https://wiki.gacrc.uga.edu/api.php?action=feedcontributions&feedformat=atom&user=Gcormier 2026-05-20T09:04:35Z User contributions MediaWiki 1.39.7 https://wiki.gacrc.uga.edu/index.php?title=Policies&diff=23005 2026-05-18T02:33:21Z

<p>Gcormier: </p> <hr /> <div><br /> ==Introduction to GACRC Policies==<br /> <br /> 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. <br /> <br /> The GACRC computational infrastructure, including its servers, clusters, data stores, and other related devices are for the exclusive use of authorized users only.<br /> <br /> 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.<br /> <br /> <br /> ==GACRC Resource Usage==<br /> <br /> 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.<br /> <br /> GACRC policies supplement UGA’s Policies on the Use of Computers, found at: [https://policy.uga.edu/policies#/programs/BJWfhwRra?group=Information%20Technology%20&amp;bc=true&amp;bcCurrent=Information%20Technology%20&amp;bcItemType=programs&amp;bc=true&amp;bcCurrent=Acceptable%20Use%20Policy&amp;bcGroup=Information%20Technology%20&amp;bcItemType=programs UGA’s Policies on the Use of Computers]<br /> <br /> <br /> ==GACRC Eligibility and Access ==<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> <br /> ==GACRC Identity Management==<br /> <br /> Below are described the procedures for validating the identity of account users.<br /> <br /> ===UGA Users and Faculty Lab Groups===<br /> <br /> *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.<br /> <br /> *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).<br /> <br /> *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. <br /> <br /> ===Affiliate Users===<br /> <br /> *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.<br /> <br /> *A request will be made by the GACRC to EITS to allocate to the Affiliate a UGA MyID.<br /> <br /> *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.<br /> <br /> ===Protection of Passwords===<br /> <br /> 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.<br /> <br /> More information is found at the following EITS website: <br /> <br /> [https://policy.uga.edu/policies#/programs/HJe8T3sH6?group=Information%20Technology%20&amp;bc=true&amp;bcCurrent=Information%20Technology%20&amp;bcItemType=programs&amp;bc=true&amp;bcCurrent=Password%20Policy&amp;bcGroup=Information%20Technology%20&amp;bcItemType=programs UGA Policy Website]<br /> <br /> <br /> ==GACRC Storage Usage ==<br /> <br /> <br /> ===Some working definitions===<br /> <br /> '''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.<br /> <br /> '''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.<br /> <br /> '''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 &quot;backup&quot; storage system.<br /> <br /> '''Active Projects''' – Projects that have on-going computational work being performed with files that are regularly created, accessed or modified.<br /> <br /> ===Policy Statement for SCRATCH File System===<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> ===Policy Statement for WORK File System===<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> ===Policy Statement for HOME File System===<br /> <br /> 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.<br /> <br /> All users have 200GB allocated for their HOME usage. <br /> <br /> 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.<br /> <br /> Users are strongly encouraged to make their own copies of critical files, while accepting any risks associated with HOME usage. <br /> <br /> 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. <br /> <br /> ===Policy Statement for PROJECT File System===<br /> <br /> The PROJECT filesystem resides on lower-performance/higher-capacity storage devices.<br /> <br /> This filesystem is accessible only from the GACRC’s transfer (xfer) nodes. PROJECT will not be accessible on Sapelo2's compute nodes.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> Users are strongly encouraged to make their own copies of critical files, while accepting any risks associated with PROJECT usage.<br /> <br /> 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.<br /> <br /> <br /> ==GACRC Software Policy==<br /> <br /> 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.<br /> <br /> 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:<br /> &lt;!--<br /> http://eits.uga.edu/access_and_security/infosec/pols_regs/policies/aup/eula<br /> --&gt;<br /> <br /> 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.<br /> <br /> <br /> <br /> == AI Workflows and GPU Usage Expectations ==<br /> 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.<br /> <br /> '''1.        Monitoring and Enforcement'''<br /> <br /> The GACRC actively monitors system usage to ensure fair access, system stability, and compliance with institutional policies. Patterns of concern include:<br /> <br /> * Long-running interactive GPU sessions with low or intermittent utilization<br /> * Persistent or service-like workloads running on shared compute nodes<br /> * Running of software on the login/head node, including remote development environments<br /> * Excessive or automated job submission that impacts scheduler performance<br /> * Large-scale filesystem activity that degrades shared storage performance<br /> <br /> 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.<br /> <br /> '''2.        GPU Usage and Interactive Work'''<br /> <br /> 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. <br /> <br /> '''3.        Persistent and Service-Like Workloads'''<br /> <br /> 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.<br /> <br /> '''4.        Login Node Usage and Development Environments'''<br /> <br /> 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.<br /> <br /> '''5.        Automated and AI-Driven Workflows'''<br /> <br /> 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.<br /> <br /> '''6.        Data, Software, and Filesystem Use'''<br /> <br /> 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.<br /> <br /> '''Finally, a reminder of the Archnews memo of March 26, 2025 from USG Chancellor Perdue in which the following software restrictions were announced:'''<br /> <br /> “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:<br /> <br /> # RedNote (social media app)<br /> # DeepSeek (AI chatbot)<br /> # Webull (online stock trading)<br /> # Tiger Brokers (online stock trading)<br /> # Moomoo (investing app)<br /> # Lemon8 (social media app) <br /> <br /> '''Please work with the GACRC to find the most appropriate way to accomplish your research goals.'''<br /> <br /> 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.<br /> <br /> ==Security==<br /> <br /> 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.<br /> <br /> ===Operating Systems===<br /> <br /> Any computer accessing the GACRC for any purpose must run a currently supported operating system, updated to the latest version and update (patch) levels.<br /> <br /> ===Anti-Virus Software===<br /> <br /> 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.<br /> <br /> More information can be found at the following EITS website:<br /> <br /> [https://policy.uga.edu/policies#/programs/BySr6vy8a?q=%20Minimum%20Security%20Standards%20Policy&amp;&amp;limit=20&amp;skip=0&amp;bc=true&amp;bcCurrent=Minimum%20Security%20Standards%20Policy&amp;bcItemType=programs Minimum Security Standards Policy]<br /> &lt;!--<br /> http://eits.uga.edu/access_and_security/infosec/protect_your_computer<br /> --&gt;<br /> ===Suspiciously Behaving Software===<br /> <br /> 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.<br /> <br /> ===Suspiciously Behaving Networks and Devices=== <br /> <br /> 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.<br /> <br /> ===Account Holder Responsibility===<br /> <br /> 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.<br /> <br /> <br /> ==Resolving Disagreements about Revocation of Privileges or Provisioning Resources==<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> <br /> ==System Maintenance and Downtime==<br /> <br /> ===Planned Maintenance===<br /> <br /> The GACRC instituted monthly maintenance windows in order to perform maintenance operations requiring system operations to be reduced or interrupted.<br /> <br /> The schedule will be as follows:<br /> <br /> *The last Wednesday of each month from 10AM to 4PM will be reserved for partial cluster maintenance.<br /> <br /> *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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> ===Unplanned Maintenance and System Outage===<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> ==Regulatory Compliance==<br /> <br /> 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. <br /> <br /> 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:<br /> <br /> http://research.uga.edu/export-control/<br /> <br /> Copyrighted materials are prohibited without proper authorization. Additionally, illegal content is prohibited.<br /> <br /> 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.<br /> <br /> ===Disclosure===<br /> <br /> 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.<br /> <br /> ===Research Data Compliance===<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> More information on data management plans can be found [http://guides.libs.uga.edu/c.php?g=349946&amp;p=2363161 here].<br /> <br /> <br /> <br /> <br /> &lt;!--<br /> ==Introduction to GACRC Policies==<br /> <br /> 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 (rcac@uga.edu).<br /> <br /> The GACRC computational infrastructure, including its servers, clusters, data stores, and other related devices are for the exclusive use of authorized users only. Individuals using these computer systems without proper authority, or in excess of their authority, are subject to having all of their activities on these systems monitored and recorded by GACRC personnel. In the course of monitoring individuals improperly using these systems, or in the course of any system maintenance, the activities of authorized users may also be monitored.<br /> <br /> Anyone using these systems expressly consents to such monitoring and is advised that if such monitoring reveals possible evidence of unauthorized activity, system personnel may provide the evidence of such monitoring to law enforcement officials.<br /> <br /> Anyone using these systems expressly consents to abide by the policies of the University of Georgia and/or the Georgia Advanced Computing Resource Center and, accordingly, is subject to account termination and/or immediate disconnection from GACRC resources.<br /> <br /> <br /> ==Definitions==<br /> ===Account===<br /> <br /> The collection of information related to an authorized user of resources, including resource usage statistics.<br /> ===Active Account===<br /> <br /> An account belonging to a person currently authorized to access resources.<br /> ===Home Directory===<br /> <br /> Disk storage space assigned to each user with an active account, used to store temporary or permanent files. At the GACRC, there is one and only one Home Directory per Active Account, regardless of the computational resource(s) used by the account holder.<br /> ===Account Holder===<br /> <br /> The authorized person responsible for an Active Account.<br /> ===Archive===<br /> <br /> A file which has been moved to offline or nearline storage because activity on the file has virtually ceased.<br /> <br /> <br /> ==GACRC Resource Usage==<br /> <br /> 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.<br /> <br /> GACRC policies supplement UGA’s Policies on the Use of Computers, found at: http://eits.uga.edu/access_and_security/infosec/pols_regs/policies/aup<br /> <br /> <br /> ==GACRC Eligibility and Access==<br /> <br /> 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 and associated with research projects sponsored by UGA.<br /> <br /> Direct affiliation in this context means faculty, staff and 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.<br /> <br /> For directly affiliated users, accounts on the GACRC computers will remain active as long as the researchers hold the above status.<br /> Access by researchers affiliated with the University of Georgia that do not meet the criteria above will be considered on a case-by-case basis, especially researchers not directly affiliated with the University of Georgia who are collaborating on research with researchers directly affiliated with UGA. Requests for access must be forwarded to the GACRC in such cases by a person directly affiliated with UGA.