectiveness of staff support, the GACRC maintains strict security requirements for access to GACRC resources. Over time, the enforcement of these requirements will become increasingly strict, with the goal of preventing any access to the GACRC resources by any person or any device that is not in strict compliance with these requirements.

===Operating Systems===

Any computer accessing the GACRC for any purpose must run a currently supported operating system, updated to the latest version and update (patch) levels.

===Anti-Virus Software===

Any computer accessing the GACRC for any purpose must meet minimum levels of anti-virus protection. Any computer used by an account holder must have anti-virus software from a source approved by UGA’s Office of Information Security must have that virus protection activated, and must have automatic updates activated.

More information can be found at the following EITS website:

[https://policy.uga.edu/policies#/programs/BySr6vy8a?q=%20Minimum%20Security%20Standards%20Policy&&limit=20&skip=0&bc=true&bcCurrent=Minimum%20Security%20Standards%20Policy&bcItemType=programs Minimum Security Standards Policy]

===Suspiciously Behaving Software===

Any software that behaves in a suspicious manner may at any time be terminated and/or deleted from GACRC resources at the sole discretion of the GACRC’s systems administrator(s), manager, Director, or EITS information security staff.

===Suspiciously Behaving Networks and Devices===

Any connection from any device to the GACRC may be terminated at any time, if the device or the connection or a network to which the device is attached appears to be not in compliance with UGA’s security requirements, is behaving suspiciously, or if a threat emerges requiring termination for intrusion prevention at the sole discretion of the GACRC’s systems administrator(s), manager, Director, or EITS information security staff.

===Account Holder Responsibility===

The account holder is responsible for diligently monitoring their account and compliance with the GACRC’s operating system, intrusion and virus protection standards. The account holder will be duly notified if GACRC personnel determine that minimum security requirements are not met. Specific actions will be requested of the account holder and compliance to these will be expected in a timely fashion. An account holder’s privileges to use GACRC facilities may be terminated by the GACRC Manager or Director at any time, without notice if, in the opinion of either, the account holder is reluctant or averse to practicing diligence in meeting the GACRC’s minimum requirements for intrusion and/or anti-viral protection.

==Resolving Disagreements about Revocation of Privileges or Provisioning Resources==

The Director of the Georgia Advanced Computing Resource Center has full authority to revoke a user's privileges or deny the request of a new resource allocation. The decision to revoke a user's privileges will be based on, but not limited to, abuses of the UGA Policies on the Use of Computers and/or abuses of the UGA Password Policy.

If an account holder is denied a request for provisioning of GACRC resources or resource privileges are revoked, the account holder’s Department Head may appeal to the Vice President for Research and the Vice President for Information Technology. Their decision will be informed by the Director of the GACRC, the Chief Technology Officer as well as the Associate Chief Information Officer for Information Security. The decision of the Vice President for Research and Vice President for Information Technology is final.

==System Maintenance and Downtime==

===Planned Maintenance===

The GACRC instituted monthly maintenance windows in order to perform maintenance operations requiring system operations to be reduced or interrupted.

The schedule will be as follows:

*The last Wednesday of each month from 10AM to 4PM will be reserved for partial cluster maintenance.

*Twice a year, a two-day shut-down of GACRC services will be scheduled for more complex maintenance operations. These will occur on the last Tuesday and Wednesday of the months of January and July.

These maintenance windows represent periods when the GACRC may choose to drain the queues of running jobs and suspend access to the Sapelo2 cluster, as well as storage devices for maintenance purposes. Interruptions will be kept as brief as possible.

The GACRC will notify all users at least 10 days in advance that a maintenance window will be in effect. The notification will describe the nature and extent (partial or full) of the interruptions of cluster and or storage services. In case a maintenance window has to be extended due to unavoidable technical reasons, adequate communications will be made to all users.

The impact of the outages will vary, and the GACRC will do its best to preserve pending and running jobs, which is often very doable. Nevertheless, users will need to plan their job submissions around the maintenance windows.

===Unplanned Maintenance and System Outage===

From time to time, hardware, software, and/or environmental factors may cause a system or subsystem to malfunction, causing disruption to service. Also, there may be circumstances or events related to possible security issues or intrusions which will cause GACRC staff to take systems offline while the nature of the apparent breach is analyzed and appropriate action is taken.

Whenever possible, account holders will be notified by e-mail of these outages in advance, but that may not always be possible. Account holders will be notified by e-mail if the disruption should last more than 30 minutes.

GACRC staff will strive to preserve the work and/or prevent disruption of jobs in process during such outages. However, there may be circumstances which cause disruption of jobs and loss of data. Users are encouraged to implement methods in their code which minimize the effect of unplanned interruption of a job’s execution, such as checkpoints. Users are also strongly encouraged to maintain copies of files of importance.

==Regulatory Compliance==

The GACRC as an infrastructure and service provider does NOT currently warrant that its practices or facilities meet government-mandated requirements for the storage and protection of sensitive, private or classified information. Users may not store such information on GACRC facilities. In other words, data that falls under HIPAA, FERPA, FISMA or similar regulatory requirements, may not be stored, computed against or otherwise transacted through, or with, GACRC infrastructure.

The GACRC and its users must comply with all existing Federal export control regulations for services and infrastructure. Research groups must agree to NOT install or use any software or data that falls under Export Control regulations. More information on the subject of Export Control is available at the following OVPR website:

http://research.uga.edu/export-control/

Copyrighted materials are prohibited without proper authorization. Additionally, illegal content is prohibited.

Non-compliance with any such Federal requirements might impact GACRC operations or delivery of services and could place the GACRC and UGA at risk. If a research group is found to be in non-compliance, then account access will be immediately suspended, while an investigation by EITS’s Information Security division is instigated.

===Disclosure===

Research groups that are involved in activities that store protected data on GACRC infrastructure must contact immediately the GACRC Director in order to address the issue. Depending on circumstances, accommodations might be possible for such activities.

===Research Data Compliance===

Research Data Management is a critical factor in both obtaining federal funding from the NSF, NIH, DoD and other federal agencies, and in the conduct of funded research. Responsibility in maintaining and preserving research data, as detailed in data management plans submitted to Federal funding agencies, is entirely placed upon the research faculty, post docs, and graduate students conducting the research. The GACRC will help by providing information and assistance, but will not be responsible to ensure compliance with a project’s data management plan.

During the phase of proposal writing, arrangements can be discussed and agreed upon as to the GACRC playing an active role, and ensuring the provision of specific services towards the compliance of a data management plan. Depending on the complexity or the nature of the proposed services, the GACRC might require the purchase of specific hardware/software and/or the availability of a %FTE salary and benefits.

More information on data management plans can be found [http://guides.libs.uga.edu/c.php?g=349946&p=2363161 here].

File:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf

2026-08-20T13:39:28Z

Chelsea: Chelsea uploaded a new version of File:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf

Training

2026-08-11T13:47:57Z

Chelsea: /* Linux Training for Linux-inexperienced Cluster New Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''September 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)

4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)

5. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|August 20th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|September 11th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|September 16th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|September 24th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|August 18th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|September 9th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|September 14th, Monday, 1:00 PM - 3:00 PM
|-
|v
|September 22nd, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|September 18th, Friday, 1:00 PM - 3:00 PM
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|September 23rd, Wednesday, 2:00 PM - 2:45 PM
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|September 25th, Friday, 1:00 PM - 3:00 PM
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

===Sapelo2 Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

===Teaching Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

===Linux Training for New Cluster Users===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

===Installing Software Packages in Virtual Environments on Sapelo2===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

===Job Parallelization with GNU Parallel and Slurm Arrays===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}



===Topical Sessions===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

===Out-Reach/In-Class Talk===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|Fall 2026
|
|[[Media:GACRC_Teaching_Cluster_Training-Python.pdf]]
|-
|Fall 2026
|
|[[Media:GACRC_Teaching_Cluster_Training-Amber.pdf]]
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2026-08-11T13:40:01Z

Chelsea: /* Event Schedule */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''August 2026''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|August 20th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|September 11th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|September 16th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|September 24th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|July 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 20th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 5th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 10th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 18th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

===Sapelo2 Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

===Teaching Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

===Linux Training for New Cluster Users===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

===Installing Software Packages in Virtual Environments on Sapelo2===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

===Job Parallelization with GNU Parallel and Slurm Arrays===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}



===Topical Sessions===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

===Out-Reach/In-Class Talk===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|Fall 2026
|
|[[Media:GACRC_Teaching_Cluster_Training-Python.pdf]]
|-
|Fall 2026
|
|[[Media:GACRC_Teaching_Cluster_Training-Amber.pdf]]
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2026-07-30T20:08:46Z

Chelsea: /* Out-Reach/In-Class Talk */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''August 2026''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|July 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|July 22nd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 7th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 12th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 20th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|July 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 20th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 5th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 10th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 18th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

===Sapelo2 Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

===Teaching Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

===Linux Training for New Cluster Users===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

===Installing Software Packages in Virtual Environments on Sapelo2===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

===Job Parallelization with GNU Parallel and Slurm Arrays===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}



===Topical Sessions===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

===Out-Reach/In-Class Talk===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|Fall 2026
|
|[[:Media:GACRC Teaching Cluster Training-Python.pdf]]
|-
|Fall 2026
|
|[[:Media:GACRC Teaching Cluster Training-Amber.pdf]]
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2026-07-30T20:08:04Z

Chelsea: /* Out-Reach/In-Class Talk */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''August 2026''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|July 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|July 22nd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 7th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 12th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 20th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|July 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 20th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 5th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 10th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 18th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

===Sapelo2 Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

===Teaching Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

===Linux Training for New Cluster Users===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

===Installing Software Packages in Virtual Environments on Sapelo2===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

===Job Parallelization with GNU Parallel and Slurm Arrays===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}



===Topical Sessions===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

===Out-Reach/In-Class Talk===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|Fall 2026
|
|[[:File:GACRC Teaching Cluster Training-Python.pdf]]
|-
|Fall 2026
|
|[[:File:GACRC Teaching Cluster Training-Amber.pdf]]
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

File:GACRC Teaching Cluster Training-Amber.pdf

2026-07-30T20:06:22Z

Chelsea:

File:GACRC Teaching Cluster Training-Python.pdf

2026-07-30T20:05:49Z

Chelsea:

Training

2026-07-30T20:04:57Z

Chelsea: /* Out-Reach/In-Class Talk */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''August 2026''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|July 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|July 22nd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 7th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 12th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 20th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|July 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 20th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 5th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 10th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 18th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

===Sapelo2 Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

===Teaching Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

===Linux Training for New Cluster Users===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

===Installing Software Packages in Virtual Environments on Sapelo2===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

===Job Parallelization with GNU Parallel and Slurm Arrays===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}



===Topical Sessions===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

===Out-Reach/In-Class Talk===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|Fall 2026
|
|
|-
|Fall 2026
|
|
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Using a Conda environment in Jupyter

2026-07-28T19:33:02Z

Chelsea: /* Open OnDemand */

== Conda environment ==
A Conda environment is a type of virtual environment. Conda environments are used to contain a set of software/packages that you install (via Conda) into that environment that may be accessed any time you activate the environment. To learn more about Conda environments, please see our wiki page on creating Conda environments at '''[[Installing Applications on Sapelo2#How to install Conda packages|Link to wiki page on how to install Conda environments]].'''

== Open OnDemand ==
Open OnDemand is a web-based service that allows users to run software with a graphical user interface (GUI) such as Jupyter Notebook. Please see our Open OnDemand [[OnDemand|wiki page]] to learn more.

== Using a Conda environment in Jupyter ==
These steps will allow you to access the software you install into a Conda environment within Jupyter Notebook running on Open OnDemand

=== Create the Conda environment ===
Create your Conda environment and install any packages you will want to use.
=== Install ipykernel ===
While your Conda environment is still activated, install ipykernel to your Conda environment with:

<pre class="gcommand">
conda install ipykernel
python -m ipykernel install --user --name=my_env
</pre>
Note: change my_env to whatever the name of your Conda environment is. This is the name that you will see in Jupyter Notebook as an available kernel.

=== Open Jupyter in Open OnDemand ===
Click on the Jupyter app in [https://ondemand.gacrc.uga.edu/ Open OnDemand] and choose your desired resources. Please ensure that you choose the Miniforge3 version of Jupyter.

Click launch at the bottom of the page to start a Jupyter Notebook session. You will be redirected to "My Interactive Sessions" where you can wait for the job to be allocated resources. 

[[File:Screenshot 2023-12-13 at 10.25.00 AM.png|alt=|border|700x700px]]

Once the job starts, click on Connect to Jupyter. This will open Jupyter in a new page in your browser.

'''For Jupyter versions < 7.0.0 please see below''' (for versions > 7.0.0, scroll down).

From here, click "new" and you should see the name of the ipykernel you created. Clicking on that will start a Jupyter notebook with a kernel that has access to all of the packages in your Conda environment.

[[File:Load_condakernel.png|alt=|border|1111x1111px]]

'''For Jupyter versions > 7.0.0 please see below.'''

From here, click File > new > notebook. A new Jupyter notebook will open and a window will appear titled "Select Kernel". Click the drop down menu and under "Start Other Kernel" you should see the name of your Conda environment. Clicking on that will start your Jupyter notebook with a kernel that has access to all of the packages in your Conda environment.

[[File:New-jupyter-interface.png|alt=|border|1111x1111px]]
[[File:Load_new_condakernel.png|alt=|border|1111x1111px]]

Transferring Files

2026-07-28T18:26:29Z

Chelsea:

[[Category:Sapelo2]][[Category:Teaching]]

=Transferring Files to and from Sapelo2=

To transfer files from your local storage device to Sapelo2 or from Sapelo2 to your local storage device, please connect to xfer.gacrc.uga.edu (use your UGA MyID, the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

==The File Transfer nodes for Sapelo2 (xfer.gacrc.uga.edu)==

Users can transfer files between their local machines and GACRC storage using various programs, such as (a) Filezilla, (b) WinSCP, and (c) a secure copy (scp). To transfer files, you must have a file transfer program installed on your local machine and a connection to the UGA campus network.

All Sapelo2 users, as well as all GACRC PIs, can access the xfer nodes using the hostname '''xfer.gacrc.uga.edu''' and using their UGA MyID (not the 810 or 811 number) and the MyID password to authenticate. Two-factor authentication using Archpass Duo is also necessary. For more details of Archpass Duo, please refer to
[https://uga.teamdynamix.com/TDClient/3190/eitsclientportal/KB/Category/23825/ArchPass-powered-by-Duo archpass_duo ].

The GACRC file transfer nodes (xfer) are configured to facilitate file transfer. These nodes, which have a hostname of '''xfer.gacrc.uga.edu''', are connected via a higher-bandwidth network connection. Hence, maximum transfer speed between a user's local machine and the GACRC systems can be achieved by transferring files to/from the host xfer.gacrc.uga.edu (instead of the login nodes of the clusters).

It is not necessary to connect to the UGA VPN when connecting to a file transfer node from off-campus. If you are transferring data from/to a server outside of campus (such as your local computer), you will get much faster transfer speeds if you are not connected to the VPN.

Note that a user's home directory on the xfer nodes is the same as the user's Sapelo2 home directory, which is '''not''' the same as the user's home directory on the teaching cluster.

The xfer node can access the following file systems using the full path:

1. Your home directory on an xfer node is the same as your Sapelo2 home directory, and the path is /home/username

2. The Sapelo2 scratch directory: /scratch/username

3. The Sapelo2 work directory: /work/groupname

4. The project file system for the lab: /project/groupname

==File Transfer Methods for Sapelo2==

===Globus===
Globus is a high-performance data-transfer platform that allows you to perform and/or automate data transfers and is the recommended method for transferring files to/from the Sapelo2 Cluster. These transfers can be to and from other institutions, your local computer, or your Sapelo2 directories, including your /project area. Collaborators can also share data with you by sharing a Collection or an "endpoint" with you. The shared Collection/Endpoint can be on another institution, on a desktop or laptop, or on their GACRC storage.
Data transfers happen unattended and are faster than SCP/SFTP, data verification is on by default, and automatic restarts or continuation of transfers happen after a disruption.

Information about how to get started with and how to use Globus can be found on our Globus [[Globus|wiki page]].

===Using FileZilla===

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and Sapelo2, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://xfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

Once the connection is established you can upload files from your local machine to Sapelo2 or download files from Sapelo2 to your local machine.

Here is the PDF to check step-by-step screen shots:
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[Media:Xfer_Filezilla_12032018.pdf]]
|-
|}

===Using WinSCP===

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and Sapelo2, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: xfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, keep the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.


===Using scp===

To transfer files using scp you must have scp on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X).

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to Sapelo2:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your Sapelo2 home directory to which files are being transferred. You will then be asked to enter your UGA MyID password. You will also be prompted for two-factor authentication with Archpass Duo.

To transfer files from Sapelo2 to your local machine, use the full path to your file on Sapelo2 followed by the location you would like to transfer the files locally. The following example transfers a file called "filename" to the local current working directory.