<br /> <br /> For indirectly affiliated users, access will be granted for a fixed period of time, according to the expected length of the collaborative project, but no longer than one (1) year. Application for extensions will be considered.<br /> <br /> 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 directories will be archived for at least 90 days, but no longer than 180 days after an account becomes inactive.<br /> <br /> Requests for access by individuals other than those listed above should first be directed to the Director of the Center using the form provided.<br /> <br /> <br /> ==GACRC Identity Management==<br /> <br /> Below are described the procedures for validating the identity of account users.<br /> ===Directly Affiliated Users===<br /> <br /> All directly affiliated persons wanting an account must apply for access to the GACRC using the instructions provided on the GACRC website (http://www.gacrc.uga.edu/accounts). The applicant must authenticate to the form using his/her MyID and password for identification.<br /> Upon acceptance of the application, the user will be notified via e-mail. The applicant’s UGA MyID in conjunction with the temporary password will be used to initially log into the requested GACRC resources . After initial login, a new password should be provided, as noted in the emailed instructions. Please note that the GACRC will NOT record a user’s MyID password or his/her Social Security number.<br /> ===Indirectly Affiliated Users===<br /> <br /> Indirectly affiliated users must be sponsored by a directly affiliated user. The directly affiliated user must apply on behalf of the applicant by contacting the GACRC staff.<br /> ===Protection of Passwords===<br /> <br /> An account holder must never divulge their login ID 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.<br /> <br /> <br /> ==GACRC Resource Allocation==<br /> ===''High-Performance Storage Provisioning''===<br /> ===Home File System===<br /> <br /> The home file system resides on a high-performance storage device and is used for long-term storage of files needed for analyses on the GACRC computing clusters. All users have a default 100GB home quota (i.e., maximum limit) on their home directory; however, justifiable requests for quotas up to 2TB can be made by contacting the GACRC IT Manager (currently Greg Derda: derda@uga.edu). Storage in the home directory to avoid archive storage fees is not a justifiable request. Requests for home quotas greater than 2TB must be submitted by the PI of a lab group, and approved by the GACRC advisory committee (via the IT Manager). Users may create lab directories for data that is shared by a lab group, but those directories count against the quota of the creating user. An example of this, for the “abclab” users, would be: /home/abclab/labdata. Home directories are backed up. <br /> ===Scratch File System===<br /> <br /> The scratch file system resides on a high-performance storage device and is to be used for temporary storage of files in use by actively running jobs. Files are to be removed from scratch when the job(s) complete. Scratch space is not backed up.<br /> <br /> The current scratch file system is mounted on the compute clusters as escratch. Researchers who need to use scratch space can type ‘make_escratch’ and a sub-directory will be created, and the user will be told the path to the sub-directory e.g., /escratch/jsmith_Oct_22. The life span of the directory will be one week longer than the longest duration queue, which is currently 30 days (i.e., life span = 37 days). At that time, the directory and its contents will be deleted. Users can create one escratch directory per day if needed.<br /> ===Archive File System===<br /> <br /> There is an archive file system available for long-term storage of data that users don’t actively need in their home directories. It is subscribed to by a PI on behalf of his/her lab group, and is mounted on the compute cluster’s login nodes (not on the compute nodes) under oflow e.g., /oflow/abclab. There is a fee for this storage, which is currently $10 / 1TB / month, with the smallest increment being 500GB @ $5 / month. Contact the GACRC staff if you would like more information on this resource. Archived files are backed up.<br /> <br /> <br /> ==Security==<br /> <br /> 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.<br /> ===''User-Managed Servers, Clusters, Networks and Desktop Computers''===<br /> ===Operating Systems===<br /> <br /> Any computer accessing the GACRC for any purpose must meet minimum levels of operating system versions and update (patch) levels. The GACRC will, from time to time, publish these minimum requirements on its website.<br /> ===Anti-Virus Software===<br /> <br /> 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 the GACRC, must have that virus protection activated, and must have automatic updates activated for the anti-virus software.<br /> ===Suspiciously Behaving Software===<br /> <br /> 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 system administrator(s), manager, director, or security staff.<br /> ===Suspiciously Behaving Networks and Devices===<br /> <br /> 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 incompliant with the GACRC’s security requirements, seems to be behaving suspiciously, or if a threat emerges requiring termination for intrusion prevention at the sole discretion of the GACRC’s system administrator(s), manager, director, or security staff.<br /> ===Account Holder Responsibility===<br /> <br /> The account holder is responsible for diligently monitoring and meeting the GACRC’s operating system, intrusion and virus protection standards.<br /> 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.<br /> <br /> <br /> ==Storing Sensitive Information on GACRC Resources==<br /> ===Sensitive, Private, or Classified Information===<br /> <br /> The GACRC 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.<br /> ===Intellectual Property===<br /> <br /> The GACRC strives to protect documents, code, and results data on behalf of account holders. However, the GACRC does not assume responsibility for unauthorized access or data loss due to human or system error.<br /> <br /> ===Resolving Disagreements about Revocation of Privileges or Provisioning===<br /> <br /> If an account holder is denied a request for provisioning of GACRC resources or resource privileges are revoked, the user’s Department Head may appeal to the Vice President for Research. The decision of the Vice President for Research is final.<br /> <br /> <br /> ==System Maintenance and Downtime==<br /> ===Planned Maintenance===<br /> <br /> Starting March 2016, the GACRC will institute monthly maintenance windows in order to perform maintenance operations requiring system operations to be reduced or interrupted.<br /> <br /> The schedule will be as follows:<br /> <br /> *The last Wednesday of each month from 10AM to 4PM will be reserved for partial cluster maintenance.<br /> *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.<br /> <br /> These maintenance windows represent periods when the GACRC may choose to drain the queues of running jobs and suspend access to either or both clusters, as well as storage devices for maintenance purposes. Interruptions will be kept as brief as possible.<br /> <br /> 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.<br /> <br /> 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. <br /> ===Unplanned Maintenance and System Outage===<br /> <br /> 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 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.<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> <br /> ==Adding Department or Grant-Sponsored Resources to the GACRC==<br /> <br /> Researchers may benefit by adding resources sponsored by grants or departments to the GACRC. In many cases, the cost of doing so will be less than the researcher’s acquisition and maintenance of the resources within their own laboratory or group.<br /> ===Usage Model===<br /> <br /> When a department or research project sponsors the addition of compute power, storage capacity, and/or software to the GACRC’s compliment of high performance computing resources, the project will have access to the resource capacities that they have sponsored, throughout the duration of the research project, or as agreed upon in a separate service level agreement. When the project could benefit from resources beyond those that the project sponsored, if those resources are available through the GACRC, they will be allocated to the project. When the resources sponsored by a project are not being used by the project, they will become available to other projects.<br /> <br /> The project will benefit from the security, environmental, and system administration provided by the GACRC.<br /> ===Usage Policy Enforcement===<br /> <br /> The GACRC strives to enforce this usage model through the use of resource management software. From time to time the software may not perform in accordance with the policy. Such events, when detected, should be reported to the GACRC system administrator or manager such that corrective action can be taken to prevent such events in the future.<br /> ===Funding Model===<br /> <br /> During the grant design and writing process, GACRC staff, in collaboration with the Office of the Vice President for Research Office of Sponsored Programs, is available to assist in estimating the level of computing, storage, network bandwidth, software, and services required to meet the objectives of the proposed research project. GACRC staff will provide the cost of acquiring, installing, and maintaining the proposed resources (in compliance with the architectures of the GACRC as well as established best-practices) over the life of the grant. If the grant is awarded, the GACRC will acquire and implement the resources sponsored by the project using funds allocated for such purposes.<br /> <br /> --&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Consulting&diff=22717 2026-03-13T17:10:12Z

<p>Gcormier: </p> <hr /> <div>===Perl and UNIX-shell scripting===<br /> <br /> Automating and simplifying tasks with command-scripts is a routine procedure in the Unix/Linux environment. We regularly help users develop scripts to suit their specific needs.<br /> <br /> ===Code Development===<br /> <br /> We provide assistance with code compilation and debugging in serial and parallel environments.<br /> <br /> ===Computational Physics===<br /> <br /> Computational physics methods are sometimes useful and applicable to problems in other fields. We provide some <br /> consultation for computational physics algorithm selection and implementation.<br /> <br /> ===Bioinformatics===<br /> <br /> From the installation of programs and data (e.g., genetic databases), to helping users get started, bioinformatics support is a key support area.<br /> <br /> ===General Usage===<br /> <br /> GACRC staff are available to provide consultation in order to facilitate and optimize the use of GACRC’s resources. We are available to meet with small groups of users, and to provide guest lectures for courses that use GACRC resources.<br /> <br /> <br /> ==People==<br /> <br /> ===Administrators===<br /> <br /> *'''Guy Cormier, Ph.D.''' &lt;br /&gt;Director, UGA Georgia Advanced Computing Resource Center&lt;br /&gt;Associate Research Scientist, Institute of Bioinformatics<br /> <br /> ===GACRC Consultants===<br /> <br /> &lt;!-- *'''Yecheng Huang, Ph.D.''' &lt;br /&gt; Bioinformatics consultant --&gt;<br /> &lt;!-- *'''Saravanaraj &quot;Raj&quot; Ayyampalayam, Ph.D.''' &lt;br /&gt; High Performance Computing Facilitator and Bioinformatics Specialist --&gt;<br /> &lt;!-- *'''Karen Bobier, Ph.D.''' &lt;br /&gt; Bioinformatics Consultant and Trainer --&gt;<br /> &lt;!-- *'''Ben Cronheim''' &lt;br /&gt; High Performance Computing User Support and Trainer --&gt;<br /> *'''Isaiah Davis''' &lt;br /&gt; Software Support Associate<br /> *'''Zhuofei Hou, Ph.D.''' &lt;br /&gt; High Performance Computing Facilitator<br /> *'''Chelsea Ware''' &lt;br /&gt; Software Support Associate<br /> *'''Shan-Ho Tsai, Ph.D.''' &lt;br /&gt; Consulting Group Lead and High Performance Computing Consultant <br /> *'''Jordan Utley, M.S.''' &lt;br /&gt; Bioinformatics Support Specialist<br /> &lt;!-- *'''Cecilia &quot;Keeko&quot; Villaveces''' &lt;br /&gt; Bioinformatics Specialist --&gt;<br /> &lt;!-- *'''Suchitra Pakala, M.S.''' &lt;br /&gt; Cluster usage and Bioinformatics Trainer --&gt;<br /> <br /> ===GACRC IT Staff===<br /> <br /> *'''Paul Brunk''' &lt;br /&gt; Principal Unix System Administrator<br /> *'''Bruce Carpenter''' &lt;br /&gt; Linux System Administrator<br /> *'''Jonathan &quot;Jon&quot; Gibson''' &lt;br /&gt; Linux System Administrator<br /> *'''Keyton Stanier''' &lt;br /&gt; Linux System Administrator<br /> *'''Kris Lamoureux''' &lt;br /&gt; Linux System Administrator<br /> &lt;!-- *'''Len Ewen''' &lt;br /&gt; Linux System Administrator --&gt;<br /> <br /> ===Emeritus===<br /> *'''Greg Derda, Ph.D.''' &lt;br /&gt; Operations Manager Extraordinaire<br /> <br /> <br /> ==Office Hours==<br /> GACRC staff are located in the Computing Services Building (formerly called Statistics Building), rooms 101 to 108. Our office is open Monday through Friday from 9am until 5pm. You are welcome to stop by and ask questions, or you can schedule an appointment using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support].<br /> <br /> ==Directions==<br /> The Computing Services Building is located at 101 Cedar Street, Athens, GA 30602, on the corner of Cedar Street and East Campus Rd. As you enter the building from the entrance on Cedar Street, on the East Campus Rd. end of the building, there are stairs leading down to the first floor. Our offices are on your left, as you come down those stairs.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=22309 2025-03-10T18:11:43Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – General overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – Software docs and how-to’s - &quot;You Are Here&quot;<br /> *[https://kaltura.uga.edu/channel/GACRC/176125031 Kaltura] – Linux and HPC training videos<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> &lt;!--<br /> &lt;div style=&quot;width=100%; margin:0; background:#FF9F40; font-size:120%; font-weight:bold; border:1px solid #FF9F40; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Scheduled maintenance underway - Sapelo2, xfer nodes, GACRC storage systems, and Open OnDemand unavailable &lt;/span&gt;&lt;/div&gt;<br /> --&gt;<br /> &lt;!--<br /> &lt;div style=&quot;width=100%; margin:0; background:#FF9F40; font-size:120%; font-weight:bold; border:1px solid #FF9F40; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Teaching cluster inaccessible while the scheduled UGA network maintenance is on-going&lt;/span&gt;&lt;/div&gt;<br /> --&gt;<br /> <br /> &lt;!--<br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Sapelo2 Cluster Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#FF9F40; font-size:120%; font-weight:bold; border:1px solid #FF9F40; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Sapelo decommissioned&lt;/span&gt;&lt;/div&gt; <br /> --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current users:<br /> <br /> * GACRC offering in-person drop-in '''[[Office Hours]]'''.<br /> <br /> *[[Changes implemented during January 28-29, 2025 maintenance]]<br /> <br /> &lt;!--<br /> &lt;blockquote style=&quot;background-color: lightyellow; border: solid thin grey;&quot;&gt; <br /> '''October Office Hours:'''<br /> *'''Wednesday October 9th, 3:00-4:30 pm''' at the McBay Science library, Main floor<br /> &lt;/blockquote&gt;<br /> --&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> *[[User Accounts]]<br /> *[[Instructional Accounts]]<br /> *[[Connecting]]<br /> *[[Transferring Files]]<br /> *[[Password | Changing your Password]]<br /> *[[Frequently Asked Questions | FAQ]]<br /> *[https://wiki.gacrc.uga.edu/wiki/Quick_Reference_Guide Command List]<br /> *[[Getting Help]]<br /> *[[Policies]]<br /> *[[Consulting]]<br /> *[[Training]]<br /> <br /> A Webinar introducing the GACRC was presented on March 10, 2025. A recording of this [https://kaltura.uga.edu/media/t/1_jfku2g8l/176125031 webinar] is found on GACRC's Kaltura channel. <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> *[[Systems]]<br /> *[[Disk Storage]]<br /> &lt;!-- * [[Sapelo2 and Sapelo2 (old) comparison]] --&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> *[[Running Jobs]]<br /> *[[Monitoring Jobs]]<br /> *[[Job Submission Partitions]]<br /> *[[Sample Scripts | Sample Job Submission Scripts]]<br /> *[[Migrating from Torque to Slurm]]<br /> *[[Troubleshooting on Sapelo2]]<br /> *[[Best Practices]]<br /> *[[Globus]]<br /> *[[OnDemand | Open OnDemand]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> *[[Software]]<br /> *[[Available Toolchains and Toolchain Compatibility]]<br /> *[[Bioinformatics Databases]]<br /> *[[OpenMP]]<br /> *[[MPI | Message Passing Interface (MPI)]]<br /> *[[Compilers]]<br /> *[[GPU|GPU and CUDA Programming]]<br /> *[[Installing Applications]]<br /> <br /> <br /> &lt;!--<br /> * [[Galaxy]]<br /> * [[Zaney]]<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;<br /> --&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Globus&diff=21932 2024-06-06T19:01:17Z

<p>Gcormier: </p> <hr /> <div><br /> ===Introduction===<br /> The GACRC, on behalf of UGA, recently procured an institutional subscription to Globus for secure, reliable management of UGA's research data. <br /> Globus is a high-performance data-transfer platform that allows you to perform and/or automate:<br /> <br /> *Data transfers between servers in your group.<br /> *Data transfers between a server and your laptop.<br /> *Sharing data with researchers at UGA and at other institutions.<br /> *Sharing data with the world.<br /> <br /> 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. A video introduction to Globus at UGA can be found '''[https://kaltura.uga.edu/media/t/1_vlprwoc7/176125031 here]'''.<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> ===Getting Started===<br /> <br /> If you are a first time user of Globus, you will need to create an Identity Account. At a minimum you will need to setup your identity using the University of Georgia organizational login in order to access UGA systems.<br /> <br /> *Go to https://www.globus.org and choose Login in the upper right corner.<br /> *Search for University of Georgia in the “Use your existing organizational login&quot; box.<br /> *Choose continue and you will be forwarded to a UGA Single Sign-On (SSO) login page. You will also need to authenticate with Duo (two-factor authentication).<br /> [[File:Globus-UGA-login.png|alt=|border|700x700px]]<br /> <br /> <br /> When you login for the first time using an existing organization login associated to UGA:<br /> <br /> *Globus will ask if you would like to link to an existing account. If you have already used another account with Globus in the past, you can choose &quot;Link to an existing account&quot;. Otherwise, click &quot;Continue&quot; to proceed.<br /> <br /> *You will need to accept Globus Terms of Service and Privacy Policy and click Continue to proceed.<br /> <br /> *You will need to give Globus permission to use your identity to access information and perform actions (like file transfers) on your behalf.<br /> <br /> These 3 steps will not be prompted after your first login.<br /> <br /> Detailed information with screenshots are provided by Globus at their [https://docs.globus.org/how-to/get-started/ Getting Started page].<br /> <br /> &lt;!--<br /> ====Key Concepts====<br /> <br /> Collection: a named location containing data you can access with Globus. Collections can be hosted on many different kinds of systems, including HPC clusters, laptops, desktops, etc. <br /> <br /> Endpoint: a server that hosts collections.<br /> <br /> Globus Connect: software used to create an endpoint.<br /> --&gt;<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> ===Access GACRC Storage===<br /> <br /> GACRC maintains a '''UGA GACRC Collection''' that can be used to access and transfer files in and out of the Sapelo2 /home, /scratch, /work, and /project file systems. <br /> <br /> After you have logged in to Globus, click the '''File Manager''' link at the top-left of the window. <br /> <br /> In the '''Collection''' search box, enter GACRC and you should see UGA GACRC Collection in the list.<br /> <br /> [[File:Globus-UGA-GACRC-Collection.png|border|900x900px]]<br /> <br /> <br /> Select the '''UGA GACRC Collection''' and authenticate with SSO to access your files on Sapelo2. By default, you will open your home directory on Sapelo2. For example:<br /> <br /> <br /> [[File:Globus-sapelo2-home.png|border|900x900px]]<br /> <br /> To access your /scratch or /project areas, enter the full path in the '''Path''' field under the '''Collection''' name (for example, enter /project/abclab) and then press the Enter or Return key on your keyboard for the change in the path to take effect.<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> ===Transfer Data Between GACRC Storage and Desktops/Laptops===<br /> <br /> There are two ways to use Globus to transfer files between a GACRC storage and desktops or laptops. The method that is best suited depends on the number and size of the files to be transferred. In both cases you would use a browser to Login into https://www.globus.org, as described above, and open the UGA GACRC Collection in the File Manager panel.<br /> ====Small number of files or small sizes downloaded or uploaded====<br /> <br /> '''Uploads''' - Once you open the UGA GACRC Collection in the File Manager panel, you can select the &quot;Upload&quot; button to upload a file from your local machine to the UGA GACRC Collection, to the path you select (e.g. your Sapelo2 /scratch dir).<br /> <br /> '''Downloads''' - Once you open the UGA GACRC Collection in the File Manager panel, you can navigate to the directory where the files are located and select the files you want to download. Then select the &quot;Download&quot; button to download the file(s) to your local machine.<br /> <br /> Here is a sample screenshot to download a file called analysis.txt from the user's home directory on Sapelo2 to the local machine:<br /> <br /> [[File:Globus-sapelo2-download-file.png|border|900x900px]]<br /> <br /> You do not need to install Globus Connect Personal on your local machine in order to use the Download and Upload features, to transfer files from e.g. the UGA GACRC Collection to your local machine. Please note that not all Collections have the Download and Upload feature. If this feature is not available, you can follow the instructions in the '''Many files or large files''' section below.<br /> <br /> ====Many files or large files====<br /> <br /> Install Globus Connect Personal (GCP) and create a Globus endpoint on your local machine. Globus Connect Personal allows faster and more reliable file transfers. Information on how to install GCP on your local machine and create an endpoint are available on the [[Globus Connect Personal|'''Globus Connect Personal''']] page.<br /> <br /> Once you have installed GCP and created an endpoint on your local machine, navigate to the UGA GACRC Collection in the File Manager panel, select the files or directories you wish to transfer, and click on the double panel icon (top right), as illustrated here:<br /> <br /> <br /> [[File:Globus-UGA-GACRC-collection-filetransfer1.png|border|900x900px]]<br /> <br /> <br /> On the right panel, enter the name of the Collection on your endpoint (e.g. called shtsai-imac in this example) and select the path where to transfer the data to (or from). By default, file integrity will be checked after the transfer is completed. You can enable other options (e.g. file encryption on transfer) by opening the '''Transfer &amp; Sync Options''' menu and selecting the options you wish to use. Once all the settings are chosen, and you are ready to perform the file transfer, click on the '''Start''' button. You can check the status of the transfer by going to the Activity panel.