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:full/path/to/filename ./
</pre>

(Note: yourUGAMyID@ can be omitted if your username on Sapelo2 is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer, for example, to upload all files with .dat extension to your sapelo2 home directory, to a subdirectory called subdir:

<pre class="gcommand">
scp *.dat yourUGAMyID@xfer.gacrc.uga.edu:subdir
</pre>

An example that uses a wildcard to download all files with .dat extension in your Sapelo2 home dir, in a subdirectory called subdir to your local machine:

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:subdir/\*.dat ./
</pre>

(Note the backslash “ \ ” preceeding * in the last example.)

A directory and all its contents can be transferred using the scp option '''-r''', for recursive file transferring. For example, to transfer a directory on your local machine called programs and all files in it to your Sapelo2 home directory, use:

<pre class="gcommand">
scp -r programs yourUGAMyID@xfer.gacrc.uga.edu:
</pre>

You can also use the scp option '''-p''' to preserve the file features, such as last modification time, file permissions, etc.

To transfer files directly to your Sapelo2 /scratch area (such as /scratch/johndoe/):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/scratch/johndoe/
</pre>

To transfer files directly to your Sapelo2 work directory:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/work/groupname/subdirname
</pre>

To transfer files directly to your lab's project file system (such as /project/groupname):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/project/groupname
</pre>

===Download directly from internet to Sapelo2===

Here is an example on how to download [http://hannonlab.cshl.edu/fastx_toolkit/index.html FastaX] software from internet directly to Sapelo2

<pre class="gcommand">
wget https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>

Some websites use indirect connections, it could be downloaded as
<pre class="gcommand">
curl -OL https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>


==Transferring Files between two file systems on Sapelo2==

Use ssh to login to xfer.gacrc.uga.edu using your UGA MyID username and password (and two-factor authentication via Archpass Duo) to transfer files between different file systems on Sapelo2, including the project area. To transfer data between two file systems that are available on the xfer node, you can use the '''cp''' or the '''rsync''' commands. If you have many files to copy, then a good option is to use the '''fpsync''' command, as that will allow the use of multiple cores.

For example, if you want to use 4 cores to transfer all files from /scratch/myid/mydata to /project/mylab/myid/mydata, you can use the following command on an xfer node shell prompt:

<pre class="gcomman">
fpsync -n 4 -t $HOME/fpsync /scratch/myid/mydata /project/mylab/myid/mydata
</pre>

When using the '''fpysnc''' command, please use the <code> -t $HOME/fpsync</code> option to set the fpsync's temporary directory to be in your home directory.



=Transferring Files to and from the Teaching Cluster=

==The File Transfer node for the Teaching Cluster (txfer.gacrc.uga.edu)==

Users can transfer files between their local machines and the teaching cluster using (a) Filezilla, (b) a secure copy (scp), or (c) WinSCP. To transfer files using scp (or SSH file transfer) you must have scp (or SSH) on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X).

Access to txfer.gacrc.uga.edu requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass archpass_duo] .

==File Transfer Methods for the Teaching Cluster==
To transfer files from your local storage device to the teaching cluster, please connect to the file transfer node, txfer.gacrc.uga.edu (use your UGA MyID and the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

===Using FileZilla===

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and the teaching cluster, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://txfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

===Using WinSCP===

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and the teaching cluster, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: txfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, kept the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.


===Using scp===

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to the teaching cluster:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your teaching cluster home directory to which files are being transferred. You will then be asked to enter your UGA MyID password.

(Note: yourUGAMyID@ can be omitted if your username on the teaching cluster is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer (e.g. all files with .dat extension):

<pre class="gcommand">
scp *.dat yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

=Transferring Files between Sapelo2 and the Teaching Cluster=

To transfer files between your Sapelo2 directories (e.g. your Sapelo2 home directory or /scratch directory) and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to copy files to/from your home directory at txfer.gacrc.uga.edu.

For example, to transfer a directory called subdir2 in your /scratch directory to your teaching cluster home directory. On xfer.gacrc.uga.edu issue the command:
<pre class="gcommand">
scp -r -p /scratch/yourUGAMyID/subdir2 txfer.gacrc.uga.edu:

UGA DUO authentication is required for SSH/SCP access to
GACRC systems.

UGA DUO is a two-factor authentication service which
requires a password (one factor) and a code, phone,
or device (second factor) to successfully authenticate.

If you are not enrolled in the UGA DUO service please
visit the UGA DUO service self-service portal to enroll
and configure or manage your DUO enabled devices.

https://eits.uga.edu/access_and_security/infosec/tools/duo/portal/

For additional help with UGA DUO authentication or to
report an issue please visit:

https://eits.uga.edu/access_and_security/infosec/tools/archpass/

Password:

Duo two-factor login for yourUGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>
When you enter your password, you will be prompted for the two-factor authentication step. Once you enter a passcode or select an option, the file transfer will start.

==Transferring Files between your Sapelo2 project area and the Teaching Cluster==

To transfer files between your /project area and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to e.g. copy files from /project to your home directory at txfer.gacrc.uga.edu (or to copy files from your home directory at txfer.gacrc.uga.edu to your /project area).

For example, to copy a file called species.fa from your teaching cluster home directory to a subdirectory called binf1234 in your /project area, use the following command on xfer.gacrc.uga.edu:

<pre class="gcommand">
scp txfer.gacrc.uga.edu:species.fa /project/abclab/binf1234
</pre>
where ''abclab'' needs to be changed to the name of your group.

==Other Methods==
===Using iCommands to access the Cyverse Data Store===
[https://cyverse.org/data-store Cyverse] is a secure data storage and management service. iCommands is a collection of commands for Linux and Mac OS operating systems that are used to interact with the CyVerse Data Store. iCommands can be used by CyVerse account users to download files that have been shared by other users and to upload files to the Data Store, as well as add metadata, change permissions, and more. A CyVerse account is not required to download a public data file via iCommands.

version 4.2.8 of iCommands is installed on Sapelo2 IRODS '''transfer node''' (xfer-irods.gacrc.uga.edu). Please note that this command is not available on the other transfer nodes.

You will need to log on a Sapelo2 transfer node xfer-irods.gacrc.uga.edu and then initialize the connection to iRODS by using the iinit command to use iCommands

More information about using iCommands can be found on the [[ICommands-Sapelo2|'''ICommands-Sapelo2''']] page. You can also read [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands Official iCommands Documentation]

Transferring Files

2026-07-28T17:49:50Z

Chelsea: /* File Transfer Methods for Sapelo2 */

[[Category:Sapelo2]][[Category:Teaching]]

=Transferring Files to and from Sapelo2=

To transfer files from your local storage device to Sapelo2 or from Sapelo2 to your local storage device, please connect to xfer.gacrc.uga.edu (use your UGA MyID, the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

==The File Transfer nodes for Sapelo2 (xfer.gacrc.uga.edu)==

Users can transfer files between their local machines and GACRC storage using various programs, such as (a) Filezilla, (b) WinSCP, and (c) a secure copy (scp). To transfer files, you must have a file transfer program installed on your local machine and a connection to the UGA campus network.

All Sapelo2 users, as well as all GACRC PIs, can access the xfer nodes using the hostname '''xfer.gacrc.uga.edu''' and using their UGA MyID (not the 810 or 811 number) and the MyID password to authenticate. Two-factor authentication using Archpass Duo is also necessary. For more details of Archpass Duo, please refer to
[https://uga.teamdynamix.com/TDClient/3190/eitsclientportal/KB/Category/23825/ArchPass-powered-by-Duo archpass_duo ].

The GACRC file transfer nodes (xfer) are configured to facilitate file transfer. These nodes, which have a hostname of '''xfer.gacrc.uga.edu''', are connected via a higher-bandwidth network connection. Hence, maximum transfer speed between a user's local machine and the GACRC systems can be achieved by transferring files to/from the host xfer.gacrc.uga.edu (instead of the login nodes of the clusters).

It is not necessary to connect to the UGA VPN when connecting to a file transfer node from off-campus. If you are transferring data from/to a server outside of campus (such as your local computer), you will get much faster transfer speeds if you are not connected to the VPN.

Note that a user's home directory on the xfer nodes is the same as the user's Sapelo2 home directory, which is '''not''' the same as the user's home directory on the teaching cluster.

The xfer node can access the following file systems using the full path:

1. Your home directory on an xfer node is the same as your Sapelo2 home directory, and the path is /home/username

2. The Sapelo2 scratch directory: /scratch/username

3. The Sapelo2 work directory: /work/groupname

4. The project file system for the lab: /project/groupname

==File Transfer Methods for Sapelo2==

===Globus===
Globus is a high-performance data-transfer platform that allows you to perform and/or automate data transfers and is the recommended method for transferring files to/from the Sapelo2 Cluster. These transfers can be to and from other institutions, your local computer, or your Sapelo2 directories, including your /project area. Collaborators can also share data with you by sharing a Collection or an "endpoint" with you. The shared Collection/Endpoint can be on another institution, on a desktop or laptop, or on their GACRC storage.
Data transfers happen unattended and are faster than SCP/SFTP, data verification is on by default, and automatic restarts or continuation of transfers happen after a disruption.

Information about how to get started with and how to use Globus can be found on our Globus wiki page [[Globus|here]].

===Using FileZilla===

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and Sapelo2, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://xfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

Once the connection is established you can upload files from your local machine to Sapelo2 or download files from Sapelo2 to your local machine.

Here is the PDF to check step-by-step screen shots:
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[Media:Xfer_Filezilla_12032018.pdf]]
|-
|}

===Using WinSCP===

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and Sapelo2, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: xfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, keep the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.


===Using scp===

To transfer files using scp you must have scp on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X).

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to Sapelo2:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your Sapelo2 home directory to which files are being transferred. You will then be asked to enter your UGA MyID password. You will also be prompted for two-factor authentication with Archpass Duo.

To transfer files from Sapelo2 to your local machine, use the full path to your file on Sapelo2 followed by the location you would like to transfer the files locally. The following example transfers a file called "filename" to the local current working directory.

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:full/path/to/filename ./
</pre>

(Note: yourUGAMyID@ can be omitted if your username on Sapelo2 is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer, for example, to upload all files with .dat extension to your sapelo2 home directory, to a subdirectory called subdir:

<pre class="gcommand">
scp *.dat yourUGAMyID@xfer.gacrc.uga.edu:subdir
</pre>

An example that uses a wildcard to download all files with .dat extension in your Sapelo2 home dir, in a subdirectory called subdir to your local machine:

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:subdir/\*.dat ./
</pre>

(Note the backslash “ \ ” preceeding * in the last example.)

A directory and all its contents can be transferred using the scp option '''-r''', for recursive file transferring. For example, to transfer a directory on your local machine called programs and all files in it to your Sapelo2 home directory, use:

<pre class="gcommand">
scp -r programs yourUGAMyID@xfer.gacrc.uga.edu:
</pre>

You can also use the scp option '''-p''' to preserve the file features, such as last modification time, file permissions, etc.

To transfer files directly to your Sapelo2 /scratch area (such as /scratch/johndoe/):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/scratch/johndoe/
</pre>

To transfer files directly to your Sapelo2 work directory:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/work/groupname/subdirname
</pre>

To transfer files directly to your lab's project file system (such as /project/groupname):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/project/groupname
</pre>

===Download directly from internet to Sapelo2===

Here is an example on how to download [http://hannonlab.cshl.edu/fastx_toolkit/index.html FastaX] software from internet directly to Sapelo2

<pre class="gcommand">
wget https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>

Some websites use indirect connections, it could be downloaded as
<pre class="gcommand">
curl -OL https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>


==Transferring Files between two file systems on Sapelo2==

Use ssh to login to xfer.gacrc.uga.edu using your UGA MyID username and password (and two-factor authentication via Archpass Duo) to transfer files between different file systems on Sapelo2, including the project area. To transfer data between two file systems that are available on the xfer node, you can use the '''cp''' or the '''rsync''' commands. If you have many files to copy, then a good option is to use the '''fpsync''' command, as that will allow the use of multiple cores.

For example, if you want to use 4 cores to transfer all files from /scratch/myid/mydata to /project/mylab/myid/mydata, you can use the following command on an xfer node shell prompt:

<pre class="gcomman">
fpsync -n 4 -t $HOME/fpsync /scratch/myid/mydata /project/mylab/myid/mydata
</pre>

When using the '''fpysnc''' command, please use the <code> -t $HOME/fpsync</code> option to set the fpsync's temporary directory to be in your home directory.



=Transferring Files to and from the Teaching Cluster=

==The File Transfer node for the Teaching Cluster (txfer.gacrc.uga.edu)==

Users can transfer files between their local machines and the teaching cluster using (a) Filezilla, (b) a secure copy (scp), or (c) WinSCP. To transfer files using scp (or SSH file transfer) you must have scp (or SSH) on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X).

Access to txfer.gacrc.uga.edu requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass archpass_duo] .

==File Transfer Methods for the Teaching Cluster==
To transfer files from your local storage device to the teaching cluster, please connect to the file transfer node, txfer.gacrc.uga.edu (use your UGA MyID and the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

===Using FileZilla===

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and the teaching cluster, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://txfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

===Using WinSCP===

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and the teaching cluster, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: txfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, kept the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.


===Using scp===

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to the teaching cluster:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your teaching cluster home directory to which files are being transferred. You will then be asked to enter your UGA MyID password.

(Note: yourUGAMyID@ can be omitted if your username on the teaching cluster is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer (e.g. all files with .dat extension):

<pre class="gcommand">
scp *.dat yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

=Transferring Files between Sapelo2 and the Teaching Cluster=

To transfer files between your Sapelo2 directories (e.g. your Sapelo2 home directory or /scratch directory) and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to copy files to/from your home directory at txfer.gacrc.uga.edu.

For example, to transfer a directory called subdir2 in your /scratch directory to your teaching cluster home directory. On xfer.gacrc.uga.edu issue the command:
<pre class="gcommand">
scp -r -p /scratch/yourUGAMyID/subdir2 txfer.gacrc.uga.edu:

UGA DUO authentication is required for SSH/SCP access to
GACRC systems.

UGA DUO is a two-factor authentication service which
requires a password (one factor) and a code, phone,
or device (second factor) to successfully authenticate.

If you are not enrolled in the UGA DUO service please
visit the UGA DUO service self-service portal to enroll
and configure or manage your DUO enabled devices.

https://eits.uga.edu/access_and_security/infosec/tools/duo/portal/

For additional help with UGA DUO authentication or to
report an issue please visit:

https://eits.uga.edu/access_and_security/infosec/tools/archpass/

Password:

Duo two-factor login for yourUGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>
When you enter your password, you will be prompted for the two-factor authentication step. Once you enter a passcode or select an option, the file transfer will start.

==Transferring Files between your Sapelo2 project area and the Teaching Cluster==

To transfer files between your /project area and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to e.g. copy files from /project to your home directory at txfer.gacrc.uga.edu (or to copy files from your home directory at txfer.gacrc.uga.edu to your /project area).

For example, to copy a file called species.fa from your teaching cluster home directory to a subdirectory called binf1234 in your /project area, use the following command on xfer.gacrc.uga.edu:

<pre class="gcommand">
scp txfer.gacrc.uga.edu:species.fa /project/abclab/binf1234
</pre>
where ''abclab'' needs to be changed to the name of your group.

==Other Methods==
===Using iCommands to access the Cyverse Data Store===
[https://cyverse.org/data-store Cyverse] is a secure data storage and management service. iCommands is a collection of commands for Linux and Mac OS operating systems that are used to interact with the CyVerse Data Store. iCommands can be used by CyVerse account users to download files that have been shared by other users and to upload files to the Data Store, as well as add metadata, change permissions, and more. A CyVerse account is not required to download a public data file via iCommands.

version 4.2.8 of iCommands is installed on Sapelo2 IRODS '''transfer node''' (xfer-irods.gacrc.uga.edu). Please note that this command is not available on the other transfer nodes.

You will need to log on a Sapelo2 transfer node xfer-irods.gacrc.uga.edu and then initialize the connection to iRODS by using the iinit command to use iCommands

More information about using iCommands can be found on the [[ICommands-Sapelo2|'''ICommands-Sapelo2''']] page. You can also read [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands Official iCommands Documentation]

Transferring Files

2026-07-28T17:49:25Z

Chelsea:

[[Category:Sapelo2]][[Category:Teaching]]

=Transferring Files to and from Sapelo2=

To transfer files from your local storage device to Sapelo2 or from Sapelo2 to your local storage device, please connect to xfer.gacrc.uga.edu (use your UGA MyID, the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

==The File Transfer nodes for Sapelo2 (xfer.gacrc.uga.edu)==

Users can transfer files between their local machines and GACRC storage using various programs, such as (a) Filezilla, (b) WinSCP, and (c) a secure copy (scp). To transfer files, you must have a file transfer program installed on your local machine and a connection to the UGA campus network.

All Sapelo2 users, as well as all GACRC PIs, can access the xfer nodes using the hostname '''xfer.gacrc.uga.edu''' and using their UGA MyID (not the 810 or 811 number) and the MyID password to authenticate. Two-factor authentication using Archpass Duo is also necessary. For more details of Archpass Duo, please refer to
[https://uga.teamdynamix.com/TDClient/3190/eitsclientportal/KB/Category/23825/ArchPass-powered-by-Duo archpass_duo ].