<br /> <br /> <br /> [[File:Globus-UGA-GACRC-collection-filetransfer2.png|border|900x900px]]<br /> <br /> ====Transfer files from/to an external hard drive====<br /> <br /> It is possible to use Globus to transfer files between an external hard drive connected to your local machine and another system, such as a GACRC storage area. The first step is to install Globus Connect Personal (GCP) on your local machine. Information on how to install GCP on your local machine and create an endpoint are available on the [[Globus Connect Personal|'''Globus Connect Personal''']] page.<br /> <br /> After you connect your external hard drive to your computer, you will need to add it to the list of Accessible Folders within the Globus Connect Personal application. Documentation on how to do that from Window and Mac are at<br /> <br /> https://docs.globus.org/how-to/globus-connect-personal-windows/#configuration<br /> <br /> https://docs.globus.org/how-to/globus-connect-personal-mac/#configuration<br /> <br /> Then you should be able to transfer files from the external drive to a GACRC storage (or vice-versa) via Globus.<br /> <br /> ====Transferring files between Sapelo2 file systems====<br /> <br /> To transfer files between two files systems on Sapelo2, navigate to the File Manager two-panel view, and select UGA GACRC Collection on both panels. Enter the path to the location of the files on one panel (e.g. your /project directory) and the location where you want to transfer the file to on the other panel (e.g. your /scratch directory). Select the files to transfer and click '''Start'''. You can check a report of the transfer by going to the Activity panel.<br /> <br /> Here is an example where a directory called inputdata is transferred from a /project directory to a /scratch directory:<br /> <br /> [[File:Globus-filetransfer-project-scratch.png|border|900x900px]]<br /> <br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> ===Access Storage Not Hosted by GACRC===<br /> <br /> Globus can be used to access, share, transfer, or manage data stored on devices outside of the GACRC. The steps described above can also be used to access and transfer data from any endpoint that has been shared with you (for example, shared by a collaborator in another institution). You can either search for an endpoint in the '''File Manager''' panel, or go to the '''Endpoints''' panel and select '''Shared with you''' to see a list of Collections shared with you.<br /> <br /> You can transfer files into your Sapelo2 file systems by using the '''UGA GACRC Collection''' and selecting the appropriate directory (e.g. your /home, /scratch, or /project directories).<br /> <br /> ===Access Shared Data===<br /> <br /> Collaborators can 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. Once you login into https://www.globus.org, you can view all Collections/Endpoints shared with you by clicking on '''Endpoints''' on the left side of the page and then open the '''Shared with you''' tab. A list of endpoints that have been shared with you will be listed on the page.<br /> <br /> You can transfer data from shared endpoints to you desktop or laptop, or directly into your GACRC storage (e.g. your /scratch area or your group's /project area). You can transfer files into your Sapelo2 file systems by using the '''UGA GACRC Collection''' and selecting the appropriate directory (e.g. your /home, /scratch, or /project directories).<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> ===Sharing Data===<br /> <br /> Globus can be used to share data from your local machine or your GACRC /project area.<br /> <br /> ====Sharing data from GACRC storage (/project)====<br /> <br /> You can allow collaborators to download or transfer files from your /project area into their local endpoints/collections or into their GACRC storage space in the UGA GACRC Collection. Your collaborators do not have to be associated with an institution that has a Globus subscription. They can login into https:///www.globus.org using a Globus ID, a Google Account, an ORCID ID, or with their institutional account if their institution has a Globus subscription. <br /> <br /> Steps to share a /project folder with a collaborator:<br /> <br /> 1. In the '''File Manager''' panel, open the '''UGA GACRC Project Sharing''' collection.<br /> <br /> 2. Navigate to the folder you wish to share (e.g. /project/abclab/shareddir) and select it. <br /> <br /> 3. Select '''Share''' and create a guest collection.<br /> <br /> 4. Add permissions to share the collection with your collaborators (they will need to have a Globus account, as indicated above). <br /> <br /> Note that your collaborators will not be able to transfer files into your shared Collection on /project, even if you choose to add '''write''' permission while sharing the Collection.<br /> <br /> If you would like your collaborators to transfer data into your GACRC storage for you to use on the cluster, please contact GACRC and we will set up a space where they can write into.<br /> <br /> To obtain the data you shared with them, your collaborators can do as follows:<br /> <br /> a. If you are only sharing a few small files, they can navigate to the File Manager panel in the Globus page (available after they login into https:///www.globus.org), open the collection you shared with them, select the files and use the Download option.<br /> <br /> b. To copy large files or a larger number of files to their desktop or laptop, they should install [[Globus Connect Personal|'''Globus Connect Personal]] on their local machine.<br /> <br /> c. If your collaborators are GACRC users, they can transfer the data into their GACRC storage, using the UGA GACRC Collection. This use case does not require that they install Globus Connect Personal on their local machine.<br /> <br /> ====Sharing data from your desktop or laptop====<br /> <br /> If you have a need to share data from your desktop or laptop with research collaborators (or if you wish to transfer data between two computers) add “University of Georgia” as your Globus Plus Sponsor in your Globus Account Settings. Please be sure you have your UGAMail (yourMyID@uga.edu) set as your contact email address in your profile. Note this is not required for normal Collections/Endpoints provided by GACRC.<br /> <br /> *Click on '''Account''' on the left side of the browser after you login into https://www.globus.org<br /> *Click on the '''Globus Plus''' tab at the top of the page<br /> *Choose '''Select a Globus Plus Sponsor''' <br /> *Find and click on “University of Georgia” in the list and complete your settings. GACRC will be notified of your request after you click Continue<br /> <br /> Once your request is approved, Globus Plus will allow you to create shared links to your own Globus Connect Personal client. These are also known as guest collections. Please note that if you allow write access to your Collection, your local hard drive can be inadvertently filled or files stored there could be deleted. Please see the [[Globus Connect Personal|'''Globus Connect Personal''']] page for more information.<br /> <br /> ====Sharing data from a multi-user system====<br /> <br /> If the data are stored (or will be stored) on a multi-user system, you can install [https://docs.globus.org/globus-connect-server/v5.4/ '''Globus Connect Server'''] and create an endpoint on this system. Please contact GACRC to request that your endpoint be associated with UGA's Globus subscription. Once your endpoint is listed in UGA's subscription, you will be able to share it.<br /> <br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> <br /> ===Summary of Collections on GACRC storage===<br /> <br /> <br /> *'''UGA GACRC Collection (All GACRC filesystems) – GACRC Users Only''': This collection allows you to access data on your Sapelo2 /home and /scratch directories, as well as your group's /work and /project areas. You can use the Upload and Download features (recommended for a few small files) or transfer large files and/or a large number of files from/to a different endpoint.<br /> <br /> *'''UGA GACRC Project Sharing (Read Only)''': You can use this collection to share a directory with a collaborator. The data to the shared needs to reside in your group's /project folder and you can select a directory to create a shared collection. Anyone with whom you share the collection will be able to copy the shared files (even if the files don't have Unix read permission open for group or for others), but they will not be able to write into your shared collection.<br /> <br /> *'''UGA GACRC read-write Sharing''': This collection has read-write access to allow external (to UGA) users to upload data to GACRC storage for a UGA user. Please contact GACRC if your external collaborator needs to upload data onto GACRC storage for you to use ('''upon request, GACRC staff will configure a space for you''').<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> <br /> ===Globus Command Line Interface===<br /> <br /> The Globus Command Line Interface (CLI) provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. The CLI can be used to integrate Globus actions into your scripts to automate your data flows.<br /> <br /> To use it on Sapelo2, you need to load the module first, for example, to use version 2.1.0, load the module with<br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ml Globus-CLI/2.1.0-GCCcore-8.3.0<br /> &lt;/pre&gt;<br /> <br /> For more information, please see the [[Globus-CLI]] page.<br /> <br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> === Documentation===<br /> <br /> [https://docs.globus.org/ Official Globus Documentation]<br /> <br /> [https://www.globus.org/subscriber-welcome-kit/key-resource-list Key Resource List]<br /> <br /> [https://docs.globus.org/how-to/ How-to]<br /> <br /> [https://docs.globus.org/faq/ FAQs]<br /> <br /> [https://docs.globus.org/how-to/get-started/ How to get started]<br /> <br /> [https://docs.globus.org/how-to/share-files/ How to share data using Globus]<br /> <br /> [https://www.youtube.com/channel/UCIuyIEG3U5wla7fV7u4dTdQ Globus youtube channel]</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Disk_Storage&diff=21192 2023-03-27T23:15:58Z

<p>Gcormier: /* Current Storage Systems */</p> <hr /> <div>[[Category:Sapelo2]][[Category:Storage]]<br /> <br /> <br /> == Storage Overview ==<br /> <br /> Network attached storage systems at the GACRC are tiered in three levels based on speed and capacity. Ranked in order of decreasing speed, the file systems are &quot;scratch&quot; and &quot;work&quot;, &quot;home&quot;, and &quot;offline&quot; storage. <br /> <br /> The home filesystem is the &quot;landing zone&quot; when users login, and the scratch filesystem is where jobs should be run. Scratch is considered temporary and files are not to be left on it long-term. The work file system is a group-shared space that can be used to store common files needed by jobs. The offline storage filesystem is where data that is currently being used should be stored when it is not being used on scratch. <br /> <br /> Each compute node has local physical hard drives that the user can utilize as temporary storage, aka lscratch. The lscratch device is a very fast storage device compared to the network attached storage systems. The drawback is that the capacity is low and it cannot be accessed from outside the compute node. The data in lscratch is not backed up and it can be deleted anytime after the job on the compute node is finished.<br /> <br /> <br /> === Home file system ===<br /> <br /> When you login into a system (e.g. sapelo2 or xfer nodes), you will land on your home directory. Home directories are &quot;auto mounted&quot; on the login nodes and xfer nodes when you login. Your home directory on the xfer nodes is the same as your home directory on sapelo2. Sapelo2 compute nodes will also mount a user's home directory when a job starts (be that interactive or batch). Users of the teaching cluster have a separate home directory, which is not the same as on Sapelo2. <br /> <br /> Home directories have a per user quota and have snapshots. Snapshots are like backups in that they are read-only moment-in-time captures of files and directories which can be used to restore files that may have been accidentally deleted or overwritten. <br /> <br /> &lt;!