The GACRC file transfer nodes (xfer) are configured to facilitate file transfer. These nodes, which have a hostname of '''xfer.gacrc.uga.edu''', are connected via a higher-bandwidth network connection. Hence, maximum transfer speed between a user's local machine and the GACRC systems can be achieved by transferring files to/from the host xfer.gacrc.uga.edu (instead of the login nodes of the clusters).

It is not necessary to connect to the UGA VPN when connecting to a file transfer node from off-campus. If you are transferring data from/to a server outside of campus (such as your local computer), you will get much faster transfer speeds if you are not connected to the VPN.

Note that a user's home directory on the xfer nodes is the same as the user's Sapelo2 home directory, which is '''not''' the same as the user's home directory on the teaching cluster.

The xfer node can access the following file systems using the full path:

1. Your home directory on an xfer node is the same as your Sapelo2 home directory, and the path is /home/username

2. The Sapelo2 scratch directory: /scratch/username

3. The Sapelo2 work directory: /work/groupname

4. The project file system for the lab: /project/groupname

==File Transfer Methods for Sapelo2==

===Globus===
Globus is a high-performance data-transfer platform that allows you to perform and/or automate data transfers and is the recommended method for transferring files to/from the Sapelo2 Cluster. These transfers can be to and from other institutions, your local computer, or your Sapelo2 directories, including your /project area. Collaborators can also share data with you by sharing a Collection or an "endpoint" with you. The shared Collection/Endpoint can be on another institution, on a desktop or laptop, or on their GACRC storage.
Data transfers happen unattended and are faster than SCP/SFTP, data verification is on by default, and automatic restarts or continuation of transfers happen after a disruption.

Information about how to get started with a use Globus cana be found on our Globus wiki page [[Globus|here]].

===Using FileZilla===

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and Sapelo2, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://xfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

Once the connection is established you can upload files from your local machine to Sapelo2 or download files from Sapelo2 to your local machine.

Here is the PDF to check step-by-step screen shots:
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[Media:Xfer_Filezilla_12032018.pdf]]
|-
|}

===Using WinSCP===

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and Sapelo2, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: xfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, keep the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.


===Using scp===

To transfer files using scp you must have scp on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X).

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to Sapelo2:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your Sapelo2 home directory to which files are being transferred. You will then be asked to enter your UGA MyID password. You will also be prompted for two-factor authentication with Archpass Duo.

To transfer files from Sapelo2 to your local machine, use the full path to your file on Sapelo2 followed by the location you would like to transfer the files locally. The following example transfers a file called "filename" to the local current working directory.

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:full/path/to/filename ./
</pre>

(Note: yourUGAMyID@ can be omitted if your username on Sapelo2 is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer, for example, to upload all files with .dat extension to your sapelo2 home directory, to a subdirectory called subdir:

<pre class="gcommand">
scp *.dat yourUGAMyID@xfer.gacrc.uga.edu:subdir
</pre>

An example that uses a wildcard to download all files with .dat extension in your Sapelo2 home dir, in a subdirectory called subdir to your local machine:

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:subdir/\*.dat ./
</pre>

(Note the backslash “ \ ” preceeding * in the last example.)

A directory and all its contents can be transferred using the scp option '''-r''', for recursive file transferring. For example, to transfer a directory on your local machine called programs and all files in it to your Sapelo2 home directory, use:

<pre class="gcommand">
scp -r programs yourUGAMyID@xfer.gacrc.uga.edu:
</pre>

You can also use the scp option '''-p''' to preserve the file features, such as last modification time, file permissions, etc.

To transfer files directly to your Sapelo2 /scratch area (such as /scratch/johndoe/):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/scratch/johndoe/
</pre>

To transfer files directly to your Sapelo2 work directory:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/work/groupname/subdirname
</pre>

To transfer files directly to your lab's project file system (such as /project/groupname):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/project/groupname
</pre>

===Download directly from internet to Sapelo2===

Here is an example on how to download [http://hannonlab.cshl.edu/fastx_toolkit/index.html FastaX] software from internet directly to Sapelo2

<pre class="gcommand">
wget https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>

Some websites use indirect connections, it could be downloaded as
<pre class="gcommand">
curl -OL https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>


==Transferring Files between two file systems on Sapelo2==

Use ssh to login to xfer.gacrc.uga.edu using your UGA MyID username and password (and two-factor authentication via Archpass Duo) to transfer files between different file systems on Sapelo2, including the project area. To transfer data between two file systems that are available on the xfer node, you can use the '''cp''' or the '''rsync''' commands. If you have many files to copy, then a good option is to use the '''fpsync''' command, as that will allow the use of multiple cores.

For example, if you want to use 4 cores to transfer all files from /scratch/myid/mydata to /project/mylab/myid/mydata, you can use the following command on an xfer node shell prompt:

<pre class="gcomman">
fpsync -n 4 -t $HOME/fpsync /scratch/myid/mydata /project/mylab/myid/mydata
</pre>

When using the '''fpysnc''' command, please use the <code> -t $HOME/fpsync</code> option to set the fpsync's temporary directory to be in your home directory.



=Transferring Files to and from the Teaching Cluster=

==The File Transfer node for the Teaching Cluster (txfer.gacrc.uga.edu)==

Users can transfer files between their local machines and the teaching cluster using (a) Filezilla, (b) a secure copy (scp), or (c) WinSCP. To transfer files using scp (or SSH file transfer) you must have scp (or SSH) on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X).

Access to txfer.gacrc.uga.edu requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass archpass_duo] .

==File Transfer Methods for the Teaching Cluster==
To transfer files from your local storage device to the teaching cluster, please connect to the file transfer node, txfer.gacrc.uga.edu (use your UGA MyID and the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

===Using FileZilla===

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and the teaching cluster, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://txfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

===Using WinSCP===

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and the teaching cluster, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: txfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, kept the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.


===Using scp===

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to the teaching cluster:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your teaching cluster home directory to which files are being transferred. You will then be asked to enter your UGA MyID password.

(Note: yourUGAMyID@ can be omitted if your username on the teaching cluster is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer (e.g. all files with .dat extension):

<pre class="gcommand">
scp *.dat yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

=Transferring Files between Sapelo2 and the Teaching Cluster=

To transfer files between your Sapelo2 directories (e.g. your Sapelo2 home directory or /scratch directory) and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to copy files to/from your home directory at txfer.gacrc.uga.edu.

For example, to transfer a directory called subdir2 in your /scratch directory to your teaching cluster home directory. On xfer.gacrc.uga.edu issue the command:
<pre class="gcommand">
scp -r -p /scratch/yourUGAMyID/subdir2 txfer.gacrc.uga.edu:

UGA DUO authentication is required for SSH/SCP access to
GACRC systems.

UGA DUO is a two-factor authentication service which
requires a password (one factor) and a code, phone,
or device (second factor) to successfully authenticate.

If you are not enrolled in the UGA DUO service please
visit the UGA DUO service self-service portal to enroll
and configure or manage your DUO enabled devices.

https://eits.uga.edu/access_and_security/infosec/tools/duo/portal/

For additional help with UGA DUO authentication or to
report an issue please visit:

https://eits.uga.edu/access_and_security/infosec/tools/archpass/

Password:

Duo two-factor login for yourUGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>
When you enter your password, you will be prompted for the two-factor authentication step. Once you enter a passcode or select an option, the file transfer will start.

==Transferring Files between your Sapelo2 project area and the Teaching Cluster==

To transfer files between your /project area and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to e.g. copy files from /project to your home directory at txfer.gacrc.uga.edu (or to copy files from your home directory at txfer.gacrc.uga.edu to your /project area).

For example, to copy a file called species.fa from your teaching cluster home directory to a subdirectory called binf1234 in your /project area, use the following command on xfer.gacrc.uga.edu:

<pre class="gcommand">
scp txfer.gacrc.uga.edu:species.fa /project/abclab/binf1234
</pre>
where ''abclab'' needs to be changed to the name of your group.

==Other Methods==
===Using iCommands to access the Cyverse Data Store===
[https://cyverse.org/data-store Cyverse] is a secure data storage and management service. iCommands is a collection of commands for Linux and Mac OS operating systems that are used to interact with the CyVerse Data Store. iCommands can be used by CyVerse account users to download files that have been shared by other users and to upload files to the Data Store, as well as add metadata, change permissions, and more. A CyVerse account is not required to download a public data file via iCommands.

version 4.2.8 of iCommands is installed on Sapelo2 IRODS '''transfer node''' (xfer-irods.gacrc.uga.edu). Please note that this command is not available on the other transfer nodes.

You will need to log on a Sapelo2 transfer node xfer-irods.gacrc.uga.edu and then initialize the connection to iRODS by using the iinit command to use iCommands

More information about using iCommands can be found on the [[ICommands-Sapelo2|'''ICommands-Sapelo2''']] page. You can also read [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands Official iCommands Documentation]

RAxML-NG-Sapelo2

2026-07-23T18:10:27Z

Chelsea: /* Version */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==
Bioinformatics
== Program On ==
Sapelo2
== Version ==
1.2.0, 1.2.2
==Author / Distributor==
Alexey M. Kozlov and Alexandros Stamatakis
==Description==
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.

== Running Program ==

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''RAxML-NG'''

To use RaxML-NG, please first load the module with
<pre class="gscript">
module load RAxML-NG/1.2.2-GCC-13.2.0
</pre>

Keep in mind that because this version doesn't use MPI, the job cannot be run on multiple nodes, though it can use multiple threads on a single node.

Example of shell script to run in the batch queue, using 8 cores on a single node:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_RAxML-NG 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=8 #this needs to be the same as the '--threads' option below! 
<nowiki>#</nowiki>SBATCH --mem=64GB 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=RAxML-NG.%j.out 
<nowiki>#</nowiki>SBATCH --error=RAxML-NG.%j.err 

cd $SLURM_SUBMIT_DIR 
ml RAxML-NG/1.2.2-GCC-12.2.0 
raxml-ng --all --msa testAA.fa --model LG+G8+F --tree pars{10} --bs-trees 200 --threads 8 
</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running Jobs on Sapelo2]].

== Documentation ==

<pre class="gcommand">

ml RAxML-NG/1.2.2-GCC-12.2.0
raxml-ng --help

RAxML-NG v. 1.2.2-master released on 30.04.2024 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

Usage: raxml-ng [OPTIONS]

Commands (mutually exclusive):
--help display help information
--version display version information
--evaluate evaluate the likelihood of a tree (with model+brlen optimization)
--search ML tree search (default: 10 parsimony + 10 random starting trees)
--bootstrap bootstrapping (default: use bootstopping to auto-detect #replicates)
--all all-in-one (ML search + bootstrapping)
--support compute bipartition support for a given reference tree (e.g., best ML tree)
and a set of replicate trees (e.g., from a bootstrap analysis)
--bsconverge test for bootstrapping convergence using autoMRE criterion
--bsmsa generate bootstrap replicate MSAs
--terrace check whether a tree lies on a phylogenetic terrace
--check check alignment correctness and remove empty columns/rows
--parse parse alignment, compress patterns and create binary MSA file
--start generate parsimony/random starting trees and exit
--rfdist compute pair-wise Robinson-Foulds (RF) distances between trees
--consense [ STRICT | MR | MR<n> | MRE ] build strict, majority-rule (MR) or extended MR (MRE) consensus tree (default: MR)
eg: --consense MR75 --tree bsrep.nw
--ancestral ancestral state reconstruction at all inner nodes
--sitelh print per-site log-likelihood values

Command shortcuts (mutually exclusive):
--search1 Alias for: --search --tree rand{1}
--loglh Alias for: --evaluate --opt-model off --opt-branches off --nofiles --log result
--rf Alias for: --rfdist --nofiles --log result

Input and output options:
--tree rand{N} | pars{N} | FILE starting tree: rand(om), pars(imony) or user-specified (newick file)
N = number of trees (default: rand{10},pars{10})
--msa FILE alignment file
--msa-format VALUE alignment file format: FASTA, PHYLIP, CATG or AUTO-detect (default)
--data-type VALUE data type: DNA, AA, BIN(ary) or AUTO-detect (default)
--tree-constraint FILE constraint tree
--prefix STRING prefix for output files (default: MSA file name)
--log VALUE log verbosity: ERROR,WARNING,RESULT,INFO,PROGRESS,DEBUG (default: PROGRESS)
--redo overwrite existing result files and ignore checkpoints (default: OFF)
--nofiles do not create any output files, print results to the terminal only
--precision VALUE number of decimal places to print (default: 6)
--outgroup o1,o2,..,oN comma-separated list of outgroup taxon names (it's just a drawing option!)
--site-weights FILE file with MSA column weights (positive integers only!)

General options:
--seed VALUE seed for pseudo-random number generator (default: current time)
--pat-comp on | off alignment pattern compression (default: ON)
--tip-inner on | off tip-inner case optimization (default: OFF)
--site-repeats on | off use site repeats optimization, 10%-60% faster than tip-inner (default: ON)
--threads VALUE number of parallel threads to use (default: 1)
--workers VALUE number of tree searches to run in parallel (default: 1)
--simd none | sse3 | avx | avx2 vector instruction set to use (default: auto-detect).
--rate-scalers on | off use individual CLV scalers for each rate category (default: ON for >2000 taxa)
--force [ <CHECKS> ] disable safety checks (please think twice!)

Model options:
--model <name>+G[n]+<Freqs> | FILE model specification OR partition file
--brlen linked | scaled | unlinked branch length linkage between partitions (default: scaled)
--blmin VALUE minimum branch length (default: 1e-6)
--blmax VALUE maximum branch length (default: 100)
--blopt nr_fast | nr_safe branch length optimization method (default: nr_fast)
nr_oldfast | nr_oldsafe
--opt-model on | off ML optimization of all model parameters (default: ON)
--opt-branches on | off ML optimization of all branch lengths (default: ON)
--prob-msa on | off use probabilistic alignment (works with CATG and VCF)
--lh-epsilon VALUE log-likelihood epsilon for optimization/tree search (default: 0.1)

Topology search options:
--spr-radius VALUE SPR re-insertion radius for fast iterations (default: AUTO)
--spr-cutoff VALUE | off relative LH cutoff for descending into subtrees (default: 1.0)
--lh-epsilon-triplet VALUE log-likelihood epsilon for branch length triplet optimization (default: 1000)

Bootstrapping options:
--bs-trees VALUE number of bootstraps replicates
--bs-trees autoMRE{N} use MRE-based bootstrap convergence criterion, up to N replicates (default: 1000)
--bs-trees FILE Newick file containing set of bootstrap replicate trees (with --support)
--bs-cutoff VALUE cutoff threshold for the MRE-based bootstopping criteria (default: 0.03)
--bs-metric fbp | tbe branch support metric: fbp = Felsenstein bootstrap (default), tbe = transfer distance
--bs-write-msa on | off write all bootstrap alignments (default: OFF)

EXAMPLES:
1. Perform tree inference on DNA alignment
(10 random + 10 parsimony starting trees, general time-reversible model, ML estimate of substitution rates and
nucleotide frequencies, discrete GAMMA model of rate heterogeneity with 4 categories):

./raxml-ng --msa testDNA.fa --model GTR+G

2. Perform an all-in-one analysis (ML tree search + non-parametric bootstrap)
(10 randomized parsimony starting trees, fixed empirical substitution matrix (LG),
empirical aminoacid frequencies from alignment, 8 discrete GAMMA categories,
200 bootstrap replicates):

./raxml-ng --all --msa testAA.fa --model LG+G8+F --tree pars{10} --bs-trees 200

3. Optimize branch lengths and free model parameters on a fixed topology
(using multiple partitions with proportional branch lengths)

./raxml-ng --evaluate --msa testAA.fa --model partitions.txt --tree test.tree --brlen scaled
</pre>

== Installation ==

Source code for RAxML 8.2.12 downloaded from [https://github.com/stamatak/standard-RAxML/archive/master.zip githhub] and compiled with intel-2019b compilers and intel MPI.

== System ==
64-bit Linux

Software

2026-07-23T18:09:51Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 22Jul2025, 29Aug2024 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.5, 3.1.0, 3.1.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2, 5.42.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2023.7, 2025.4, 2025.10, 2026.04 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.0, 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

QIIME2-Sapelo2

2026-07-23T18:06:21Z

Chelsea: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==

2023.7, 2025.4, 2025.10, 2026.04

== Author / Distributor ==

[https://qiime2.org/ QIIME2]

== Description ==
QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed."

More details are at [https://qiime2.org/ QIIME2]

== Running Program ==

Also refer to [[Running Jobs on Sapelo2]]

*Version 2023.7 installed at /apps/eb/QIIME2/2023.7
*Version 2025.4 installed at /apps/eb/QIIME2/2025.4-amplicon
*Version 2025.10 installed at /apps/eb/QIIME2/2025.10-amplicon
*Version 2026.04 installed at /apps/eb/QIIME2/2026.04

To use version 2023.7, please first load the module with

<pre class="gscript">
module load QIIME2/2023.7
</pre>

To use version 2025.4 please first load the module with

<pre class="gscript">
module load QIIME2/2025.4-amplicon
</pre>

To use version 2025.10, please first load the module with

<pre class="gscript">
module load QIIME2/2025.10-amplicon
</pre>

To use version 2026.04, please first load the module with

<pre class="gscript">
module load QIIME2/2026.04
</pre>

Example of a shell script sub.sh to run QIIME2 2023.7 at the batch queue:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_qiime2 # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU by default
#SBATCH --cpus-per-task=1 # Number of CPU cores per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=48:00:00 # Time limit hrs:min:sec
#SBATCH --output=log.%j.out # Standard output log
#SBATCH --error=log.%j.err # Standard error log

#SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu # Where to send mail

cd $SLURM_SUBMIT_DIR

ml QIIME2/2023.7

echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
qiime [OPTIONS] COMMAND [ARGS]...
</pre>

where [OPTIONS], COMMAND, and [ARGS] need to be replaced by the options, command, and arguments you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.