-- A user's snapshot is stored within his/her home file system, thus snapshots consume a user's home directory quota. If files are created and deleted with frequency, the snapshots will grow and might end up using a large fraction (or all) the space available within a user's home file system. <br /> --&gt;<br /> The recommended data workflow is to have files in the home directory *change* as little as possible. These should be databases, applications that you use frequently but do not need to modify that often and other things that you, primarily, *read from*. &lt;!-- Think of snapshots as the memory of the files that were stored there - no matter if you add, change or delete the files, the total sum of that activity will build up over time and may exceed your quota. --&gt;<br /> <br /> Summary of the home directory characteristics for a sample user 'jsmith' in 'abclab':<br /> &lt;pre&gt;<br /> sapelo2<br /> home dir quota = 200GB<br /> home dir path = /home/jsmith<br /> snapshots = yes<br /> subject to 30-day purge = no<br /> &lt;/pre&gt;<br /> <br /> <br /> === Scratch file system ===<br /> <br /> The scratch file system resides on a high-speed storage device and it should be used to store temporary files needed for current jobs. Files that are not needed for current jobs should not be left on the scratch file system. This file system is mounted on the login nodes, xfer nodes, and compute nodes.<br /> <br /> The recommended data workflow will have jobs write output files, including intermediate data, such as checkpoint files, and final results into the scratch file system. Final results, intermediate files, and other data should then be transferred out of and immediately deleted from the scratch file system, if these are not needed for other jobs that are being submitted soon. <br /> <br /> Because the scratch file system stores large amounts of data that change a lot, it is does not have snapshots turned on and it is not backed up in anyway. Files deleted from a scratch directory cannot be recovered. <br /> <br /> There is no per user quota in the scratch file system, but a file retention policy is implemented to help prevent this file system from filling up. <br /> <br /> <br /> '''Scratch file system &quot;30-day purge&quot; policy'''<br /> <br /> &lt;blockquote style=&quot;background-color: lightyellow; border: solid thin grey;&quot;&gt; <br /> 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.<br /> <br /> 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, request/force users to clean up their /scratch directories or reduce temporarily the 30 day limit to a lower limit. <br /> <br /> Please see [[Policies#Policy_Statement_for_SCRATCH_File_System|purge policy]] for more info.<br /> &lt;/blockquote&gt;<br /> <br /> <br /> Summary of the scratch directory characteristics for a sample user 'jsmith' in 'abclab':<br /> &lt;pre&gt;<br /> sapelo2<br /> scratch dir quota = Currently no per user quota<br /> scratch dir path = /scratch/jsmith<br /> snapshots = no<br /> subject to 30-day purge = yes<br /> &lt;/pre&gt;<br /> <br /> === Work file system ===<br /> <br /> The work file system resides on a high-speed storage device and it should be used to store files needed for jobs. Each group has a directory in the work file system and this space can be used to store files needed by multiple users within a group. The work file system has a per group quota and files stored there are not subject to the auto-purge policy that is applied to the scratch file system.<br /> <br /> The work file system is mounted on the login nodes, xfer nodes, and compute nodes.<br /> <br /> The recommended data workflow is to have files that are often needed for repeated jobs, possibly by multiple users within a group, such as reference data and model data, be stored in the group's work directory. This directory is not intended as a place for jobs to write output files. <br /> <br /> The work file system does not have snapshots turned on and it is not backed up in anyway. Files deleted from a work directory cannot be recovered. <br /> <br /> Summary of the work directory characteristics for a sample user 'jsmith' in 'abclab':<br /> &lt;pre&gt;<br /> sapelo2<br /> work dir group quota = 500GB and a maximum of 100,000 files<br /> work dir path = /work/abclab<br /> snapshots = no<br /> subject to 30-day purge = no<br /> &lt;/pre&gt;<br /> <br /> === lscratch file system ===<br /> <br /> Each compute node has local physical hard drives that the user can utilize as temporary storage. The file system defined on the hard drives is called /lscratch. The lscratch device is a very fast storage device compared to the network attached storage systems. The drawback is that the capacity is low and it cannot be accessed from outside the compute node. This file system can be used for single-core jobs and for multi-thread jobs that run within a single node. In general, parallel jobs that use more than one node (e.g. MPI jobs) cannot use the /lscratch file system.<br /> <br /> The data in lscratch is not backed up and it needs to be deleted when job on the compute node is finished.<br /> <br /> Jobs that do not need to write large output files, but that need to access the files often (for example, to write small amounts of data into disk), can benefit from using /lscratch. Jobs that use /lscratch should request the amount of space in /lscratch. For information on how to request lscratch space for jobs, please refer to [https://wiki.gacrc.uga.edu/wiki/Running_Jobs_on_Sapelo2#How_to_run_a_job_using_the_local_scratch_.2Flscratch_on_a_compute_node How to run a job from lscratch]<br /> <br /> Summary of the lscratch directory characteristics for a sample user 'jsmith' in 'abclab':<br /> &lt;pre&gt;<br /> sapelo2<br /> quota = Limited by device size (Approx. 210GB on the AMD nodes and 800GB on the Intel nodes)<br /> path = /lscratch<br /> snapshots = no<br /> subject to purge = yes (files to be deleted when job exits the node) <br /> &lt;/pre&gt;<br /> <br /> <br /> === Project file system ===<br /> <br /> The offline storage filesystem is named &quot;project&quot; and is configured for use by lab groups. By default, each lab group has a 1TB quota. Individual members of a lab group can create subdirectories under their lab's project directory. PI's of lab groups can request additional storage on project as needed. Please note that this storage is not meant for long-term (e.g., archive) storage of data. That type of storage is the responsibility of the user.<br /> <br /> The project filesystem is not mounted on the compute nodes and cannot be accessed by running jobs. It is mounted on the &quot;xfer&quot; nodes when it is first accessed using its full path. <br /> <br /> The project filesystem has snapshots turned on. <br /> <br /> The recommended data workflow is to have data not needed for current jobs, but that are still needed for future jobs on the cluster, be transferred into the project file system and deleted from the scratch area.<br /> <br /> Summary of the project directory characteristics for a sample group 'abclab':<br /> &lt;pre&gt;<br /> sapelo2<br /> quota = default of 1TB per group<br /> path = /project/abclab<br /> snapshots = yes<br /> subject to 30-day purge = no<br /> &lt;/pre&gt;<br /> <br /> <br /> [[#top|Back to Top]]<br /> <br /> <br /> == Storage Architecture Summary ==<br /> <br /> Mount path for home, scratch, work, and lscratch filesystems using an example user 'jsmith' in a lab group 'abclab':<br /> &lt;pre&gt;<br /> sapelo2<br /> <br /> home= /home/jsmith<br /> scratch= /scratch/jsmith<br /> work= /work/abclab <br /> lscratch= /lscratch<br /> <br /> &lt;/pre&gt;<br /> <br /> <br /> Quota for home, scratch, work, and lscratch filesystems:<br /> &lt;pre&gt;<br /> sapelo2<br /> <br /> home= 200GB<br /> scratch= Currently no quota<br /> work= (to be added)<br /> lscratch= Limited by device size (Approx. 210GB on the AMD nodes and 800GB on the Intel nodes)<br /> <br /> &lt;/pre&gt;<br /> <br /> <br /> <br /> == Auto Mounting Filesystems ==<br /> <br /> Some filesystems are &quot;auto mounted&quot; when they are first accessed on a server. For the xfer nodes, this includes Sapelo2 home directories and the project filesystems. Sapelo2 compute nodes will mount a user's home directory when a job starts. <br /> <br /> <br /> == Snapshots ==<br /> <br /> '''Home directories'''<br /> <br /> Home directories are snapshotted. Snapshots are like backups in that they are read-only moment-in-time captures of files and directories which can be used to restore files that may have been accidentally deleted or overwritten.<br /> <br /> Home directories on Sapelo2 have snapshots taken once a day and are maintained on Sapelo2 for 14 days, giving the user the ability to retrieve old files for up to 14 days after they have deleted them. <br /> <br /> '''Note: Users can access the previous 14 days of snapshots of their own home directories and restore their files.'''<br /> <br /> If you would like to recover a file that you have deleted from your home directory within the last 14 days, you can check if the file is available in any of the snapshots and, if so, copy the file back. This can be done on a transfer node (xfer.gacrc.uga.edu) or on a Sapelo2 compute node. <br /> <br /> Here is an example for user jsmith, on an xfer node:<br /> <br /> &lt;pre&gt;<br /> [jsmith@xfer1 ]$ pwd<br /> /home/jsmith<br /> <br /> [jsmith@xfer1 ]$ ls /home/.zfs/snapshot/<br /> zrepl_20220907_063420_000 zrepl_20220920_220422_000 zrepl_20220921_200422_000<br /> zrepl_20220908_070420_000 zrepl_20220920_230422_000 zrepl_20220921_210422_000<br /> zrepl_20220909_073421_000 zrepl_20220921_000422_000 zrepl_20220921_220422_000<br /> zrepl_20220910_073421_000 zrepl_20220921_010422_000 zrepl_20220921_230422_000<br /> zrepl_20220911_073421_000 zrepl_20220921_020422_000 zrepl_20220922_000422_000<br /> zrepl_20220912_073421_000 zrepl_20220921_030422_000 zrepl_20220922_010421_000<br /> zrepl_20220913_073421_000 zrepl_20220921_040422_000 zrepl_20220922_020422_000<br /> zrepl_20220914_073421_000 zrepl_20220921_050422_000 zrepl_20220922_030422_000<br /> zrepl_20220915_073421_000 zrepl_20220921_060422_000 zrepl_20220922_040422_000<br /> zrepl_20220916_073421_000 zrepl_20220921_070422_000 zrepl_20220922_050421_000<br /> zrepl_20220917_073421_000 zrepl_20220921_080422_000 zrepl_20220922_060422_000<br /> zrepl_20220918_080421_000 zrepl_20220921_090421_000 zrepl_20220922_070422_000<br /> zrepl_20220919_080422_000 zrepl_20220921_100422_000 zrepl_20220922_080422_000<br /> zrepl_20220920_083422_000 zrepl_20220921_113421_000 zrepl_20220922_090422_000<br /> zrepl_20220920_143422_000 zrepl_20220921_123422_000 zrepl_20220922_100422_000<br /> zrepl_20220920_153422_000 zrepl_20220921_133423_000 zrepl_20220922_110422_000<br /> zrepl_20220920_163422_000 zrepl_20220921_150422_000 zrepl_20220922_120422_000<br /> zrepl_20220920_173422_000 zrepl_20220921_160422_000 zrepl_20220922_130422_000<br /> zrepl_20220920_190421_000 zrepl_20220921_170422_000 zrepl_20220922_140422_000<br /> zrepl_20220920_200422_000 zrepl_20220921_180421_000 zrepl_20220922_143422_000<br /> zrepl_20220920_210422_000 zrepl_20220921_190422_000 zrepl_20220922_150422_000<br /> <br /> [jsmith@xfer1 ]$ cd /home/.zfs/snapshot/zrepl_20220907_063420_000/jsmith<br /> <br /> [jsmith@xfer1 ]$ cp my-to-restore-file /home/jsmith<br /> &lt;/pre&gt;<br /> <br /> Weekly and monthly snapshots are also made going as far back as 6 months, but GACRC staff must retrieve these snapshots for you upon [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25844 request].<br /> <br /> <br /> '''Project file systems'''<br /> <br /> The project file systems are also snapshotted and the method to recover a file from a snapshot depends on whether your project directory is located on the Panasas storage device or on a ZFS storage device (SN13). One of the two methods below should work for you. <br /> <br /> '''Note: ANY user in a lab can access the snapshots of his/her group project file system and restore files he/she has there.'''<br /> <br /> '''Method 1 (for project folders on the Panasas)'''<br /> <br /> Each /project filesystem on the Panasas contains a completely invisible directory named &quot;.snapshot&quot;. This directory cannot be listed with ls or viewed by any program at all. Only the &quot;cd&quot; command can be used to enter this directory. Users of /project directories may retrieve files from these snapshots by changing into their snapshot directory /project/abclab/.snapshot and then cd into an appropriate snapshot directory and copying files from the that snapshot to any location they would like.<br /> <br /> Here is an example for user jsmith who is in the abclab group, on an xfer node:<br /> <br /> &lt;pre&gt;<br /> [jsmith@xfer1 ]$ pwd<br /> /home/jsmith<br /> <br /> [jsmith@xfer1 ]$ cd /project/abclab/.snapshot<br /> <br /> [jsmith@xfer1 .snapshot]$ ls <br /> 2019.02.17.04.00.03.Weekly 2019.03.01.06.00.03.Daily<br /> 2019.02.26.06.00.03.Daily 2019.03.02.06.00.03.Daily<br /> 2019.02.27.06.00.03.Daily 2019.03.03.04.00.03.Weekly<br /> 2019.02.28.06.00.03.Daily 2019.03.03.06.00.03.Daily<br /> <br /> [jsmith@xfer1 snapshot]$ cd 2019.03.03.06.00.03.Daily<br /> <br /> [jsmith@xfer1 2019.03.03.06.00.03.Daily]$ cp my-to-restore-file /home/jsmith/test<br /> &lt;/pre&gt;<br /> <br /> '''Method 2 (for project folders on SN13)'''<br /> <br /> Each /project filesystem on SN13 contains a hidden directory called .zfs and the snapshots are located in the directory /project/abclab/.zfs/snapshot (you can &lt;code&gt;cd&lt;/code&gt; into this directory and list the snapshots with the &lt;code&gt;ls&lt;/code&gt; command).<br /> <br /> Here is an example for user jsmith who is in the abclab group, on an xfer node:<br /> <br /> &lt;pre&gt;<br /> [jsmith@xfer1 ]$ pwd<br /> /home/jsmith<br /> [jsmith@xfer1 ]$ date<br /> Wed Aug 18 11:40:59 EDT 2021<br /> <br /> [jsmith@xfer1 ]$ cd /project/abclab/.zfs/snapshot<br /> <br /> [jsmith@xfer1 snapshot]$ ls <br /> zrepl_20210729_211245_000 zrepl_20210811_052246_000 zrepl_20210818_012411_000<br /> zrepl_20210730_215245_000 zrepl_20210812_054245_000 zrepl_20210818_022410_000<br /> zrepl_20210731_222244_000 zrepl_20210813_201246_000 zrepl_20210818_035041_000<br /> zrepl_20210801_225245_000 zrepl_20210816_152410_000 zrepl_20210818_052018_000<br /> zrepl_20210802_235244_000 zrepl_20210817_152411_000 zrepl_20210818_062051_000<br /> zrepl_20210804_003245_000 zrepl_20210817_172411_000 zrepl_20210818_075046_000<br /> zrepl_20210805_021244_000 zrepl_20210817_182411_000 zrepl_20210818_092039_000<br /> zrepl_20210806_025245_000 zrepl_20210817_202410_000 zrepl_20210818_115019_000<br /> zrepl_20210807_035245_000 zrepl_20210817_212410_000 zrepl_20210818_125036_000<br /> zrepl_20210808_045245_000 zrepl_20210817_222410_000 zrepl_20210818_135021_000<br /> zrepl_20210809_050244_000 zrepl_20210817_232411_000 zrepl_20210818_145018_000<br /> zrepl_20210810_050245_000 zrepl_20210818_002411_000 zrepl_20210818_152028_000<br /> <br /> [jsmith@xfer1 snapshot]$ cd zrepl_20210818_152028_000<br /> [jsmith@xfer1 zrepl_20210818_152028_000]$ cp my-to-restore-file /home/jsmith/test<br /> &lt;/pre&gt;<br /> <br /> [[#top|Back to Top]]<br /> <br /> <br /> == Current Storage Systems ==<br /> <br /> (1) ZFS storage chain (300TB) - $HOME on Sapelo2<br /> <br /> (2) DDN SFA14KX Lustre appliance (2.5PB) - $SCRATCH &amp; $WORK on Sapelo2<br /> <br /> (3) Panasas ActiveStor 100H (1PB) - $PROJECT research groups' long-term space - only for active projects requiring Sapelo2 access<br /> <br /> (4) ZFS storage chain (1.2PB) - $PROJECT research groups' long-term space - only for active projects requiring Sapelo2 access<br /> <br /> (4) ZFS storage chains (2.4PB) - backup environment for $HOME and $PROJECT.<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- <br /> <br /> (1) Panasas ActiveStor 12 storage cluster with 133TB usable capacity, running PanFS parallel file system. Currently supporting the home filesystem on the zcluster<br /> <br /> (1) Seagate (Xyratex) Lustre appliance with 480TB usable capacity. Currently supporting the scratch filesystem on sapelo<br /> <br /> (3) Penguin IceBreakers storage chains running ZFS mounted through NFS for a total of 84TB usable capacity. Currently supporting home directories on sapelo<br /> <br /> (2) Penguin IceBreakers storage chains running ZFS mounted through NFS for a total of 374TB usable capacity. This storage is used as an active project repository<br /> <br /> (1) Penguin IceBreaker storage chains running ZFS mounted through NFS for a total of 142TB usable capacity. This storage is used as a backup resource for the home and project filesystems<br /> --&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Systems&diff=21074 2022-10-19T19:20:26Z

<p>Gcormier: </p> <hr /> <div>[[Category:Sapelo2]]<br /> [[Category:Teaching]]<br /> <br /> &lt;!--<br /> === Sapelo ===<br /> <br /> Sapelo is a Linux cluster that runs a 64-bit CentOS 6.5 operating system<br /> and the login nodes has Intel Xeon processors. A QDR Infiniband network (40Gbps) provides internodal communication among <br /> compute nodes, and between the compute nodes and the storage systems serving the home directories and the <br /> scratch directories.<br /> <br /> The cluster is currently comprised of the following resources: <br /> <br /> * 16 compute nodes with AMD Opteron processors (48 cores and 128GB of RAM per node) <br /> * four 48-core 256GB RAM nodes with AMD Opteron processors (n16, n17, n18, n19)<br /> * one 48-core 512GB RAM nodes with AMD Opteron processors (n20)<br /> <br /> ====[[Connecting]]====<br /> <br /> ====[[Code Compilation on Sapelo]]====<br /> <br /> ====[[Running Jobs on Sapelo]]====<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> --&gt;<br /> <br /> <br /> === Sapelo2 ===<br /> <br /> Sapelo2 is a Linux cluster that runs a 64-bit CentOS 7.9 operating system and it is managed using xCAT and Puppet. Several virtual login nodes are available, with Intel Xeon Gold 6230 processors, 32GB of RAM, and 16 cores per node. The queueing system on Sapelo2 is Slurm.<br /> <br /> For a subset of compute nodes, internodal communication among them and between these nodes and the storage systems serving the home directories and the scratch directories is provided by a QDR Infiniband network(40Gbps). For another (larger) subset of compute nodes, these communications are provided by an EDR Infiniband network (100Gbps).<br /> <br /> <br /> The cluster is currently comprised of the following resources: <br /> <br /> '''Regular nodes'''<br /> <br /> * 72 compute nodes with AMD EPYC (Milan 3rd gen) processors (128 cores and 512GB of RAM per node)<br /> * 4 compute nodes with AMD EPYC (Milan 3rd gen) processors (64 cores and 256GB of RAM per node)<br /> * 2 compute nodes with AMD EPYC (Milan 3rd gen) processors (64 cores and 128GB of RAM per node)<br /> * 123 compute nodes with AMD EPYC (Rome 2nd gen) processors (64 cores and 128GB of RAM per node)<br /> * 64 compute nodes with AMD EPYC (Naples 1st gen) processors (32 cores and 128GB of RAM per node)<br /> * 42 compute nodes with Intel Xeon Skylake processors (32 cores and 192GB of RAM per node)<br /> * 34 compute nodes with Intel Xeon Broadwell processors (28 cores and 64GB of RAM per node)<br /> <br /> <br /> '''High memory nodes (2TB/node)'''<br /> <br /> * 2 compute nodes with AMD EPYC processors (32 cores and 2TB of RAM per node)<br /> <br /> <br /> '''High memory nodes (1TB/node)'''<br /> <br /> * 2 compute nodes with AMD EPYC (Milan 3rd gen) processors (128 cores and 1TB of RAM per node)<br /> * 4 compute nodes with AMD EPYC (Naples 1st gen) processors (64 cores and 1TB of RAM per node)<br /> * 5 compute nodes with Intel Xeon Broadwell processors (28 cores and 1TB of RAM per node)<br /> <br /> <br /> '''High memory nodes (512GB/node)'''<br /> <br /> * 18 compute nodes with AMD EPYC (Naples 1st gen) processors (32 cores and 512GB of RAM per node)<br /> &lt;!-- * 1 compute node with Intel Xeon Nehalem processors (32 cores and 512GB of RAM per node) --&gt;<br /> <br /> <br /> '''GPU nodes'''<br /> <br /> * 1 compute node with AMD EPYC (Milan 3rd gen) processors (64 cores and 1TB of RAM) and 4x NVIDIA A100 GPU cards.<br /> * 4 compute nodes with Intel Xeon Skylake processors (32 cores and 187GB of RAM) and 1x NVIDIA P100 GPU card per node<br /> * 2 compute nodes with Intel Xeon processors (16 cores and 128GB of RAM) and 8x NVIDIA K40m GPU cards per node<br /> <br /> <br /> '''Buy-in nodes'''<br /> <br /> * Various configurations<br /> <br /> <br /> &lt;!--<br /> '''Notes'''<br /> <br /> &lt;blockquote style=&quot;background-color: lightyellow; border: solid thin grey;&quot;&gt; <br /> Your home directory and /lustre1 directory on Sapelo2 are the same as on Sapelo. Therefore, there is no need to transfer data between your Sapelo and Sapelo2 home directories and /lustre1 directories. <br /> &lt;/blockquote&gt;<br /> <br /> The queueing system on Sapelo2 is Torque/Moab.<br /> <br /> ====[[Sapelo2 Frequently Asked Questions]]==== <br /> <br /> ====[[Sapelo and Sapelo2 comparison]]====<br /> <br /> --&gt;<br /> ====[[Connecting#Connecting_to_Sapelo2 |Connecting to Sapelo2]]====<br /> <br /> ====[[Transferring Files]]====<br /> <br /> ====[[Disk Storage]]====<br /> <br /> ====[[Software on Sapelo2]]====<br /> <br /> ====[[Available Toolchains and Toolchain Compatibility]]====<br /> <br /> ====[[Code Compilation on Sapelo2]]====<br /> <br /> ====[[Running Jobs on Sapelo2]]====<br /> <br /> ====[[Monitoring Jobs on Sapelo2]]====<br /> <br /> ====[[Migrating from Torque to Slurm]]====<br /> <br /> <br /> <br /> '''Training material'''<br /> <br /> To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the GACRC's Kaltura channel at https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required). Training sessions and slides are available at https://wiki.gacrc.uga.edu/wiki/Training<br /> <br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> &lt;!--<br /> === Slurm Test Cluster (Sap2test) ===<br /> <br /> GACRC is planning to switch the queueing system on Sapelo2 from Torque/Moab to Slurm later this year. At the same time, we will update the cluster OS, from CentOS 7.5 to CentOS 7.8, the compiler toolchains, and the application software packages. Older versions of the applications, currently on Sapelo2, will only be installed in the updated cluster if necessary, upon user request.<br /> <br /> In preparation for implementing this major change in the Fall, we are deploying a Slurm development (dev) cluster, that will be available ahead of time. The goal is to give users an environment to modify their workflow scripts to use Slurm and possibly to use newer versions of the applications, prior to the major change. All job submission scripts will need to be changed, because Slurm uses different syntax from Torque/Moab, as summarized in [[Migrating from Torque to Slurm]]. We strongly encourage everyone to fully test their ported workflow scripts on the Slurm dev cluster, to ensure a smooth transition to the new system later in the year.<br /> <br /> This dev cluster is intended to allow users to port their workflow scripts to Slurm, and it is not a platform for users to run jobs extensively. This dev cluster currently has the following resources:<br /> <br /> '''Regular nodes'''<br /> <br /> * 40 compute nodes with AMD Opteron processors (48 cores, 128GB RAM per node)<br /> * 24 compute nodes with AMD EPYC processors (64 cores, 128GB RAM per node)<br /> * 6 compute nodes with AMD EPYC processors (32 cores, 128GB RAM per node)<br /> * 4 compute nodes with AMD Opteron processors (48 cores, 256GB RAM per node)<br /> * 1 compute node with Intel Broadwell processors (28 cores, 64GB RAM per node)<br /> * 1 compute node with Intel Skylake processors (32 cores, 192GB RAM per node)<br /> <br /> '''High memory nodes (512GB)'''<br /> <br /> * 2 compute nodes with AMD EPYC processors (32 cores, 512GB RAM per node)<br /> * 4 compute nodes with AMD Opteron processors (48 cores, 512GB RAM per node)<br /> <br /> '''GPU node'''<br /> <br /> * 1 compute node with Intel Skylake processors (32 cores, 192GB RAM per node) and a P100 GPU card<br /> <br /> '''Storage'''<br /> <br /> The user's home directory (/home), scratch directory (/scratch), and each group's work directory (/work) on the Slurm test cluster are the same file systems as on Sapelo2. So there is no need to transfer data between Sapelo2 and Slurm test cluster. If you have Sapelo2 specific settings in your dotfiles (for example in .bashrc or in software specific configuration files), those might need to get changed when you work on Sap2test. The environment variable GACRC_CLUSTER stores the test cluster name, and can be used to set up a cluster specific dotfile to use on the test cluster.