Example of job submission
<pre class="gcommand">
sbatch ./sub.sh
</pre>

== Documentation ==

<pre class="gcommand">
[cft07037@b1-24 singularity-images]$ ml QIIME2/2023.2
[cft07037@b1-24 singularity-images]$ qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]...

QIIME 2 command-line interface (q2cli)
--------------------------------------

To get help with QIIME 2, visit https://qiime2.org.

To enable tab completion in Bash, run the following command or add it to
your .bashrc/.bash_profile:

source tab-qiime

To enable tab completion in ZSH, run the following commands or add them to
your .zshrc:

autoload -Uz compinit && compinit
autoload bashcompinit && bashcompinit
source tab-qiime

Options:
--version Show the version and exit.
--help Show this message and exit.

Commands:
info Display information about current deployment.
tools Tools for working with QIIME 2 files.
dev Utilities for developers and advanced users.
alignment Plugin for generating and manipulating alignments.
composition Plugin for compositional data analysis.
cutadapt Plugin for removing adapter sequences, primers, and
other unwanted sequence from sequence data.
dada2 Plugin for sequence quality control with DADA2.
deblur Plugin for sequence quality control with Deblur.
demux Plugin for demultiplexing & viewing sequence quality.
diversity Plugin for exploring community diversity.
diversity-lib Plugin for computing community diversity.
emperor Plugin for ordination plotting with Emperor.
feature-classifier Plugin for taxonomic classification.
feature-table Plugin for working with sample by feature tables.
fragment-insertion Plugin for extending phylogenies.
gneiss Plugin for building compositional models.
greengenes2 Methods for interaction with Greengenes2
longitudinal Plugin for paired sample and time series analyses.
metadata Plugin for working with Metadata.
phylogeny Plugin for generating and manipulating phylogenies.
quality-control Plugin for quality control of feature and sequence data.
quality-filter Plugin for PHRED-based filtering and trimming.
sample-classifier Plugin for machine learning prediction of sample
metadata.
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.
</pre>
[[#top|Back to Top]]

== Installation ==

source code from [https://qiime2.org/ QIIME2]

== System ==
64-bit Linux

QIIME2-Sapelo2

2026-07-23T18:03:30Z

Chelsea: /* Version */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==

2023.7, 2025.4, 2025.10, 2026.04

== Author / Distributor ==

[https://qiime2.org/ QIIME2]

== Description ==
QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed."

More details are at [https://qiime2.org/ QIIME2]

== Running Program ==

Also refer to [[Running Jobs on Sapelo2]]

*Version 2020.6 installed as a conda environment at /apps/eb/QIIME2/2020.6
*Version 2023.2 installed as a conda environment at /apps/eb/QIIME2/2023.2
*Version 2023.5.1 installed as a conda environment at /apps/eb/QIIME2/2023.5.1-foss-2022a
*Version 2023.7 installed as a conda environment at /apps/eb/QIIME2/2023.7

To use version 2020.6, please first load the module with

<pre class="gscript">
module load QIIME2/2020.6
</pre>

To use version2023.2, please first load the module with

<pre class="gscript">
module load QIIME2/2023.2
</pre>

To use version 2023.5.1, please first load the module with

<pre class="gscript">
module load QIIME2/2023.5.1-foss-2022a
</pre>

To use version 2023.7, please first load the module with

<pre class="gscript">
module load QIIME2/2023.7
</pre>

Example of a shell script sub.sh to run QIIME2 2023.7 at the batch queue:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_qiime2 # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU by default
#SBATCH --cpus-per-task=1 # Number of CPU cores per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=48:00:00 # Time limit hrs:min:sec
#SBATCH --output=log.%j.out # Standard output log
#SBATCH --error=log.%j.err # Standard error log

#SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu # Where to send mail

cd $SLURM_SUBMIT_DIR

ml QIIME2/2023.7

echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
qiime [OPTIONS] COMMAND [ARGS]...
</pre>

where [OPTIONS], COMMAND, and [ARGS] need to be replaced by the options, command, and arguments you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.

Example of job submission
<pre class="gcommand">
sbatch ./sub.sh
</pre>

== Documentation ==

<pre class="gcommand">
[cft07037@b1-24 singularity-images]$ ml QIIME2/2023.2
[cft07037@b1-24 singularity-images]$ qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]...

QIIME 2 command-line interface (q2cli)
--------------------------------------

To get help with QIIME 2, visit https://qiime2.org.

To enable tab completion in Bash, run the following command or add it to
your .bashrc/.bash_profile:

source tab-qiime

To enable tab completion in ZSH, run the following commands or add them to
your .zshrc:

autoload -Uz compinit && compinit
autoload bashcompinit && bashcompinit
source tab-qiime

Options:
--version Show the version and exit.
--help Show this message and exit.

Commands:
info Display information about current deployment.
tools Tools for working with QIIME 2 files.
dev Utilities for developers and advanced users.
alignment Plugin for generating and manipulating alignments.
composition Plugin for compositional data analysis.
cutadapt Plugin for removing adapter sequences, primers, and
other unwanted sequence from sequence data.
dada2 Plugin for sequence quality control with DADA2.
deblur Plugin for sequence quality control with Deblur.
demux Plugin for demultiplexing & viewing sequence quality.
diversity Plugin for exploring community diversity.
diversity-lib Plugin for computing community diversity.
emperor Plugin for ordination plotting with Emperor.
feature-classifier Plugin for taxonomic classification.
feature-table Plugin for working with sample by feature tables.
fragment-insertion Plugin for extending phylogenies.
gneiss Plugin for building compositional models.
greengenes2 Methods for interaction with Greengenes2
longitudinal Plugin for paired sample and time series analyses.
metadata Plugin for working with Metadata.
phylogeny Plugin for generating and manipulating phylogenies.
quality-control Plugin for quality control of feature and sequence data.
quality-filter Plugin for PHRED-based filtering and trimming.
sample-classifier Plugin for machine learning prediction of sample
metadata.
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.
</pre>
[[#top|Back to Top]]

== Installation ==

source code from [https://qiime2.org/ QIIME2]

== System ==
64-bit Linux

Software

2026-07-23T18:03:06Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 22Jul2025, 29Aug2024 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.5, 3.1.0, 3.1.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2, 5.42.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2023.7, 2025.4, 2025.10, 2026.04 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Software

2026-07-23T18:01:46Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 22Jul2025, 29Aug2024 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.5, 3.1.0, 3.1.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2, 5.42.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Python-Teaching

2026-07-23T17:59:52Z

Chelsea: /* Program On */

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
== Category ==

Programming

== Program On ==

Teaching

== Version ==
2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2

== Author / Distributor ==

[http://python.org/ Python]

== Description ==
"Python is a programming language that lets you work more quickly and integrate your systems more effectively."
More details are at [http://python.org/ Python]

== Running Program ==

Please also see [[Python-Sapelo2]] as that documentation applies to the teaching cluster as well.

To see all versions of Python installed on the cluster, use:
<pre class="gscript">
ml spider Python
</pre>

For example:

'''Version 2.7.18'''

Installed in /apps/eb/Python/2.7.18-GCCcore-11.3.0

To use this version, please load the module with
<pre class="gscript">
ml Python/2.7.18-GCCcore-11.3.0
</pre>

'''Version 3.12.3'''

Installed in /apps/eb/Python/3.12.3-GCCcore-13.3.0

To use this version, please load the module with
<pre class="gscript">
ml Python/3.12.3-GCCcore-13.3.0
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Python 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Python.%j.out 
<nowiki>#</nowiki>SBATCH --error=Python.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Python/3.12.3-GCCcore-13.3.0 
python [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

== Documentation ==

<pre class="gcommand">
ml Python/3.12.3-GCCcore-13.3.0
python -h

usage: python [option] ... [-c cmd | -m mod | file | -] [arg] ...
Options (and corresponding environment variables):
-b : issue warnings about converting bytes/bytearray to str and comparing
bytes/bytearray with str or bytes with int. (-bb: issue errors)
-B : don't write .pyc files on import; also PYTHONDONTWRITEBYTECODE=x
-c cmd : program passed in as string (terminates option list)
-d : turn on parser debugging output (for experts only, only works on
debug builds); also PYTHONDEBUG=x
-E : ignore PYTHON* environment variables (such as PYTHONPATH)
-h : print this help message and exit (also -? or --help)
-i : inspect interactively after running script; forces a prompt even
if stdin does not appear to be a terminal; also PYTHONINSPECT=x
-I : isolate Python from the user's environment (implies -E and -s)
-m mod : run library module as a script (terminates option list)
-O : remove assert and __debug__-dependent statements; add .opt-1 before
.pyc extension; also PYTHONOPTIMIZE=x
-OO : do -O changes and also discard docstrings; add .opt-2 before
.pyc extension
-P : don't prepend a potentially unsafe path to sys.path; also
PYTHONSAFEPATH
-q : don't print version and copyright messages on interactive startup
-s : don't add user site directory to sys.path; also PYTHONNOUSERSITE=x
-S : don't imply 'import site' on initialization
-u : force the stdout and stderr streams to be unbuffered;
this option has no effect on stdin; also PYTHONUNBUFFERED=x
-v : verbose (trace import statements); also PYTHONVERBOSE=x
can be supplied multiple times to increase verbosity
-V : print the Python version number and exit (also --version)
when given twice, print more information about the build
-W arg : warning control; arg is action:message:category:module:lineno
also PYTHONWARNINGS=arg
-x : skip first line of source, allowing use of non-Unix forms of #!cmd
-X opt : set implementation-specific option
--check-hash-based-pycs always|default|never:
control how Python invalidates hash-based .pyc files
--help-env: print help about Python environment variables and exit
--help-xoptions: print help about implementation-specific -X options and exit
--help-all: print complete help information and exit

Arguments:
file : program read from script file
- : program read from stdin (default; interactive mode if a tty)
arg ...: arguments passed to program in sys.argv[1:]

</pre>
[[#top|Back to Top]]

== Installation ==

Source code is obtained from [http://python.org/ Python]

== System ==
64-bit Linux

Python-Sapelo2

2026-07-23T17:59:39Z

Chelsea: /* Version */

[[Category:Sapelo2]][[Category:Software]][[Category:Programming]]
== Category ==
Programming
== Program On ==
Sapelo2
== Version ==
2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5, 3.14.2

== Author / Distributor ==
[http://www.python.org/ The Python Software Foundation]

== Description ==

Python is a programming language.

== Running Program ==

Also refer to [[Running Jobs on Sapelo2]]

There is no default python command on the system. The OS comes with a default /usr/bin/python3 command that provides Python v. 3.9.21. Scripts that have the first line:
<pre class="gscript">
#!/usr/bin/python
</pre>
will not work on Sapelo2 (with the Rocky 9 OS). We recommend that you change this line to
<pre class="gscript">
#!/usr/bin/env python
</pre>
and load one of the Python modules before running the script.

We have a set of Python versions installed on Sapelo2 via environment modules. To find out which Python modules are installed, please run the following command on the cluster:

<pre class="gscript">
ml spider Python
</pre>

For example, this output could look like this:
<pre class="gscript">
ml spider Python

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Python:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Python is a programming language that lets you work more quickly and integrate your systems more effectively.

Versions:
Python/2.7.18-GCCcore-11.3.0-bare
Python/2.7.18-GCCcore-11.3.0
Python/2.7.18-GCCcore-12.3.0
Python/2.7.18-GCCcore-13.2.0
Python/2.7.18-GCCcore-13.3.0
Python/3.9.6-GCCcore-11.2.0-bare
Python/3.9.6-GCCcore-11.2.0
Python/3.10.4-GCCcore-11.3.0-bare
Python/3.10.4-GCCcore-11.3.0
Python/3.10.8-GCCcore-12.2.0-bare
Python/3.10.8-GCCcore-12.2.0
Python/3.11.3-GCCcore-12.3.0-eb520
Python/3.11.3-GCCcore-12.3.0
Python/3.11.5-GCCcore-13.2.0
Python/3.12.3-GCCcore-13.3.0
Python/3.13.1-GCCcore-14.2.0
Python/3.13.5-GCCcore-14.3.0
Other possible modules matches:
Biopython Boost.Python Brotli-python GitPython IPython Python-bundle-PyPI bx-python flatbuffers-python graphviz-python intervaltree-python libxml2-python ...

----------------------------------------------------------------------------------
To find other possible module matches execute:

$ module -r spider '.*Python.*'

----------------------------------------------------------------------------------
For detailed information about a specific "Python" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:

$ module spider Python/3.12.3-GCCcore-13.3.0
----------------------------------------------------------------------------------

</pre>

----
[[#top|Back to Top]]

==About Python packages==

Some common third-party Python packages are installed individually as separate modules on the cluster.

===numpy, scipy, pandas===

The numpy, scipy, pandas, mpi4py, mpmath, and deap packages are installed in SciPy-bundle module:

<pre class="gscript">
ml spider SciPy-bundle

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
SciPy-bundle:
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Description:
Bundle of Python packages for scientific software

Versions:
SciPy-bundle/2021.10-foss-2021b
SciPy-bundle/2022.05-foss-2022a
SciPy-bundle/2023.07-gfbf-2023a
SciPy-bundle/2023.07-iimkl-2023a
SciPy-bundle/2023.11-gfbf-2023b
SciPy-bundle/2024.05-gfbf-2024a
SciPy-bundle/2024.06-foss-2023a-Python-2.7.18
SciPy-bundle/2025.06-gfbf-2025a

------------------------------------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "SciPy-bundle" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:

$ module spider SciPy-bundle/2025.06-gfbf-2025a
------------------------------------------------------------------------------------------------------------------------------------------------------------------

</pre>

Note that, when you load SciPy-bundle module, a specific version of Python that the package is built for will be loaded at first. This means that you don't have to load the Python module separately from loading SciPy-bundle module. For example:

*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when SciPy-bundle/2022.05-foss-2022a is loaded.

*Python/2.7.18-GCCcore-12.3.0 will be automatically loaded when SciPy-bundle/2024.06-foss-2023a-Python-2.7.18 is loaded.

*Python/3.12.3-GCCcore-13.3.0 will be automatically loaded when SciPy-bundle/2024.05-gfbf-2024a is loaded.

----
[[#top|Back to Top]]

===matplotlib===

The matplotlib package is installed in matplotlib module.

<pre class="gscript">
ml spider matplotlib

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
matplotlib:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Description:
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python
scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.

Versions:
matplotlib/2.2.5-foss-2023a-Python-2.7.18
matplotlib/3.5.2-foss-2022a
matplotlib/3.7.2-gfbf-2023a
matplotlib/3.8.2-gfbf-2023b
matplotlib/3.9.2-gfbf-2024a

----------------------------------------------------------------------------------
For detailed information about a specific "matplotlib" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:

$ module spider matplotlib/3.9.2-gfbf-2024a
----------------------------------------------------------------------------------
</pre>

Same as SciPy-bundle, when you load matplotlib module, a specific version of Python that matplotlib is built for will be loaded at first, which means you don't have to load the Python module separately from loading matplotlib module. For example:

*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when you load matplotlib/3.5.2-foss-2022a.

*Python/2.7.18-GCCcore-12.3.0 will be automatically loaded when you load matplotlib/2.2.5-foss-2023a-Python-2.7.18.

----
[[#top|Back to Top]]

===Biopython===

The Biopython package is installed in Biopython module.

<pre class="gscript">
ml spider biopython

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Biopython:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Description:
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries
and applications which address the needs of current and future work in bioinformatics.

Versions:
Biopython/1.79-foss-2022a
Biopython/1.83-foss-2023a
Biopython/1.84-foss-2023b
Biopython/1.84-foss-2024a

----------------------------------------------------------------------------------
For detailed information about a specific "Biopython" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:

$ module spider Biopython/1.84-foss-2024a
----------------------------------------------------------------------------------
</pre>

Same as above SciPy-bundle and matplotlib, when you load Biopython module, a specific version of Python that the package is built for will be loaded at first. You don't have to load the Python module separately from loading Biopython module. For ecample:

*Python/3.10.4-GCCcore-11.3.0 will be automatically loaded when Biopython/1.79-foss-2022a is loaded.

*Python/3.12.3-GCCcore-13.3.0 will be automatically loaded when Biopython/1.84-foss-2024a is loaded.

----
[[#top|Back to Top]]

==Examples==

===Example of using Python3===

To use Python 3.10.4, you can use the following in the first line of your Python code:

<pre class="gscript">
#!/apps/eb/Python/3.10.4-GCCcore-11.3.0/bin/python3
</pre>

Or use the following line in the first line of your Python code:
<pre class="gscript">
#!/usr/bin/env python
</pre>
an then you run your program as:

<pre class="gcommand">
module load Python/3.10.4-GCCcore-11.3.0

python myProgram.py
</pre>

===Example of using Python2===

To use Python 2.7.18, you can use the following in the first line of your Python code:

<pre class="gscript">
#!/apps/eb/Python/2.7.18-GCCcore-11.3.0/bin/python
</pre>

Or use the following line in the first line of your Python code:
<pre class="gscript">
#!/usr/bin/env python
</pre>
an then you run your program as:

<pre class="gcommand">
module load Python/2.7.18-GCCcore-11.3.0

python myProgram.py
</pre>

----
[[#top|Back to Top]]

== Documentation ==
Please see http://www.python.org/
== Installation ==
EasyBuild recipes

== System ==
64-bit Linux

Perl-Teaching

2026-07-23T17:58:21Z

Chelsea: /* Program On */

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
== Category ==

Programming

== Program On ==

Teaching

== Version ==
5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2, 5.42.0

== Author / Distributor ==

[http://www.perl.org/ Perl]

== Description ==
Larry Wall's Practical Extraction and Report Language. More information is at [http://www.perl.org/ Perl]

== Running Program ==

Use the command <pre>ml spider Perl</pre> to see all the Perl versions installed on the cluster. For example:

'''Version 5.38.2'''

It is installed in /apps/eb/Perl/5.38.2-GCCcore-13.3.0

To use this version, please load the module with
<pre class="gscript">
ml Perl/5.38.2-GCCcore-13.3.0
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Perl 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Perl.%j.out 
<nowiki>#</nowiki>SBATCH --error=Perl.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Perl/5.38.2-GCCcore-13.3.0 
perl [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Perl/5.38.2-GCCcore-13.3.0
perl -h

Usage: perl [switches] [--] [programfile] [arguments]
-0[octal/hexadecimal] specify record separator (\0, if no argument)
-a autosplit mode with -n or -p (splits $_ into @F)
-C[number/list] enables the listed Unicode features
-c check syntax only (runs BEGIN and CHECK blocks)
-d[t][:MOD] run program under debugger or module Devel::MOD
-D[number/letters] set debugging flags (argument is a bit mask or alphabets)
-e commandline one line of program (several -e's allowed, omit programfile)
-E commandline like -e, but enables all optional features
-f don't do $sitelib/sitecustomize.pl at startup
-F/pattern/ split() pattern for -a switch (//'s are optional)
-i[extension] edit <> files in place (makes backup if extension supplied)
-Idirectory specify @INC/#include directory (several -I's allowed)
-l[octnum] enable line ending processing, specifies line terminator
-[mM][-]module execute "use/no module..." before executing program
-n assume "while (<>) { ... }" loop around program
-p assume loop like -n but print line also, like sed
-s enable rudimentary parsing for switches after programfile
-S look for programfile using PATH environment variable
-t enable tainting warnings
-T enable tainting checks
-u dump core after parsing program
-U allow unsafe operations
-v print version, patchlevel and license
-V[:configvar] print configuration summary (or a single Config.pm variable)
-w enable many useful warnings
-W enable all warnings
-x[directory] ignore text before #!perl line (optionally cd to directory)
-X disable all warnings

Run 'perldoc perl' for more help with Perl.

</pre>
[[#top|Back to Top]]

== Installation ==

Source code is obtained from [http://www.perl.org/ Perl]

== System ==
64-bit Linux

Software

2026-07-23T17:58:11Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 22Jul2025, 29Aug2024 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.5, 3.1.0, 3.1.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2, 5.42.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

OrthoFinder-Sapelo2

2026-07-23T17:53:54Z

Chelsea: /* Program On */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==
2.5.5, 3.1.0, 3.1.5

== Author / Distributor ==

[https://github.com/davidemms/OrthoFinder OrthoFinder]

== Description ==
"OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format."
More details are at [https://github.com/davidemms/OrthoFinder OrthoFinder]

== Running Program ==

Please refer to [[Running Jobs on Sapelo2]]

 
'''Version 2.5.5'''

Version 2.5.5, installed at
*/apps/eb/OrthoFinder/2.5.5-foss-2022a/

To use version 2.5.5, please first load the module with

<pre class="gscript">
ml OrthoFinder/2.5.5-foss-2022a
</pre>
'''Version 3.1.0'''

Version 3.1.0, installed at
*/apps/eb/OrthoFinder/3.1.0-foss-2023a/

To use version 2.5.5, please first load the module with

<pre class="gscript">
ml OrthoFinder/3.1.0-foss-2023a
</pre>
'''Version 3.1.5'''

Version 3.1.5, installed at
*/apps/eb/OrthoFinder/3.1.5-foss-2025a/

To use version 2.5.5, please first load the module with

<pre class="gscript">
ml OrthoFinder/3.1.5-foss-2025a
</pre>
 
Note that if the option<pre class="gscript">-M msa</pre>is used as shown in the documentation below, this will allow for both multiple sequence alignment building as well as tree inference. The default methods for these processes (MAFFT and FastTree, respectively) are loaded with OrthoFinder/2.5.5-foss-2022a, but if you wish to use alternative methods as described in the documentation, you will need to load the modules for these methods yourself. Please refer to [[Available Toolchains and Toolchain Compatibility]] if you are unsure of what installations of these software will be compatible with our installation of OrthoFinder.

Here is an example of a shell script sub.sh to run OrthoFinder v2.5.5 at the batch queue:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_OrthoFinder
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32gb
#SBATCH --time=120:00:00
#SBATCH --output=log.%j.out
#SBATCH --error=log.%j.err
#SBATCH --mail-user=username@uga.edu
#SBATCH --mail-type=ALL

cd $SLURM_SUBMIT_DIR

ml OrthoFinder/2.5.5-foss-2022a

orthofinder -t 8 -a 8 [options]
</pre>

Here is an example of job submission
<pre class="gcommand">
sbatch ./sub.sh
</pre>

== Documentation ==

<pre class="gcommand">
ml OrthoFinder/2.5.5-foss-2022a
orthofinder -h

OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms

SIMPLE USAGE:
Run full OrthoFinder analysis on FASTA format proteomes in <dir>
orthofinder [options] -f <dir>

Add new species in <dir1> to previous run in <dir2> and run new analysis
orthofinder [options] -f <dir1> -b <dir2>

OPTIONS:
-t <int> Number of parallel sequence search threads [Default = 16]
-a <int> Number of parallel analysis threads
-d Input is DNA sequences
-M <txt> Method for gene tree inference. Options 'dendroblast' & 'msa'
[Default = dendroblast]
-S <txt> Sequence search program [Default = diamond]
Options: blast, diamond, diamond_ultra_sens, blast_gz, mmseqs, blast_nucl
-A <txt> MSA program, requires '-M msa' [Default = mafft]
Options: mafft, muscle
-T <txt> Tree inference method, requires '-M msa' [Default = fasttree]
Options: fasttree, raxml, raxml-ng, iqtree
-s <file> User-specified rooted species tree
-I <int> MCL inflation parameter [Default = 1.5]
--fewer-files Only create one orthologs file per species
-x <file> Info for outputting results in OrthoXML format
-p <dir> Write the temporary pickle files to <dir>
-1 Only perform one-way sequence search
-X Don't add species names to sequence IDs
-y Split paralogous clades below root of a HOG into separate HOGs
-z Don't trim MSAs (columns>=90% gap, min. alignment length 500)
-n <txt> Name to append to the results directory
-o <txt> Non-default results directory
-h Print this help text

WORKFLOW STOPPING OPTIONS:
-op Stop after preparing input files for BLAST
-og Stop after inferring orthogroups
-os Stop after writing sequence files for orthogroups
(requires '-M msa')
-oa Stop after inferring alignments for orthogroups
(requires '-M msa')
-ot Stop after inferring gene trees for orthogroups

WORKFLOW RESTART COMMANDS:
-b <dir> Start OrthoFinder from pre-computed BLAST results in <dir>
-fg <dir> Start OrthoFinder from pre-computed orthogroups in <dir>
-ft <dir> Start OrthoFinder from pre-computed gene trees in <dir>

LICENSE:
Distributed under the GNU General Public License (GPLv3). See License.md

CITATION:
When publishing work that uses OrthoFinder please cite:
Emms D.M. & Kelly S. (2019), Genome Biology 20:238

If you use the species tree in your work then please also cite:
Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278
Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914
</pre>
[[#top|Back to Top]]

== Installation ==

source code from [https://github.com/davidemms/OrthoFinder/releases OrthoFinder]

== System ==
64-bit Linux

Software

2026-07-23T17:51:39Z

Chelsea:

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 22Jul2025, 29Aug2024 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.5, 3.1.0, 3.1.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Software

2026-07-15T18:57:28Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 22Jul2025, 29Aug2024 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.4, 2.5.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

LAMMPS-Sapelo2

2026-07-14T21:49:44Z

Chelsea: /* Version */

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
== Category ==

Chemistry

== Program On ==

Sapelo2

== Version ==

22Jul2025, 29Aug2024

== Author / Distributor ==

Please see http://lammps.sandia.gov/authors.html

== Description ==

From http://lammps.sandia.gov/ :
"LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. "

== Running Program ==

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 23Jun2022'''

*Using the foss/2022a toolchain

This version was compiled with the foss/2022a toolchain (GNU 1.3.0 compilers and OpenMPI 4.1.4) and it is installed in /apps/eb/LAMMPS/23Jun2022-foss-2022a-kokkos

The binary is called lmp and it was compiled with the following packages:

Enabled packages: ASPHERE;ATC;AWPMD;BOCS;BODY;BPM;BROWNIAN;CG-DNA;CLASS2;COLLOID;COLVARS;COMPRESS;CORESHELL;DIELECTRIC;DIFFRACTION;DIPOLE;DPD-BASIC;DPD-MESO;DPD-REACT;DPD-SMOOTH;DRUDE;EFF;ELECTRODE;EXTRA-COMPUTE;EXTRA-DUMP;EXTRA-FIX;EXTRA-MOLECULE;EXTRA-PAIR;FEP;GRANULAR;H5MD;INTERLAYER;KIM;KOKKOS;KSPACE;LATBOLTZ;MACHDYN;MANIFOLD;MANYBODY;MC;MDI;MEAM;MGPT;MISC;ML-IAP;ML-PACE;ML-RANN;ML-SNAP;MOFFF;MOLECULE;MOLFILE;MPIIO;NETCDF;OPENMP;OPT;ORIENT;PERI;PHONON;PLUGIN;PLUMED;POEMS;PTM;PYTHON;QEQ;QTB;REACTION;REAXFF;REPLICA;RIGID;SCAFACOS;SHOCK;SMTBQ;SPH;SPIN;SRD;TALLY;UEF;VORONOI;VTK;YAFF

To use this version of Lammps, first load the modules with
<pre class="gcommand">
ml LAMMPS/23Jun2022-foss-2022a-kokkos
</pre>

'''Example of shell scripts to run LAMMPS on the batch queue:'''

'''To use version 23Jun2022 with the foss-2022a toolchain'''

To run lmp version 23Jun2022 as a parallel job, using e.g. 2 node2 and 16 cores per node (sub.sh)
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=lammpsjob # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --nodes=2 # Number of nodes
#SBATCH --ntasks=32 # Number of MPI ranks
#SBATCH --ntasks-per-node=16 # How many tasks on each node
#SBATCH --cpus-per-task=1 # Number of cores per MPI rank
#SBATCH --mem-per-cpu=600mb # Memory per processor
#SBATCH --time=02:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

cd $SLURM_SUBMIT_DIR

ml LAMMPS/23Jun2022-foss-2022a-kokkos

srun lmp -in file.in > file.out

</pre>
Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.



== Documentation ==

Please see links from http://lammps.sandia.gov/

A user manual is available at http://lammps.sandia.gov/doc/Manual.html
== Installation ==

Source code downloaded from https://www.lammps.org/download.html

== System ==
64-bit Linux

Software

2026-07-14T21:49:25Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 22Jul2025, 29Aug2024 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023a, R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.4, 2.5.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

File:Linux Training For New Users Of Cluster Suchi 04252019.pdf

2026-07-14T19:49:06Z

Chelsea: Chelsea uploaded a new version of File:Linux Training For New Users Of Cluster Suchi 04252019.pdf

File:Using Sapelo2 Cluster at the GACRC Part II Rocky8.pdf

2026-07-14T19:48:35Z

Chelsea: Chelsea uploaded a new version of File:Using Sapelo2 Cluster at the GACRC Part II Rocky8.pdf

== Summary ==
Sapelo2 partII training, Rocky8

Training

2026-07-13T17:10:58Z

Chelsea: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''August 2026''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|July 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|July 22nd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 7th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 12th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 20th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|July 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 20th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 5th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 10th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 18th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

===Sapelo2 Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

===Teaching Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

===Linux Training for New Cluster Users===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

===Installing Software Packages in Virtual Environments on Sapelo2===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

===Job Parallelization with GNU Parallel and Slurm Arrays===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}



===Topical Sessions===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

===Out-Reach/In-Class Talk===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Training

2026-07-13T17:10:36Z

Chelsea: /* Event Schedule */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''June 2026''', the GACRC is hosting 6 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

==Event Schedule==

This section describes the training workshops that we offer, along with the sessions that are currently scheduled.

===Sapelo2 Cluster New User Training===

This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.

'''Prerequisites:'''

*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Workshop Training Goals:'''

*Understand the layout of Sapelo2

*Understand the Sapelo2 file systems

*Understand the Sapelo2 partitions

*Understand the Sapelo2 software environment

*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

*Understand how to initiate an interactive job

*Understand how to transfer files to and from the cluster

*Understand how to get support from GACRC support team when you have any issues on cluster

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|June 18th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|July 10th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|July 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|July 22nd, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 7th, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 12th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|August 20th, Thursday, 2:00 PM - 4:00 PM
|}

===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.

The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.

'''Prerequisite:'''

Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.

*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|June 16th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 8th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 14th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|July 20th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 5th, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 10th, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|August 18th, Tuesday, 1:00 PM - 3:00 PM
|}

===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Learn about high-performance computing framework

2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?

3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?

4. How can I make my job run more efficiently (through the correct use of software and hardware)?

5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|
|}

===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Learn how to create a virtual environment on Sapelo2

2. Be able to install software packages into both Conda and Python virtual environments

3. Understand how to manage dependencies of their virtual environments

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|
|}

===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

'''Prerequisite:'''

Must already have strong understanding of the Linux environment and Sapelo2.

'''Training Goals:'''

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

'''Scheduled Sessions:'''

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|
|}



==How to Register==

The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 GACRC User Account Request Form].

If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.



== Download==

This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.

===Sapelo2 Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}

===Teaching Cluster Training===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2026.pdf]]
|-
|}

===Linux Training for New Cluster Users===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

===Installing Software Packages in Virtual Environments on Sapelo2===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_virtual_environments_training_v1.2.pdf]]
|}

===Job Parallelization with GNU Parallel and Slurm Arrays===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.1.pdf]]
|}



===Topical Sessions===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]

|}

===Out-Reach/In-Class Talk===

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|GEOG - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop-python-Spring2026.pdf]]
|-
|BCMB8330 - Spring2026 || In-Class || [[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2026.pdf]]
|-
|PHYS8601 - Spring2026 || In-Class || [[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2026.pdf]] ; [[Media:Gacrc_handout2026_phys8601.pdf]]
|-
|Anthropology Department || Out-Reach || [[Media:GACRC_overview_20251117_Anthropology.pdf]]
|-
|CSP seminar - Fall 2025|| Out-Reach || [[Media:GACRC_overview_20250819-CSP.pdf]]

|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

Trinity-Sapelo2

2026-07-09T16:22:56Z

Chelsea: /* Utilizing /lscratch in Trinity Job Submission Script */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==

2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2

== Author / Distributor ==

Trinity is now published online at [http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html Nature Biotechnology]. The Broad Institute’s [http://www.broadinstitute.org/blog/suite-tools-takes-flight blog] has a story on how the Trinity project came together.

More details at [https://github.com/trinityrnaseq/trinityrnaseq/ Trinity github page]

== Description ==

From https://github.com/trinityrnaseq/trinityrnaseq/wiki:

"Trinity, developed at the [http://www.broadinstitute.org/ Broad Institute], represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:

Inchworm assembles the RNA-Seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.

Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.

Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes."

[[#top|Back to Top]]

== Running Program ==

===General Instructions===

Also refer to [[Running Jobs on Sapelo2]]

Trinity versions 2.5.1, 2.8.4, 2.8.5, 2.15.1, and 2.15.2 are installed on Sapelo2.

* Mostly trinity needs to run at large memory queue, namely highmem_p, as in the sample script below.
* '''Trinity is best run utilizing /lscratch, please see [[Trinity-Sapelo2#Utilizing .2Flscratch in Trinity Job Submission Script|Utilizing /lscratch for Trinity Jobs]] or scroll down to see how to configure your job submission script to use /lscratch'''
* To run Trinity in conjunction with HpcGridRunner, please see [[Trinity-HpcGridRunner|our wiki page on Trinity HpcGridRunner]].