<br /> <br /> However, Sapelo2's /usr/local file system and therefore the applications installed on Sapelo2 are not available on the Slurm test cluster. <br /> <br /> <br /> '''Training material'''<br /> <br /> To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the GACRC's Kaltura channel at https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required). Training sessions and slides are available at https://wiki.gacrc.uga.edu/wiki/Training<br /> <br /> <br /> '''Getting Help'''<br /> <br /> If you run into any issues on the test cluster or have any questions or suggestions, please let me know via the online form below, as it will reach all the GACRC staff members:<br /> <br /> [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=41600 Support for Slurm test cluster]<br /> <br /> <br /> ====[[Connecting to the Slurm test cluster]]====<br /> <br /> ====[[Sapelo2 and Sap2test comparison]]====<br /> <br /> ====[[Software on sap2test | Software Installed on the Slurm test cluster]]====<br /> <br /> ====[[Code Compilation on Sap2test]]====<br /> <br /> ====[[Available Toolchains and Toolchain Compatibility]]====<br /> <br /> ====[[Running Jobs on Sap2test | Running Jobs on the Slurm test cluster]]====<br /> <br /> ====[[Monitoring Jobs on Sap2test | Monitoring Jobs on Slurm test cluster]]====<br /> <br /> ====[[Sample batch job submission scripts on the Slurm test cluster]]====<br /> <br /> ====[[Migrating from Torque to Slurm]]====<br /> <br /> <br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> --&gt;<br /> <br /> === Teaching cluster ===<br /> <br /> The teaching cluster is a Linux cluster that runs a 64-bit Linux, with Centos 7.8. The login node is a VM that has 4 cores (Intel Xeon Gold 6230 processor) and 16GB of RAM. An Ethernet network (1Gbps) provides internodal communication among compute nodes, and between the compute nodes and the storage systems serving the home directories and the work directories.<br /> <br /> The cluster is currently comprised of the following resources: <br /> <br /> *30 compute nodes with Intel Xeon X5650 2.67GHz processors (12 cores and 48GB of RAM per node) <br /> * 2 compute nodes with Intel Xeon L7555 1.87GHz processors (32 cores and 512GB of RAM per node)<br /> * 4 NVIDIA Tesla (Kepler) K20Xm GPU cards. These cards are installed on one host that has dual 6-core Intel Xeon CPUs and 48GB of RAM<br /> <br /> The queueing system on the teaching cluster is Slurm.<br /> <br /> ====[[Connecting#Connecting_to_the_teaching_cluster |Connecting to the teaching cluster]]====<br /> <br /> ====[[Transferring Files]]====<br /> <br /> ====[[Disk Storage]]====<br /> <br /> ====Software Installed on the teaching cluster====<br /> <br /> The list of installed application is available at [[Software]] page.<br /> <br /> ====[[Code Compilation on the teaching cluster]]====<br /> <br /> ====[[Running Jobs on the teaching cluster]]====<br /> <br /> ====[[Monitoring Jobs on the teaching cluster]]====</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Job_Submission_partitions_on_Sapelo2&diff=21073 2022-10-19T19:03:18Z

<p>Gcormier: </p> <hr /> <div>[[category:sapelo2]]<br /> <br /> ===Batch partitions (queues) defined on the Sapelo2===<br /> <br /> There are different partitions defined on Sapelo2. The Slurm queueing system refers to queues as partition. Users are required to specify, in the job submission script or as job submission command line arguments, the partition and the resources needed by the job in order for it to be assigned to compute node(s) that have enough available resources (such as number of cores, amount of memory, GPU cards, etc). Please note, Slurm will not allow a job to be submitted if there are no resources matching your request. Please refer to [[Migrating from Torque to Slurm]] for more info about Slurm queueing system.<br /> <br /> The following partitions are defined on the Sapelo2 cluster:<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Partition Name<br /> ! scope=&quot;col&quot; | Time limit<br /> ! scope=&quot;col&quot; | Max jobs running<br /> ! scope=&quot;col&quot; | Max jobs able to be submitted<br /> ! scope=&quot;col&quot; | Notes<br /> |-<br /> |-<br /> | batch || 7 days || 250 || 10,000 || Regular nodes.<br /> |-<br /> | batch_30d || 30 days || 1 || 2 || Regular nodes. A given user can have up to one job running at a time here, plus one pending, or two pending and none running. A user's attempt to submit a third job into this partition will be rejected.<br /> |-<br /> | highmem_p || 7 days || 15 || 100 || For high memory jobs<br /> |-<br /> | highmem_30d_p || 30 days || 1 || 2 || For high memory jobs. A given user can have up to one job running at a time here, plus one pending, or two pending and none running. A user's attempt to submit a third job into this partition will be rejected.<br /> |-<br /> |hugemem_p<br /> |7 days<br /> |4<br /> |4<br /> |For jobs needing up to 2TB of memory<br /> |-<br /> |hugemem_30d_p<br /> |30 days<br /> |4<br /> |4<br /> |For jobs needing up to 2TB of memory<br /> |-<br /> | gpu_p || 7 days || 18 || 20 || For GPU-enabled jobs.<br /> |-<br /> | gpu_30d_p || 30 days || 2 || 2 || For GPU-enabled jobs. A given user can have up to one job running at a time here, plus one pending, or two pending and none running. A user's attempt to submit a third job into this partition will be rejected.<br /> |-<br /> | inter_p || 2 days || 3 || 20 || Regular nodes, for interactive jobs.<br /> |-<br /> | '''name'''_p || style=&quot;text-align: center&quot; colspan=&quot;2&quot;| variable || Partitions that target different groups' buy-in nodes. The '''name''' string is specific to each group. <br /> |-<br /> |}<br /> <br /> <br /> When defining the resources for your job, you'll want to make sure you stay within the bounds of the resources available for the partition that you're using. The below table outlines the resources available per type of node, with the red values being the maximum for that corresponding partition.<br /> <br /> {| width=&quot;75%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=0&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Partition Name<br /> ! scope=&quot;col&quot; | # of Nodes<br /> ! scope=&quot;col&quot; | Max Mem(GB)/Node<br /> ! scope=&quot;col&quot; | Max Cores/Node<br /> ! scope=&quot;col&quot; | Processor Type<br /> ! scope=&quot;col&quot; | GPU Cards/Node<br /> |-<br /> | rowspan=&quot;8&quot; style=&quot;text-align: center&quot; | batch, batch_30d<br /> |-<br /> | 72 || style=&quot;color:red&quot; |'''500''' || style=&quot;color:red&quot;| '''128''' || AMD EPYC Milan (3rd gen) || rowspan=&quot;11&quot; style=&quot;text-align: center&quot; | N/A<br /> |-<br /> |4<br /> |250<br /> |64<br /> |AMD EPYC Milan (3rd gen)<br /> |-<br /> | 2 || rowspan=&quot;3&quot; | 120 || 64 || AMD EPYC Milan (3rd gen)<br /> |-<br /> | 123 || 64 || AMD EPYC Rome (2nd gen)<br /> |-<br /> | 64 <br /> | 32 <br /> | AMD EPYC Naples (1st gen)<br /> |-<br /> | 42 || 180 || 32 || Intel Xeon Skylake <br /> |-<br /> | 34 || 58 || 28 || Intel Xeon Broadwell<br /> |-<br /> | rowspan=&quot;3&quot; style=&quot;text-align: center&quot; | highmem_p, highmem_30d_p<br /> | 18 || 500 || 32 || AMD EPYC Naples (1st gen)<br /> |-<br /> | 4 || rowspan=&quot;2&quot; style=&quot;color:red&quot; |'''990'''|| style=&quot;color:red&quot; |'''64'''|| AMD EPYC Naples (1st gen)<br /> |-<br /> | 5 || 28 || Intel Xeon Broadwell<br /> |-<br /> | style=&quot;text-align: center&quot;|hugemem_p, hugemem_30d_p<br /> | 2<br /> | style=&quot;color:red&quot;|'''2000'''<br /> | style=&quot;color:red&quot;|'''32'''<br /> |AMD EPYC Rome (2nd gen)<br /> |-<br /> | rowspan=&quot;3&quot; style=&quot;text-align: center&quot; | gpu_p, gpu_30d_p || 4 || 180 || 32 || Intel Xeon Skylake || 1 NVDIA P100 <br /> |-<br /> | 2 || 120 || 16 || Intel Xeon || 8 NVIDIA K40m <br /> |-<br /> |1<br /> |style=&quot;color:red&quot; |'''1000'''<br /> |style=&quot;color:red&quot; |'''64'''<br /> |AMD EPYC Milan (3rd gen)<br /> |4 NVIDIA A100<br /> |-<br /> | style=&quot;text-align: center&quot; | '''name'''_p || style=&quot;text-align: center&quot; colspan=&quot;5&quot; | variable<br /> |-<br /> |}</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Job_Submission_partitions_on_Sapelo2&diff=21072 2022-10-19T18:46:38Z

<p>Gcormier: </p> <hr /> <div>[[category:sapelo2]]<br /> <br /> ===Batch partitions (queues) defined on the Sapelo2===<br /> <br /> There are different partitions defined on Sapelo2. The Slurm queueing system refers to queues as partition. Users are required to specify, in the job submission script or as job submission command line arguments, the partition and the resources needed by the job in order for it to be assigned to compute node(s) that have enough available resources (such as number of cores, amount of memory, GPU cards, etc). Please note, Slurm will not allow a job to be submitted if there are no resources matching your request. Please refer to [[Migrating from Torque to Slurm]] for more info about Slurm queueing system.<br /> <br /> The following partitions are defined on the Sapelo2 cluster:<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Partition Name<br /> ! scope=&quot;col&quot; | Time limit<br /> ! scope=&quot;col&quot; | Max jobs running<br /> ! scope=&quot;col&quot; | Max jobs able to be submitted<br /> ! scope=&quot;col&quot; | Notes<br /> |-<br /> |-<br /> | batch || 7 days || 250 || 10,000 || Regular nodes.<br /> |-<br /> | batch_30d || 30 days || 1 || 2 || Regular nodes. A given user can have up to one job running at a time here, plus one pending, or two pending and none running. A user's attempt to submit a third job into this partition will be rejected.<br /> |-<br /> | highmem_p || 7 days || 15 || 100 || For high memory jobs<br /> |-<br /> | highmem_30d_p || 30 days || 1 || 2 || For high memory jobs. A given user can have up to one job running at a time here, plus one pending, or two pending and none running. A user's attempt to submit a third job into this partition will be rejected.<br /> |-<br /> |hugemem_p<br /> |7 days<br /> |4<br /> |4<br /> |For jobs needing up to 2TB of memory<br /> |-<br /> |hugemem_30d_p<br /> |30 days<br /> |4<br /> |4<br /> |For jobs needing up to 2TB of memory<br /> |-<br /> | gpu_p || 7 days || 18 || 20 || For GPU-enabled jobs.<br /> |-<br /> | gpu_30d_p || 30 days || 2 || 2 || For GPU-enabled jobs. A given user can have up to one job running at a time here, plus one pending, or two pending and none running. A user's attempt to submit a third job into this partition will be rejected.<br /> |-<br /> | inter_p || 2 days || 3 || 20 || Regular nodes, for interactive jobs.<br /> |-<br /> | '''name'''_p || style=&quot;text-align: center&quot; colspan=&quot;2&quot;| variable || Partitions that target different groups' buy-in nodes. The '''name''' string is specific to each group. <br /> |-<br /> |}<br /> <br /> <br /> When defining the resources for your job, you'll want to make sure you stay within the bounds of the resources available for the partition that you're using. The below table outlines the resources available per type of node, with the red values being the maximum for that corresponding partition.<br /> <br /> {| width=&quot;75%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=0&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Partition Name<br /> ! scope=&quot;col&quot; | # of Nodes<br /> ! scope=&quot;col&quot; | Max Mem(GB)/Node<br /> ! scope=&quot;col&quot; | Max Cores/Node<br /> ! scope=&quot;col&quot; | Processor Type<br /> ! scope=&quot;col&quot; | GPU Cards/Node<br /> |-<br /> | style=&quot;text-align: center&quot; rowspan=&quot;7&quot; | batch, batch_30d <br /> |-<br /> | 72 || style=&quot;color:red&quot; |'''500''' || style=&quot;color:red&quot;| '''128''' || AMD EPYC Milan (3rd gen) || rowspan=&quot;12&quot; style=&quot;text-align: center&quot; | N/A<br /> <br /> |-<br /> | 123 || rowspan=&quot;3&quot; | 120 || 64 || AMD EPYC Rome (2nd gen)<br /> |-<br /> | 64 || 32 || AMD EPYC Naples (1st gen)<br /> |-<br /> | || || <br /> |-<br /> | 42 || 180 || 32 || Intel Xeon Skylake <br /> |-<br /> | 34 || 58 || 28 || Intel Xeon Broadwell<br /> |-<br /> | style=&quot;text-align: center&quot; rowspan=&quot;5&quot;| highmem_p, highmem_30d_p<br /> | 18 ||rowspan=&quot;2&quot;| 500 || 32 || AMD EPYC Naples (1st gen)<br /> |-<br /> | || || <br /> |-<br /> | 4 || style=&quot;color:red&quot; rowspan=&quot;3&quot;| '''990''' || style=&quot;color:red&quot;| '''64''' || AMD EPYC Naples (1st gen)<br /> |-<br /> | 5 || 28 || Intel Xeon Broadwell<br /> |-<br /> | || || <br /> |-<br /> | style=&quot;text-align: center&quot;|hugemem_p, hugemem_30d_p<br /> | 2<br /> | style=&quot;color:red&quot;|'''2000'''<br /> | style=&quot;color:red&quot;|'''32'''<br /> |AMD EPYC Rome (2nd gen)<br /> |-<br /> | rowspan=&quot;4&quot; style=&quot;text-align: center&quot; | gpu_p, gpu_30d_p || 4 || 180 || 32 || Intel Xeon Skylake || 1 NVDIA P100 <br /> |-<br /> | 2 || 120 || 16 || rowspan=&quot;2&quot;| Intel Xeon || 8 NVIDIA K40m <br /> |-<br /> | || || || <br /> |-<br /> |1<br /> |style=&quot;color:red&quot; |'''1000'''<br /> |style=&quot;color:red&quot; |'''64'''<br /> |AMD EPYC Milan (3rd gen)<br /> |4 NVIDIA A100<br /> |-<br /> | style=&quot;text-align: center&quot; | '''name'''_p || style=&quot;text-align: center&quot; colspan=&quot;5&quot; | variable<br /> |-<br /> |}</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=14482 2018-10-15T19:12:48Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current users.