* Memory estimates according to an old Trinity documentation: For a 4 billion base mouse, it uses about 50 GB memory at peak.

* Do not ask for more than 24 CPU cores at the command and double the quantity of requesting CPU from queue. e.g. at the following, command ask for 8 CPU cores and at the header, it asks for --cpus-per-task=8.

* Using --normalize_reads could tremendously reduce the needs of memory. For this feature, please ensure there is no space in sequence name and quality score names, and adding "/1", "/2" to sequence name to make each seq name unique for pair reads in fasta /fq header.

* '''Please use the --full_cleanup option to make sure Trinity cleans up after itself.''' This helps a lot in keeping the number of files on Lustre storage under control.

* If previous jobs left dir trinity_out_dir, remove it before start another trinity job.

===Trinity versions 2.5.1, 2.8.4, and 2.8.5 Singularity Container on Sapelo2===

On the Sapelo2 cluster, singularity containers have access to the users home directory ($HOME), scratch directory (/scratch), lscratch directory (/lscratch), /tmp directory (/tmp) inside the container.

All environment variables set before executing singularity command is available inside the container.

To run Trinity v2.5.1, sample command is as below:

<pre class="gcommand">
singularity exec /apps/singularity-images/trinity-2.5.1.simg COMMAND
</pre>

where COMMAND should be replaced by the command you want to use.

To run Trinity v2.8.4, sample command is as below:

<pre class="gcommand">
singularity exec /apps/singularity-images/trinity-2.8.4.simg COMMAND
</pre>

To run Trinity v2.8.5, sample command is as below:

<pre class="gcommand">
singularity exec /apps/singularity-images/trinity-2.8.5.simg COMMAND
</pre>

where COMMAND should be replaced by the command you want to use.

Example of a shell script sub.sh to run Trinity v2.8.4 on the batch partition:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_Trinity # Job name (j_Trinity)
#SBATCH --partition=batch # Partition name (batch or highmem_p)
#SBATCH --ntasks=1 # Run job in single task
#SBATCH --cpus-per-task=8 # CPU core count per task
#SBATCH --mem=100G # Memory per node (100GB)
#SBATCH --time=48:00:00 # Time limit hrs:min:sec or days-hours:minutes:seconds
#SBATCH --export=NONE # Do not export any user’s explicit environment variables to compute node
#SBATCH --output=log.%j.out # Standard output log
#SBATCH --error=log.%j.err # Standard error log

#SBATCH --mail-user=username@uga.edu # Where to send mail
#SBATCH --mail-type=ALL # Mail events (BEGIN, END, FAIL, ALL)

cd $SLURM_SUBMIT_DIR

singularity exec /apps/singularity-images/trinity-2.8.4.simg Trinity --seqType <string> --max_memory 100G --CPU 8 --no_version_check --full_cleanup --normalize_reads
</pre>

Example to run Trinity script align_and_estimate_abundance.pl:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_Trinity # Job name (j_Trinity)
#SBATCH --partition=batch # Partition name (batch or highmem_p)
#SBATCH --ntasks=1 # Run job in single task
#SBATCH --cpus-per-task=1 # CPU core count per task
#SBATCH --mem=20G # Memory per node (100GB)
#SBATCH --time=48:00:00 # Time limit hrs:min:sec or days-hours:minutes:seconds
#SBATCH --export=NONE # Do not export any user’s explicit environment variables to compute node
#SBATCH --output=%x_%j.out # Standard output log
#SBATCH --error=%x_%j.err # Standard error log

#SBATCH --mail-user=username@uga.edu # Where to send mail
#SBATCH --mail-type=ALL # Mail events (BEGIN, END, FAIL, ALL)

cd $SLURM_SUBMIT_DIR

singularity exec /apps/singularity-images/trinity-2.8.4.simg /usr/local/bin/trinityrnaseq/util/align_and_estimate_abundance.pl [options]
</pre>

Where [options] need to be added as appropriate. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.

[[#top|Back to Top]]

===Trinity versions 2.15.1 and 2.15.2 Software Module on Sapelo2 ===

*version 2.15.1 running with Python3 is installed at /apps/eb/Trinity/2.15.1-foss-2022a

To run Trinity v2.15.1, please load the module:

<pre class="gcommand">
module load Trinity/2.15.1-foss-2022a
</pre>

*version 2.15.2 running with Python3 is installed at /apps/eb/Trinity/2.15.2-foss-2023a

To run Trinity v2.15.2, please load the module:

<pre class="gcommand">
module load Trinity/2.15.2-foss-2023a
</pre>

Example of a shell script sub.sh to run Trinity v2.15.1 on the batch partition:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_Trinity # Job name (j_Trinity)
#SBATCH --partition=batch # Partition name (batch or highmem_p)
#SBATCH --ntasks=1 # Run job in single task
#SBATCH --cpus-per-task=8 # CPU core count per task
#SBATCH --mem=100G # Memory per node (100GB)
#SBATCH --time=48:00:00 # Time limit hrs:min:sec or days-hours:minutes:seconds
#SBATCH --export=NONE # Do not export any user’s explicit environment variables to compute node
#SBATCH --output=log.%j.out # Standard output log
#SBATCH --error=log.%j.err # Standard error log

#SBATCH --mail-user=username@uga.edu # Where to send mail
#SBATCH --mail-type=ALL # Mail events (BEGIN, END, FAIL, ALL)

cd $SLURM_SUBMIT_DIR

module load Trinity/2.15.1-foss-2022a

Trinity --seqType <string> --max_memory 100G --CPU 8 --no_version_check --full_cleanup --normalize_reads
</pre>

Example to run Trinity script align_and_estimate_abundance.pl:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_Trinity # Job name (j_Trinity)
#SBATCH --partition=batch # Partition name (batch or highmem_p)
#SBATCH --ntasks=1 # Run job in single task
#SBATCH --cpus-per-task=1 # CPU core count per task
#SBATCH --mem=20G # Memory per node (100GB)
#SBATCH --time=48:00:00 # Time limit hrs:min:sec or days-hours:minutes:seconds
#SBATCH --export=NONE # Do not export any user’s explicit environment variables to compute node
#SBATCH --output=%x_%j.out # Standard output log
#SBATCH --error=%x_%j.err # Standard error log

#SBATCH --mail-user=username@uga.edu # Where to send mail
#SBATCH --mail-type=ALL # Mail events (BEGIN, END, FAIL, ALL)

cd $SLURM_SUBMIT_DIR

module load Trinity/2.15.1-foss-2022a

${EBROOTTRINITY}/trinityrnaseq-v2.10.0/util/align_and_estimate_abundance.pl [options]
</pre>

Where EBROOTTRINITY is the env variable storing Trinity installation pat, i.e., /apps/eb/Trinity/2.15.1-foss-2022a ; [options] need to be added as appropriate. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.

[[#top|Back to Top]]

==Utilizing /lscratch in Trinity Job Submission Script==
* Utilizing /lscratch allows Trinity jobs to run much faster and smoother and also negates the effects of heavy IO traffic.
* This /lscratch directory resides on the local hard drive of the compute node that your job gets allocated to (which means you cannot access this directory outside the job submission script).
* Below is a sample job submission script including steps so you can see what you need to add to your job submission script in order to make your Trinity job utilize /lscratch.
** As well as adding the 6 steps below, please also add the Slurm header --gres=lscratch:___ which requests space in /lscratch. The default units for this is GB and in the example submission script below, we are requesting 200GB of space with the line '''''#SBATCH --gres=lscratch:200''''' (it is the last Slurm header). Please only request as much space in /lscratch as is needed for your job.

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_Trinity # Job name (j_Trinity)
#SBATCH --partition=batch # Partition name (batch or highmem_p)
#SBATCH --ntasks=1 # Run job in single task
#SBATCH --cpus-per-task=36 # CPU core count per task
#SBATCH --mem=128G # Memory per node (100GB)
#SBATCH --time=48:00:00 # Time limit hrs:min:sec or days-hours:minutes:seconds
#SBATCH --export=NONE # Do not export any user’s explicit environment variables to compute node
#SBATCH --output=log.%j.out # Standard output log
#SBATCH --error=log.%j.err # Standard error log
#SBATCH --mail-user=username@uga.edu # Where to send mail
#SBATCH --mail-type=ALL # Mail events (BEGIN, END, FAIL, ALL)
#SBATCH --gres=lscratch:200

cd $SLURM_SUBMIT_DIR

# Step 1: create a directory in /lscratch

mkdir -p /lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs

# Step 2: copy over any input files.

cp file1.fastq.gz /lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs
cp file2.fastq.gz /lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs
cp file3.bam /lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs

# Step 3: change directories into /lscratch

cd /lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs

# Step 4: your normal job lines (loading Trinity and running Trinity command)

module load Trinity/2.15.1-foss-2022a

Trinity --seqType fq --left 'file1.fastq.gz' --right 'file2.fastq.gz' --CPU 36 --max_memory 120G --output '/lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs/trinity'

Trinity --genome_guided_bam 'file3.bam' --genome_guided_max_intron 10000 --CPU 36 --max_memory 120G --output '/lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs/trinity'

### NOTE: the directory specified in --output is the directory created in step 1 with the addition of /trinity at the end. This is because Trinity writes some files in the --output dir and some right above it.

# Step 5: copy output files back over to a certain location in /scratch which you can change below

cp -r /lscratch/${USER}/${SLURM_JOB_ID}/ /scratch/${USER}/some/directory

# Step 6: clean up /lscratch directory **VERY IMPORTANT STEP**

rm -rf /lscratch/${USER}/${SLURM_JOB_ID}
</pre>

* Please feel free to submit a ticket to us if you would like further help, explanations of how /lscratch works, or to even look over your submission script to ensure it is correctly utilizing /lscratch!

==Job Submission==

Submit a job submission script (sub.sh) to Sapelo2:

<pre class="gcommand">
sbatch sub.sh
</pre>

[[#top|Back to Top]]

==Documentation ==

More details at [https://github.com/trinityrnaseq/trinityrnaseq/wiki/ Trinity wiki page]

<pre class="gcommand">
[cft07037@b1-24 ~]$ ml Trinity/2.15.1-foss-2022a
To execute picard run: java -jar $EBROOTPICARD/picard.jar
[cft07037@b1-24 ~]$ Trinity --show_full_usage_info

###############################################################################
#

______ ____ ____ ____ ____ ______ __ __
| || \ | || \ | || || | |
| || D ) | | | _ | | | | || | |
|_| |_|| / | | | | | | | |_| |_|| ~ |
| | | \ | | | | | | | | | |___, |
| | | . \ | | | | | | | | | | |
|__| |__|\_||____||__|__||____| |__| |____/

Trinity-v2.15.1

#
#
# Required:
#
# --seqType <string> :type of reads: ('fa' or 'fq')
#
# --max_memory <string> :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
# provided in Gb of RAM, ie. '--max_memory 10G'
#
# If paired reads:
# --left <string> :left reads, one or more file names (separated by commas, no spaces)
# --right <string> :right reads, one or more file names (separated by commas, no spaces)
#
# Or, if unpaired reads:
# --single <string> :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )
#
# Or,
# --samples_file <string> tab-delimited text file indicating biological replicate relationships.
# ex.
# cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq
# cond_A cond_A_rep2 A_rep2_left.fq A_rep2_right.fq
# cond_B cond_B_rep1 B_rep1_left.fq B_rep1_right.fq
# cond_B cond_B_rep2 B_rep2_left.fq B_rep2_right.fq
#
# # if single-end instead of paired-end, then leave the 4th column above empty.
#
####################################
## Misc: #########################
#
# --SS_lib_type <string> :Strand-specific RNA-Seq read orientation.
# if paired: RF or FR,
# if single: F or R. (dUTP method = RF)
# See web documentation.
#
# --CPU <int> :number of CPUs to use, default: 2
# --min_contig_length <int> :minimum assembled contig length to report
# (def=200, must be >= 100)
#
# --long_reads <string> :fasta file containing error-corrected or circular consensus (CCS) pac bio reads
# (** note: experimental parameter **, this functionality continues to be under development)
#
# --genome_guided_bam <string> :genome guided mode, provide path to coordinate-sorted bam file.
# (see genome-guided param section under --show_full_usage_info)
#
# --long_reads_bam <string> :long reads to include for genome-guided Trinity
# (bam file consists of error-corrected or circular consensus (CCS) pac bio read aligned to the genome)
#
# --jaccard_clip :option, set if you have paired reads and
# you expect high gene density with UTR
# overlap (use FASTQ input file format
# for reads).
# (note: jaccard_clip is an expensive
# operation, so avoid using it unless
# necessary due to finding excessive fusion
# transcripts w/o it.)
#
# --trimmomatic :run Trimmomatic to quality trim reads
# see '--quality_trimming_params' under full usage info for tailored settings.
#
# --output <string> :name of directory for output (will be
# created if it doesn't already exist)
# default( your current working directory: "/home/cft07037/trinity_out_dir"
# note: must include 'trinity' in the name as a safety precaution! )
#
# --full_cleanup :only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta
#
# --cite :show the Trinity literature citation
#
# --verbose :provide additional job status info during the run.
#
# --version :reports Trinity version (Trinity-v2.15.1) and exits.
#
# --show_full_usage_info :show the many many more options available for running Trinity (expert usage).

#
# --no_super_reads :turn off super-reads mode
#
# --prep :Only prepare files (high I/O usage) and stop before kmer counting.
#
# --no_cleanup :retain all intermediate input files.
#
# --no_version_check :dont run a network check to determine if software updates are available.
#
# --no_symlink :dont symlink, just copy files instead (sets env var NO_SYMLINK=TRUE)
#
# --monitoring :use collectl to monitor all steps of Trinity
# --monitor_sec <int> : number of seconds for each interval of runtime monitoring (default: 60)
#
# --no_distributed_trinity_exec :do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
#
# --workdir <string> :where Trinity phase-2 assembly computation takes place (defaults to --output setting).
# (can set this to a node-local drive or RAM disk)
#
####################################################
# Inchworm and K-mer counting-related options: #####
#
# --min_kmer_cov <int> :min count for K-mers to be assembled by
# Inchworm (default: 1)
# --inchworm_cpu <int> :number of CPUs to use for Inchworm, default is min(6, --CPU option)
#
# --no_run_inchworm :stop after running jellyfish, before inchworm. (phase 1, read clustering only)
#
###################################
# Chrysalis-related options: ######
#
# --max_reads_per_graph <int> :maximum number of reads to anchor within
# a single graph (default: 200000)
# --min_glue <int> :min number of reads needed to glue two inchworm contigs
# together. (default: 2)
#
# --max_chrysalis_cluster_size <int> :max number of Inchworm contigs to be included in a single Chrysalis cluster. (default: 25)
#
# --no_bowtie :dont run bowtie to use pair info in chrysalis clustering.
#
# --no_run_chrysalis :stop after running inchworm, before chrysalis. (phase 1, read clustering only)
#
#####################################
### Butterfly-related options: ####
#
# --bfly_algorithm <string> : assembly algorithm to use. Options: ORIGINAL PASAFLY
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
# (see butterfly options: java -jar Butterfly.jar ).
# (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).
#
#
# Butterfly read-pair grouping settings (used to define 'pair paths'):
#
# --group_pairs_distance <int> :maximum length expected between fragment pairs (default: 500)
# (reads outside this distance are treated as single-end)
#
# ///////////////////////////////////////////////
# Butterfly default reconstruction mode settings.
#
# --path_reinforcement_distance <int> :minimum overlap of reads with growing transcript
# path (default: PE: 25, SE: 25)
# Set to 1 for the most lenient path extension requirements.
#
#
# /////////////////////////////////////////
# Butterfly transcript reduction settings:
#
# --no_path_merging : all final transcript candidates are output (including SNP variations, however, some SNPs may be unphased)
#
# By default, alternative transcript candidates are merged (in reality, discarded) if they are found to be too similar, according to the following logic:
#
# (identity=(numberOfMatches/shorterLen) > 98.0% or if we have <= 2 mismatches) and if we have internal gap lengths <= 10
#
# with parameters as:
#
# --min_per_id_same_path <int> default: 98 min percent identity for two paths to be merged into single paths
# --max_diffs_same_path <int> default: 2 max allowed differences encountered between path sequences to combine them
# --max_internal_gap_same_path <int> default: 10 maximum number of internal consecutive gap characters allowed for paths to be merged into single paths.
#
# If, in a comparison between two alternative transcripts, they are found too similar, the transcript with the greatest cumulative
# compatible read (pair-path) support is retained, and the other is discarded.
#
#
# //////////////////////////////////////////////
# Butterfly Java and parallel execution settings.
#
# --bflyHeapSpaceMax <string> :java max heap space setting for butterfly
# (default: 10G) => yields command
# 'java -Xmx10G -jar Butterfly.jar ... $bfly_opts'
# --bflyHeapSpaceInit <string> :java initial heap space settings for
# butterfly (default: 1G) => yields command
# 'java -Xms1G -jar Butterfly.jar ... $bfly_opts'
# --bflyGCThreads <int> :threads for garbage collection
# (default: 2))
# --bflyCPU <int> :CPUs to use (default will be normal
# number of CPUs; e.g., 2)
# --bflyCalculateCPU :Calculate CPUs based on 80% of max_memory
# divided by maxbflyHeapSpaceMax
#
# --bfly_jar <string> : /path/to/Butterfly.jar, otherwise default
# Trinity-installed version is used.
#
#
################################################################################
#### Quality Trimming Options ####
#
# --quality_trimming_params <string> defaults to: "ILLUMINACLIP:/apps/eb/Trinity/2.15.1-foss-2022a/trinityrnaseq-v2.15.1/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25"
#
################################################################################
#### In silico Read Normalization Options ###
#
# --normalize_max_read_cov <int> defaults to 200
# --normalize_by_read_set run normalization separate for each pair of fastq files,
# then one final normalization that combines the individual normalized reads.
# Consider using this if RAM limitations are a consideration.
#
# --just_normalize_reads stop after performing read normalization
#
# --no_normalize_reads :Do *not* run in silico normalization of reads. Defaults to max. read coverage of 200.
# see '--normalize_max_read_cov' under full usage info for tailored settings.
# (Note, as of Sept 21, 2016, normalization is on by default)
# (*Turning off normalization is not recommended for most applications)
#
# --no_parallel_norm_stats :Do not try to run the high-mem normalization stats generator in parallel for paired-end fastqs.
#
###############################################################################
#### Genome-guided de novo assembly
#
# * required:
#
# --genome_guided_max_intron <int> :maximum allowed intron length (also maximum fragment span on genome)
#
# * optional:
#
# --genome_guided_min_coverage <int> :minimum read coverage for identifying and expressed region of the genome. (default: 1)
#
# --genome_guided_min_reads_per_partition <int> :default min of 10 reads per partition
#
#
#######################################################################
# Trinity phase 2 (parallel assembly of read clusters) Options: #######
#
# --grid_exec <string> :your command-line utility for submitting jobs to the grid.
# This should be a command line tool that accepts a single parameter:
# ${your_submission_tool} /path/to/file/containing/commands.txt
# and this submission tool should exit(0) upon successful
# completion of all commands.
#
# --grid_node_CPU <int> number of threads for each parallel process to leverage. (default: 1)
#
# --grid_node_max_memory <string> max memory targeted for each grid node. (default: 1G)
#
# The --grid_node_CPU and --grid_node_max_memory are applied as
# the --CPU and --max_memory parameters for the Trinity jobs run in
# Trinity Phase 2 (assembly of read clusters)
#
# --FORCE ignore failed commands from earlier run, continue on.
# (Note, this should only be used after you've
# already dealt with these failed commands directly as needed)
#
########################################################################
# Singularity-related options
#
# --singularity_img <string> :path to a Trinity singularity image to use
#
# --singularity_extra_params <string> :additional parameters to include for the singularity command execution
#
#

#
#
###############################################################################
#
# *Note, a typical Trinity command might be:
#
# Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6
#
# (if you have multiple samples, use --samples_file ... see above for details)
#
# and for Genome-guided Trinity, provide a coordinate-sorted bam:
#
# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G
# --genome_guided_max_intron 10000 --CPU 6
#
# see: /apps/eb/Trinity/2.15.1-foss-2022a/trinityrnaseq-v2.15.1/sample_data/test_Trinity_Assembly/
# for sample data and 'runMe.sh' for example Trinity execution
#
# For more details, visit: http://trinityrnaseq.github.io
#
###############################################################################
</pre>
[[#top|Back to Top]]

== Installation==

Sources are downloaded from https://github.com/trinityrnaseq/trinityrnaseq

==System==
64-bit Linux

[[#top|Back to Top]]

Jupyter-Teaching

2026-07-08T13:59:43Z

Chelsea:

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
=== Category ===

Programming

=== Program On ===

Teaching

=== Version ===

6.4.12

===Author / Distributor===

[https://jupyter.readthedocs.io/en/latest/releases.html#jupyter-notebook Jupyter]

===Description===

"The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text" [https://jupyter.readthedocs.io/en/latest/index.html Jupyter]

===Running Program===

====Versions====

Please also refer to [[Running Jobs on the teaching cluster]].

*Jupyter 6.4.12 can be accessed through Anaconda version 2022.10 which is installed at /apps/eb/Anaconda3/2022.10

'''Please note: You do not have to install jupyter notebook on your local machine.'''


===To use Jupyter notebook on Teaching cluster with an interactive job===
====Step 1====
'''The port number for the jupyter notebook server should be some random value between 8000 and 10000. Assign this value to the variable 'NOTEBOOKPORT' in the submission script below replacing 8888. Please do not use 8888. If more than one person uses that same value you cannot establish the ssh tunnel'''

Sample steps to use jupyter 6.4.12, once you are connected to Teaching cluster, type each line below one by one, pressing enter after each one:

<pre class="gcommand">
interact # wait for interactive session to start

NOTEBOOKPORT=8888 # must change this to a random number between 8000 and 10000

IPUSED=$(hostname -i)

echo "NOTEBOOKPORT is " $NOTEBOOKPORT

echo "IPUSED is " $IPUSED

module load Anaconda3/2022.10

jupyter-notebook --port $NOTEBOOKPORT --ip=$IPUSED --no-browser

</pre>

====Step 2====
After running the steps above, '''establish another ssh tunnel''' from your desktop or laptop to Teaching cluster login node at port NOTEBOOKPORT.

To establish another ssh tunnel, follow the steps below for your OS

* '''For Mac/Linux Users'''

If you are using a Linux or Apple machine for your desktop or laptop, open a new terminal use the following command to establish the ssh tunnel between the two terminals

'''Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using ''' (see the output of the '''echo''' commands above)
<pre class="gcommand">
ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@teach.gacrc.uga.edu
</pre>

Unless you have ssh key configured, you will be prompted for your MyID password and for Archpass Duo authentication. Once authentication is established, this session prompt will hang and you are ready to go to the next step.

* '''For Windows Users'''

If you are using a Windows machine for your desktop or laptop

# Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' to use in place of the ssh client
# Open a Windows Terminal
# Navigate to the location where the plink.exe file was downloaded
## For example, if plink.exe was downloaded to your Downloads folder you could type '''cd C:\Users\yourusername\Downloads'''
## You can check that you are in the same location as plink.exe by simply typing dir into the Windows Terminal. This command works the same as ls for linux and just lists the contents of your current location so if you see plink.exe in the output of the dir command, then you know you are in the same location as the plink.exe file
# Then you can type the command below into the Windows Terminal:

'''Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using ''' (see the output of the '''echo''' commands above)
<pre class="gcommand">
plink -ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@teach.gacrc.uga.edu
</pre>
====Step 3====
Once you establish the ssh tunnel by running the command above you can access the Jupyter notebook by copy and pasting on the URLs from your interactive session into a browser OR by going to '''http://localhost:NOTEBOOKPORT''' using the browser on your desktop or laptop (make sure you replace NOTEBOOKPORT with the port number you used in the interactive session). If the page displayed on the browser asks for a token or password, you can check the token shown in your interactive session and copy and paste it into the token field in the page displayed in your browser. For example, the interact terminal might show something like this:

<pre class="gcommand">
[I 14:34:50.423 NotebookApp] Serving notebooks from local directory: /home/zhuofei
[I 14:34:50.423 NotebookApp] The Jupyter Notebook is running at:
[I 14:34:50.424 NotebookApp] http://10.31.32.126:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
[I 14:34:50.424 NotebookApp] or http://127.0.0.1:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
[I 14:34:50.424 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 14:34:50.431 NotebookApp]

To access the notebook, open this file in a browser:
file:///home/zhuofei/.local/share/jupyter/runtime/nbserver-3690-open.html
Or copy and paste one of these URLs:
http://10.31.32.126:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
or http://127.0.0.1:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
</pre>

Copy and paste the token, which in the example above is cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf, into the proper field in the page displayed in your browser.

===Documentation===

Details at https://jupyter.readthedocs.io/en/latest/index.html

===System===
64-bit Linux

LAMMPS-Sapelo2

2026-07-08T13:59:09Z

Chelsea:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
== Category ==

Chemistry

== Program On ==

Sapelo2

== Version ==

23Jun2022

== Author / Distributor ==

Please see http://lammps.sandia.gov/authors.html

== Description ==

From http://lammps.sandia.gov/ :
"LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. "

== Running Program ==

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 23Jun2022'''

*Using the foss/2022a toolchain

This version was compiled with the foss/2022a toolchain (GNU 1.3.0 compilers and OpenMPI 4.1.4) and it is installed in /apps/eb/LAMMPS/23Jun2022-foss-2022a-kokkos

The binary is called lmp and it was compiled with the following packages:

Enabled packages: ASPHERE;ATC;AWPMD;BOCS;BODY;BPM;BROWNIAN;CG-DNA;CLASS2;COLLOID;COLVARS;COMPRESS;CORESHELL;DIELECTRIC;DIFFRACTION;DIPOLE;DPD-BASIC;DPD-MESO;DPD-REACT;DPD-SMOOTH;DRUDE;EFF;ELECTRODE;EXTRA-COMPUTE;EXTRA-DUMP;EXTRA-FIX;EXTRA-MOLECULE;EXTRA-PAIR;FEP;GRANULAR;H5MD;INTERLAYER;KIM;KOKKOS;KSPACE;LATBOLTZ;MACHDYN;MANIFOLD;MANYBODY;MC;MDI;MEAM;MGPT;MISC;ML-IAP;ML-PACE;ML-RANN;ML-SNAP;MOFFF;MOLECULE;MOLFILE;MPIIO;NETCDF;OPENMP;OPT;ORIENT;PERI;PHONON;PLUGIN;PLUMED;POEMS;PTM;PYTHON;QEQ;QTB;REACTION;REAXFF;REPLICA;RIGID;SCAFACOS;SHOCK;SMTBQ;SPH;SPIN;SRD;TALLY;UEF;VORONOI;VTK;YAFF

To use this version of Lammps, first load the modules with
<pre class="gcommand">
ml LAMMPS/23Jun2022-foss-2022a-kokkos
</pre>

'''Example of shell scripts to run LAMMPS on the batch queue:'''

'''To use version 23Jun2022 with the foss-2022a toolchain'''

To run lmp version 23Jun2022 as a parallel job, using e.g. 2 node2 and 16 cores per node (sub.sh)
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=lammpsjob # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --nodes=2 # Number of nodes
#SBATCH --ntasks=32 # Number of MPI ranks
#SBATCH --ntasks-per-node=16 # How many tasks on each node
#SBATCH --cpus-per-task=1 # Number of cores per MPI rank
#SBATCH --mem-per-cpu=600mb # Memory per processor
#SBATCH --time=02:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

cd $SLURM_SUBMIT_DIR

ml LAMMPS/23Jun2022-foss-2022a-kokkos

srun lmp -in file.in > file.out

</pre>
Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.



== Documentation ==

Please see links from http://lammps.sandia.gov/

A user manual is available at http://lammps.sandia.gov/doc/Manual.html
== Installation ==

Source code downloaded from https://www.lammps.org/download.html

== System ==
64-bit Linux

Jupyter-Teaching

2026-07-08T13:19:00Z

Chelsea:

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
=== Category ===

Programming

=== Program On ===

Teaching

=== Version ===

6.4.12, test

===Author / Distributor===

[https://jupyter.readthedocs.io/en/latest/releases.html#jupyter-notebook Jupyter]

===Description===

"The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text" [https://jupyter.readthedocs.io/en/latest/index.html Jupyter]

===Running Program===

====Versions====

Please also refer to [[Running Jobs on the teaching cluster]].

*Jupyter 6.4.12 can be accessed through Anaconda version 2022.10 which is installed at /apps/eb/Anaconda3/2022.10

'''Please note: You do not have to install jupyter notebook on your local machine.'''


===To use Jupyter notebook on Teaching cluster with an interactive job===
====Step 1====
'''The port number for the jupyter notebook server should be some random value between 8000 and 10000. Assign this value to the variable 'NOTEBOOKPORT' in the submission script below replacing 8888. Please do not use 8888. If more than one person uses that same value you cannot establish the ssh tunnel'''

Sample steps to use jupyter 6.4.12, once you are connected to Teaching cluster, type each line below one by one, pressing enter after each one:

<pre class="gcommand">
interact # wait for interactive session to start

NOTEBOOKPORT=8888 # must change this to a random number between 8000 and 10000

IPUSED=$(hostname -i)

echo "NOTEBOOKPORT is " $NOTEBOOKPORT

echo "IPUSED is " $IPUSED

module load Anaconda3/2022.10

jupyter-notebook --port $NOTEBOOKPORT --ip=$IPUSED --no-browser

</pre>

====Step 2====
After running the steps above, '''establish another ssh tunnel''' from your desktop or laptop to Teaching cluster login node at port NOTEBOOKPORT.

To establish another ssh tunnel, follow the steps below for your OS

* '''For Mac/Linux Users'''

If you are using a Linux or Apple machine for your desktop or laptop, open a new terminal use the following command to establish the ssh tunnel between the two terminals

'''Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using ''' (see the output of the '''echo''' commands above)
<pre class="gcommand">
ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@teach.gacrc.uga.edu
</pre>

Unless you have ssh key configured, you will be prompted for your MyID password and for Archpass Duo authentication. Once authentication is established, this session prompt will hang and you are ready to go to the next step.

* '''For Windows Users'''

If you are using a Windows machine for your desktop or laptop

# Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' to use in place of the ssh client
# Open a Windows Terminal
# Navigate to the location where the plink.exe file was downloaded
## For example, if plink.exe was downloaded to your Downloads folder you could type '''cd C:\Users\yourusername\Downloads'''
## You can check that you are in the same location as plink.exe by simply typing dir into the Windows Terminal. This command works the same as ls for linux and just lists the contents of your current location so if you see plink.exe in the output of the dir command, then you know you are in the same location as the plink.exe file
# Then you can type the command below into the Windows Terminal:

'''Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using ''' (see the output of the '''echo''' commands above)
<pre class="gcommand">
plink -ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@teach.gacrc.uga.edu
</pre>
====Step 3====
Once you establish the ssh tunnel by running the command above you can access the Jupyter notebook by copy and pasting on the URLs from your interactive session into a browser OR by going to '''http://localhost:NOTEBOOKPORT''' using the browser on your desktop or laptop (make sure you replace NOTEBOOKPORT with the port number you used in the interactive session). If the page displayed on the browser asks for a token or password, you can check the token shown in your interactive session and copy and paste it into the token field in the page displayed in your browser. For example, the interact terminal might show something like this:

<pre class="gcommand">
[I 14:34:50.423 NotebookApp] Serving notebooks from local directory: /home/zhuofei
[I 14:34:50.423 NotebookApp] The Jupyter Notebook is running at:
[I 14:34:50.424 NotebookApp] http://10.31.32.126:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
[I 14:34:50.424 NotebookApp] or http://127.0.0.1:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
[I 14:34:50.424 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 14:34:50.431 NotebookApp]

To access the notebook, open this file in a browser:
file:///home/zhuofei/.local/share/jupyter/runtime/nbserver-3690-open.html
Or copy and paste one of these URLs:
http://10.31.32.126:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
or http://127.0.0.1:8888/?token=cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf
</pre>

Copy and paste the token, which in the example above is cf8fbaace953bbae0b31df9556a97d0930702fd65b7cfaaf, into the proper field in the page displayed in your browser.

===Documentation===

Details at https://jupyter.readthedocs.io/en/latest/index.html

===System===
64-bit Linux

Jupyter-Sapelo2

2026-07-08T13:17:29Z

Chelsea:

[[Category:Sapelo2]][[Category:Software]][[Category:Programming]]
== Category ==

Programming

== Program On ==

Sapelo2

== Version ==

6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7

== Author / Distributor ==

[https://jupyter.readthedocs.io/en/latest/index.html Jupyter]

== Description ==

"The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text" [https://jupyter.readthedocs.io/en/latest/index.html Jupyter]

== Running Program ==

===Versions===

Please also refer to [[Running Jobs on Sapelo2]].

*Jupyter 6.5.6 is installed as a module called JupyterNotebook/6.5.6-GCCcore-11.3.0 and it uses Python 3.10.4

*Jupyter 7.0.2 is installed as a module called JupyterNotebook/7.0.2-GCCcore-12.3.0 and it uses Python 3.11.3

*Jupyter 7.2.0 is installed as a module called JupyterNotebook/7.2.0-GCCcore-13.2.0 and it uses Python 3.11.5

*Jupyter 7.2.3 is installed as a module called JupyterNotebook/7.2.3-GCCcore-13.3.0 and it uses Python 3.12.3

*Jupyter 7.4.4 is installed as a module called JupyterNotebook/7.4.4-GCCcore-14.2.0 and it uses Python 3.13.1

*Jupyter 7.4.7 is installed as a module called JupyterNotebook/7.4.7-GCCcore-14.3.0 and it uses Python 3.13.5

'''Please note: You do not have to install jupyter notebook on your local machine.'''

For example, to use Jupyter 7.2.3, please load the module:
<pre class="gcommand">
module load JupyterNotebook/7.2.3-GCCcore-13.3.0
</pre>



There are three options to use Jupyter notebook on Sapelo2.

===Option 1: Use the Jupyter notebook interactive app in the Open OnDemand interface (highly recommended)===

The best way to run a Jupyter notebook on Sapelo2 is using the Jupyter notebook interactive app in the [[OnDemand]] interface to Sapelo2.

Some Important Notes about requesting resources for a Jupyter Notebook session through Open OnDemand:

* With this option, you are able to use jupyter-notebook from centrally installed JupyterNotebook modules, which you can choose under "Jupyter Environment Setup".
* You can also choose which directory to start Jupyter from using the "Notebook Directory" option
** For example, if you put /scratch/MyID in that box, it will start your session from your scratch dir and you will only have access to the files and folders there.
** If you want to be able to access files in multiple directories (like both /home/MyID and /scratch/MyID) in one Jupyter session, you can set the starting Notebook Directory to simply / (root) which will allow you to access all of your directories.
* You are also able to load other modules before launching the Jupyter Notebook with "Extra Modules to Load". Please ensure that the modules you load here are compatible with the toolchain and Python version selected in the "Jupyter Environment Setup"
* The rest of the options are similar to the resources you would request in a normal job submission script (number of cores, time, memory, etc).

[[File:OOD_JupyterNotebook_example.png|alt=|border|850x850px]]

If you would like to use /lscratch for your jupyter notebook, open a Terminal in the jupyter notebook and there you can create an /lscratch/$USER directory and copy files to it. If you use /lscratch for your jupyter session, remember to copy any files you need to keep back to /scratch before closing this application.

To add a Conda virtual environment to Jupyter Notebook please see [[Using a Conda environment in Jupyter]]

To add a Python virtual environment to Jupyter Notebook please see [[Using a Python environment in Jupyter]]

=== Option 2: Use the Jupyter notebook in an X Desktop session in the Open OnDemand interface===

Another option to run jupyter-notebook from the Open OnDemand interface is to first start an X Desktop session in the [[OnDemand]] interface and run jupyter-notebook from that desktop. This option is helpful if
you would like to use a jupyter-notebook that is not installed as a central module, for example, one that is installed in a conda environment in the user's home dir.

Steps to follow:

*2.1: Open a browser on your local machine and point it to https://ondemand.gacrc.uga.edu (if accessing from off-campus, please connect to the UGA VPN first). Authenticate with UGA's SSO.*

*2.2: Start an X Desktop session on Sapelo2, choose the resources to use (e.g. number of cores, memory, walltime, partition, gres, etc) and click Launch.

*2.3: Once the session starts, click on "Launch X Desktop Session on Sapelo2"

*2.4: In the X Desktop session, click on the Terminal icon in the panel at the bottom to start a Terminal session on the compute node allocated to your job.

*2.5: If you would like to use /lscratch for your jupyter notebook, from the Terminal you can create an /lscratch/$USER directory and copy files to it.

*2.6: In the Terminal, load any modules you want to use and/or activate a conda environment, if using jupyter-notebook from a conda environment. For example, if you would like to use the central module JupyterNotebook/6.5.6-GCCcore-11.3.0, you could load it with
<pre class="gcommand">
ml JupyterNotebook/6.5.6-GCCcore-11.3.0
</pre>
You can also load other modules that are compatible with this one (in the example above, you could load other modules that use the GCCcore-11.3.0, GCC-11.3.0, gompi-2022a, or foss-2022a toolchains).

*2.7: Start jupyter-notebook in the Terminal with
<pre class="gcommand">
NOTEBOOKPORT=8888
jupyter-notebook --port $NOTEBOOKPORT --no-browser
</pre>
where NOTEBOOKPORT should be set to some random value between 8000 and 10000. The example above uses 8888, but please choose a different value.

In the terminal you should see some output ending with something like this:
<pre class="gcommand">

[I 09:26:53.882 NotebookApp] Jupyter Notebook 6.4.12 is running at:
[I 09:26:53.882 NotebookApp] http://10.2.1.91:8999/?token=83da4f2fb1f7f95bba6ba1e6d4d6ce5c81cadc09a602c811
[I 09:26:53.883 NotebookApp] or http://127.0.0.1:8999/?token=83da4f2fb1f7f95bba6ba1e6d4d6ce5c81cadc09a602c811
[I 09:26:53.883 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 09:26:53.887 NotebookApp]

To access the notebook, open this file in a browser:
file:///home/shtsai/.local/share/jupyter/runtime/nbserver-1942279-open.html
Or copy and paste one of these URLs:
http://10.2.1.91:8999/?token=83da4f2fb1f7f95bba6ba1e6d4d6ce5c81cadc09a602c811
or http://127.0.0.1:8999/?token=83da4f2fb1f7f95bba6ba1e6d4d6ce5c81cadc09a602c811
</pre>

*2.8: Start another Terminal in the X Desktop session and in it start firefox with
<pre class="gcommand">
/apps/eb/Firefox/141.0/firefox
</pre>

*2.9: In the firefox browser that opens in your X Desktop session, paste the html file listed in the output of the jupyter-notebook command. In the example above the line is
'''file:///home/shtsai/.local/share/jupyter/runtime/nbserver-1942279-open.html'''. This should open the jupyter notebook.

*2.10: If you use /lscratch for your jupyter session, remember to copy any files you need to keep back to /scratch before closing this X Desktop session.

To add a Conda environment to Jupyter Notebook please see [[Using a Conda environment in Jupyter]]

===Option 3: To use Jupyter notebook on sapelo2 with an interactive job (not recommended)===

'''The port number for the jupyter notebook server should be some random value between 8000 and 10000. Assign this value to the variable 'NOTEBOOKPORT' in the submission script below replacing 8888. Please do not use 8888. If more than one person uses that same value you cannot establish the ssh tunnel'''

Sample steps to use jupyter 6.4.12, once you connect to sapelo2:
<pre class="gcommand">
interact [OPTIONS]

NOTEBOOKPORT=8888

IPUSED=$(hostname -i)

echo "NOTEBOOKPORT is " $NOTEBOOKPORT

echo "IPUSED is " $IPUSED

module load Anaconda3/2022.10

jupyter-notebook --port $NOTEBOOKPORT --ip=$IPUSED --no-browser

</pre>

After running the steps above, establish a another ssh tunnel from your desktop or laptop to sapelo2 login node at port NOTEBOOKPORT.

'''For Mac/Linux Users'''

If you are using a Linux or Apple machine for your desktop or laptop you can use the following command to establish the ssh tunnel

'''Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using ''' (see the output of the '''echo''' commands above)
<pre class="gcommand">
ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@sapelo2.gacrc.uga.edu
</pre>

Unless you have ssh key configured, you will be prompted for your MyID password and for Archpass Duo authentication. Once authentication is established, this session prompt will hang and you are ready to go to the next step.

'''For Windows Users'''

If you are using a Windows machine for your desktop or laptop download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' to use in place of the ssh client.
The command for windows would be as follows:
Assuming the plink.exe is in the current directory where you have a command window open.

'''Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using ''' (see the output of the '''echo''' commands above)
<pre class="gcommand">
plink -ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@sapelo2.gacrc.uga.edu
</pre>

Once you establish the ssh tunnel by running the command above you can access the Jupyter notebook by going to '''http://localhost:NOTEBOOKPORT''' using the browser on your desktop or laptop (make sure you replace NOTEBOOKPORT with the port number you used in the qlogin session). If the page displayed on the browser asks for a token or password, you can check the token shown in your qlogin session and copy and paste it into the token field in the page displayed in your browser. For example, the qlogin terminal might show something like this:

<pre class="gcommand">
[I 11:16:00.939 NotebookApp] JupyterLab extension loaded from /apps/eb/Anaconda3/2022.10/lib/python3.7/site-packages/jupyterlab
[I 11:16:00.939 NotebookApp] JupyterLab application directory is /apps/eb/Anaconda3/2022.10/share/jupyter/lab
[I 11:16:00.942 NotebookApp] Serving notebooks from local directory: /home/zhuofei
[I 11:16:00.942 NotebookApp] The Jupyter Notebook is running at:
[I 11:16:00.942 NotebookApp] http://10.2.1.30:8888/?token=857f8a9f63cf42f698ac1845db64219516a23e248019cdeb
[I 11:16:00.942 NotebookApp] or http://127.0.0.1:8888/?token=857f8a9f63cf42f698ac1845db64219516a23e248019cdeb
[I 11:16:00.942 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 11:16:00.947 NotebookApp]

To access the notebook, open this file in a browser:
file:///home/zhuofei/.local/share/jupyter/runtime/nbserver-14353-open.html
Or copy and paste one of these URLs:
http://10.2.1.30:8888/?token=857f8a9f63cf42f698ac1845db64219516a23e248019cdeb
or http://127.0.0.1:8888/?token=857f8a9f63cf42f698ac1845db64219516a23e248019cdeb
</pre>

Copy and paste the token, which in the example above is 857f8a9f63cf42f698ac1845db64219516a23e248019cdeb, into the proper field in the page displayed in your browser.

==Documentation==

Details at https://jupyter.readthedocs.io/en/latest/index.html

==System==
64-bit Linux

LAMMPS-Sapelo2

2026-07-08T13:13:14Z

Chelsea: /* Version */

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
== Category ==

Chemistry

== Program On ==

Sapelo2

== Version ==

23Jun2022, test

== Author / Distributor ==

Please see http://lammps.sandia.gov/authors.html

== Description ==

From http://lammps.sandia.gov/ :
"LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. "

== Running Program ==

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 23Jun2022'''

*Using the foss/2022a toolchain

This version was compiled with the foss/2022a toolchain (GNU 1.3.0 compilers and OpenMPI 4.1.4) and it is installed in /apps/eb/LAMMPS/23Jun2022-foss-2022a-kokkos

The binary is called lmp and it was compiled with the following packages:

Enabled packages: ASPHERE;ATC;AWPMD;BOCS;BODY;BPM;BROWNIAN;CG-DNA;CLASS2;COLLOID;COLVARS;COMPRESS;CORESHELL;DIELECTRIC;DIFFRACTION;DIPOLE;DPD-BASIC;DPD-MESO;DPD-REACT;DPD-SMOOTH;DRUDE;EFF;ELECTRODE;EXTRA-COMPUTE;EXTRA-DUMP;EXTRA-FIX;EXTRA-MOLECULE;EXTRA-PAIR;FEP;GRANULAR;H5MD;INTERLAYER;KIM;KOKKOS;KSPACE;LATBOLTZ;MACHDYN;MANIFOLD;MANYBODY;MC;MDI;MEAM;MGPT;MISC;ML-IAP;ML-PACE;ML-RANN;ML-SNAP;MOFFF;MOLECULE;MOLFILE;MPIIO;NETCDF;OPENMP;OPT;ORIENT;PERI;PHONON;PLUGIN;PLUMED;POEMS;PTM;PYTHON;QEQ;QTB;REACTION;REAXFF;REPLICA;RIGID;SCAFACOS;SHOCK;SMTBQ;SPH;SPIN;SRD;TALLY;UEF;VORONOI;VTK;YAFF

To use this version of Lammps, first load the modules with
<pre class="gcommand">
ml LAMMPS/23Jun2022-foss-2022a-kokkos
</pre>

'''Example of shell scripts to run LAMMPS on the batch queue:'''

'''To use version 23Jun2022 with the foss-2022a toolchain'''

To run lmp version 23Jun2022 as a parallel job, using e.g. 2 node2 and 16 cores per node (sub.sh)
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=lammpsjob # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --nodes=2 # Number of nodes
#SBATCH --ntasks=32 # Number of MPI ranks
#SBATCH --ntasks-per-node=16 # How many tasks on each node
#SBATCH --cpus-per-task=1 # Number of cores per MPI rank
#SBATCH --mem-per-cpu=600mb # Memory per processor
#SBATCH --time=02:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

cd $SLURM_SUBMIT_DIR

ml LAMMPS/23Jun2022-foss-2022a-kokkos

srun lmp -in file.in > file.out

</pre>
Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.



== Documentation ==

Please see links from http://lammps.sandia.gov/

A user manual is available at http://lammps.sandia.gov/doc/Manual.html
== Installation ==

Source code downloaded from https://www.lammps.org/download.html

== System ==
64-bit Linux

Software

2026-07-08T13:00:18Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3, 7.4.4, 7.4.5, 7.4.7 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 23Jun2022 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023a, R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.4, 2.5.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Java-Teaching

2026-07-08T12:51:18Z

Chelsea: /* Version */

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
== Category ==

Programming

== Program On ==

Teaching

== Version ==
1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36

== Author / Distributor ==

[http://java.com/ Java]

== Description ==
"Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers."
More details are at [http://java.com/ Java]

== Running Program ==

Please use the following command to search for all Java versions installed on the cluster:
<pre class="gscript">
ml spider Java
</pre>

For example:

'''Version 1.8.0_241'''

Installed in /apps/eb/Java/1.8.0_241

To use this version, please load the module with
<pre class="gscript">
ml Java/1.8.0_241
</pre>

'''Version 11.0.20'''

Installed in /apps/eb/Java/11.0.20

To use this version, please load the module with
<pre class="gscript">
ml Java/11.0.20
</pre>

Here is an example of a shell script, sub.sh, to run Java 1.8.0_241 on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Java 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Java.%j.out 
<nowiki>#</nowiki>SBATCH --error=Java.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Java/1.8.0_241 
java [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

== Documentation ==

<pre class="gcommand">
ml Java/1.8.0_241
java
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-server to select the "server" VM
The default VM is server,
because you are running on a server-class machine.

-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A : separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose:[class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
Warning: this feature is deprecated and will be removed
in a future release.
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
Warning: this feature is deprecated and will be removed
in a future release.
include/exclude user private JREs in the version search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.

</pre>
[[#top|Back to Top]]

== Installation ==

Source code is obtained from [http://java.com/ Java]

== System ==
64-bit Linux

Software

2026-07-08T12:51:08Z

Chelsea: /* Partial List of Installed Software */

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold 2]] || 2.3.1, 2.3.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
| [[AlphaFold3-Sapelo2|AlphaFold 3]] || 3.0.0, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22.4, 24.3 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->














| | [[Bactopia-Sapelo2|Bactopia]] || 3.2.0, 4.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1, 1.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|[[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.7, 2.7.3, 2.7.7, 10.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










| [[BioPython-Sapelo2|BioPython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.76, 1.79, 1.80, 1.83, 1.84, 1.85 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.13.0, 2.14.1, 2.16.0, 2.17.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Bowtie2-Sapelo2|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Bowtie2-Teaching|Bowtie2]] || 2.4.4, 2.4.5, 2.5.1, 2.5.2, 2.5.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Bracken-Sapelo2|Bracken]] || 3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[BRAKER-Sapelo2|BRAKER]] || 3.0.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



| [[BUSCO-Sapelo2|BUSCO]] || 5.8.3, 6.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 1.2.3, 2.0.3, 2.4.3, 2.4.4, 2.5.0, 2.6.0, 2.6.7, 2.6.9, 2.7.0, 2.9.0, 2.9.3, 2.9.9, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.3||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.7.0, 11.8.0, 12.1.1, 12.4.0, 12.6.0, 12.8.0, 13.1.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Cytoscape-Sapelo2|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1, 3.10.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



























|-->
| [[dMRIharmonization-Sapelo2|dMRIharmonization]] || 20240227 || [[:Category:Engineering|Engineering]]|| [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-->





| [[EGAPx-Sapelo2|EGAPx]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || N/A || [[File:Up20.png|20px|link=#top]]
|- -->


| [[EIGENSOFT-Sapelo2|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || N/A || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































|-
| [[Funannotate-Sapelo2|Funannotate]] || 1.8.15, 1.8.17 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMark-ET]] || 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





























|[[gocryptfs-Sapelo2|gocryptfs]] || 2.2.1, 2.5.2 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[GROMACS-Sapelo2 |GROMACS]] || 2023.4, 2024.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


















| [[HISAT2-Sapelo2|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.75-106.0, 5.76-107.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[IQ-Tree-Sapelo2|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[IQ-Tree-Teaching|IQ-Tree]] || 2.2.2.7, 2.3.5, 2.3.6, 3.0.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 1.8.0_311, 8.402, 11.0.20, 17.0.6, 21.0.2, 21.0.5, 25.36 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 6.5.6, 7.0.2, 7.2.0, 7.2.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 23Jun2022 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.27-1, 2.28-27 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023a, R2023b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-













| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1, 4.0.6, 4.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









































| [[Nsight-Compute-CLI-Sapelo2|Nsight Compute CLI]] || 2024.3.0.0, 2025.1.0.0, 2025.4.0.0 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 6.5.7 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6, 2.2.8 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.4, 2.5.5 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[PAML-Teaching|PAML]] || 4.9j, 4.10.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->









| [[PASA-Sapelo2|PASA]] || 2.5.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[Perl-Teaching|Perl]] || 5.34.0, 5.34.1, 5.36.0, 5.36.1, 5.38.0, 5.38.2, 5.40.0, 5.40.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.21.2-5419 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.9.6, 3.10.4, 3.10.8, 3.11.3, 3.11.5, 3.12.3, 3.13.1, 3.13.5 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.5.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[RAxML-NG-Sapelo2 |RAxML-NG]] || 1.2.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Sapelo2 |RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0, 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2021.16.61629, 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->









































| [[snpEff-Sapelo2|snpEff]] || 5.0e || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->





















| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 3.0.1, 3.0.3 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.3, 3.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]