<br /> &lt;!-- * [[zcluster Decommissioning]] --&gt;<br /> <br /> &lt;!-- * [[The Sapelo2 Project]] --&gt;<br /> <br /> * ''' [[Upcoming Maintenance - November 16-22, 2018]]''' <br /> <br /> * [[Sapelo2 Frequently Asked Questions]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Sapelo and Sapelo2 comparison]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Troubleshooting]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> * [[Build Applications]]<br /> * [[Zaney]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=14481 2018-10-15T19:10:58Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current users.<br /> &lt;!-- * [[zcluster Decommissioning]] --&gt;<br /> <br /> &lt;!-- * [[The Sapelo2 Project]] --&gt;<br /> <br /> '''* [[Upcoming Maintenance - November 16-22, 2018]]''' <br /> <br /> * [[Sapelo2 Frequently Asked Questions]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Sapelo and Sapelo2 comparison]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Troubleshooting]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> * [[Build Applications]]<br /> * [[Zaney]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Upcoming_Maintenance_-_November_16-22,_2018&diff=14480 2018-10-15T19:09:36Z

<p>Gcormier: Created page with &quot;GACRC is planning a maintenance, beginning at 5 p.m. Friday, November 16 and ending at 8 a.m., Thursday, November 22. The Sapelo cluster will be decommissioned during the m...&quot;</p> <hr /> <div>GACRC is planning a maintenance, beginning at 5 p.m. Friday, November 16 and ending at 8 a.m., Thursday, November 22. <br /> <br /> The Sapelo cluster will be decommissioned during the maintenance and will no longer be available. <br /> <br /> The Sapelo2 cluster will be unavailable beginning at 5 p.m. on Friday, November 16 and should be available again no later than 8 a.m. on Thursday, November 22. <br /> <br /> Please be aware that, except for the teaching cluster, all GACRC compute and storage resources, including login nodes, transfer nodes, and compute nodes will be affected by this downtime. This maintenance will require that we power down all storage and cluster systems, as we will be bringing new systems online, and updating operating systems and various clients on all compute nodes and storage servers. <br /> <br /> As a result, all jobs still running when the maintenance begins at 5 p.m. on Friday, November 16, will be lost. Please note that we have implemented a standing reservation on the queueing system that will only dispatch jobs that request a walltime that will not extend beyond the beginning of the maintenance window.<br /> <br /> After this maintenance window, Sapelo2 will have a new Lustre scratch file system, which has more capacity and offers better performance than the current /lustre1. All files in /lustre1 at the start of the maintenance window will be copied into the new Lustre scratch storage system, but file retention and purging policies will be implemented soon thereafter and we will communicate those policies in a separate message.<br /> <br /> Sapelo will be fully decommissioned. All remaining nodes on Sapelo will be migrated into Sapelo2 during the maintenance window.<br /> <br /> Please note that the teaching cluster and its transfer node will not be affected by this maintenance window.<br /> <br /> <br /> == IMPORTANT DATES TO REMEMBER: ==<br /> <br /> <br /> '''Friday, November 16th, 2018 at 5PM''' - start of maintenance window<br /> <br /> '''Saturday, November 17th, 2018''' - the Sapelo cluster will be fully decommissioned<br /> <br /> '''Thursday, November 22nd, 2018 at 8AM''' - end of maintenance window<br /> <br /> As always, we understand the inconvenience experienced by the maintenance, but these operations are imperative to maintaining stable systems and expanding the cluster resources. We thank you for your understanding and patience.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=14479 2018-10-15T19:07:42Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current users.<br /> &lt;!-- * [[zcluster Decommissioning]] --&gt;<br /> <br /> &lt;!-- * [[The Sapelo2 Project]] --&gt;<br /> <br /> * [[Upcoming Maintenance - November 16-22, 2018]] <br /> <br /> * [[Sapelo2 Frequently Asked Questions]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Sapelo and Sapelo2 comparison]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Troubleshooting]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> * [[Build Applications]]<br /> * [[Zaney]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=14478 2018-10-15T19:05:44Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current users.<br /> &lt;!-- * [[zcluster Decommissioning]] --&gt;<br /> <br /> &lt;!-- * [[The Sapelo2 Project]] --&gt;<br /> <br /> * [[Sapelo2 Frequently Asked Questions]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Sapelo and Sapelo2 comparison]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Troubleshooting]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> * [[Build Applications]]<br /> * [[Zaney]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=14477 2018-10-15T19:04:24Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current users.<br /> &lt;!-- * [[zcluster Decommissioning]] --&gt;<br /> <br /> * [[The Sapelo2 Project]]<br /> <br /> * [[Sapelo2 Frequently Asked Questions]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Sapelo and Sapelo2 comparison]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Troubleshooting]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> * [[Build Applications]]<br /> * [[Zaney]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Borg_backup&diff=14113 2018-09-17T19:26:13Z

<p>Gcormier: /* Initializing a borg repository */</p> <hr /> <div>= Introduction =<br /> The [https://borgbackup.readthedocs.io/en/stable/index.html Borg backup software] is a deduplicating backup program. It supports compression using various codecs as well.<br /> <br /> The borg backup software is installed on all xfer nodes. You can use this software to archive your files. If you have a large amount of data this could possibly reduce storage by deduplicating and compressing your data. This is especially true for large genomic datasets.<br /> <br /> == Example showing archiving Lustre data into your lab's project directory ==<br /> === Initializing a borg repository ===<br /> Borg uses a repository (a special directory in your filesystem) to store the backup data. You will have to initialize a repository before writing backup data to it.<br /> You can create the repository in any filesystem. In this example, I am storing the repository in my project filesystem.<br /> '''Please note that you will need to be logged on the xfer node to issue these commands.'''<br /> Run the following command to initialize the repository.<br /> &lt;pre&gt;<br /> $ borg init --encryption none /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> If successful, the command will not return/print anything.<br /> <br /> === Creating a backup ===<br /> The next step is to create a backup to the repository.<br /> Run the following command to create a backup with deduplication and fast compression.<br /> &lt;pre&gt;<br /> $ borg create -s --compression auto,lz4 /project/gclab/raj76/my_project::lustre1-{now} /lustre1/raj76/my_project<br /> &lt;/pre&gt;<br /> In the above command ::lustre1-{now} is the name of the archive that will be created by this backup. The {now} shorthand tells borg backup to use the current time stamp as part of the archive name. This will be useful later to identify archives.<br /> The above command should be run in a screen or tmux session as this will take a while for large datasets.<br /> === Checking the repository ===<br /> You can check the repository for consistency using the following command.<br /> &lt;pre&gt;<br /> $ borg check /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> You can list the contents of the repository using the following command. This will lists the archives in the repo.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project<br /> lustre-2018-09-01T23:26:59 Sat, 2018-09-01 23:27:00 [d2365ef51f205d20428c3df74bc9ae9ffadb779283f806722acc6e282b6abd27]<br /> &lt;/pre&gt;<br /> You can list the files in each archive using a similar command.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project::lustre-2018-09-01T23:26:59<br /> drwxrwx--- raj76 jlmlab 0 Wed, 2018-04-11 23:39:20 scratch/raj76/Dogwood<br /> drwx------ raj76 jlmlab 0 Wed, 2017-08-30 08:40:08 scratch/raj76/Dogwood/PASA_runs<br /> drwxr-xr-x raj76 jlmlab 0 Tue, 2017-09-05 01:37:31 scratch/raj76/Dogwood/PASA_runs/run_2<br /> drwxr-xr-x raj76 jlmlab 0 Mon, 2017-09-04 15:54:19 scratch/raj76/Dogwood/PASA_runs/run_2/compreh_init_build<br /> -rw-r--r-- raj76 jlmlab 141790367 Wed, 2017-08-30 22:53:47 scratch/raj76/Dogwood/PASA_runs/run_2/StringTie-Merged.gtf.fasta<br /> -rw-r--r-- raj76 jlmlab 80133357 Mon, 2017-09-04 17:18:08 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep<br /> -rw------- raj76 jlmlab 63993718 Tue, 2017-09-05 01:37:46 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep-longest-ORFs.fasta<br /> drwxr-xr-x raj76 jlmlab 0 Wed, 2017-08-30 21:44:27 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir<br /> -rw-r--r-- raj76 jlmlab 37565886 Wed, 2017-08-30 13:37:15 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 51667326 Wed, 2017-08-30 21:36:05 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:36:48 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1.completed<br /> -rw-r--r-- raj76 jlmlab 36687377 Wed, 2017-08-30 13:37:55 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 49636612 Wed, 2017-08-30 21:36:01 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.top_1<br /> &lt;/pre&gt;<br /> === Accessing the data in the backup archives ===<br /> One of the nice features of borg backup is the ability to mount a backup archive as a FUSE filesystem and access the files in the backup as if they are in a real directory tree.<br /> Create a mount point in your home directory and mount the borg backup repo using the following commands.<br /> &lt;pre&gt;<br /> $ mkdir /home/raj76/backup_mount<br /> $ borg mount /project/gclab/raj76/my_project /home/raj76/backup_mount<br /> $ cd /home/raj76/backup_mount<br /> $ ls -l<br /> total 0<br /> drwxr-xr-x. 1 raj76 rccstaff 0 Sep 1 23:27 lustre-2018-09-01T23:26:59<br /> &lt;/pre&gt;<br /> You can browse the archive directories and access the files in the backup and if need be copy the files to an area outside of the backup.<br /> The borg backup mount is a read-only mount and files and directories cannot be changed or deleted from the archive.<br /> You can unmount the backup using the following command.<br /> &lt;pre&gt;<br /> $ cd<br /> $ borg umount /home/raj76/backup_mount<br /> &lt;/pre&gt;<br /> <br /> === More information ===<br /> Please refer to the Borg backup manual for more information and detailed explanation of the available options. <br /> https://borgbackup.readthedocs.io/en/stable/index.html</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Borg_backup&diff=14112 2018-09-17T19:21:38Z

<p>Gcormier: /* Accessing the data in the backup archives */</p> <hr /> <div>= Introduction =<br /> The [https://borgbackup.readthedocs.io/en/stable/index.html Borg backup software] is a deduplicating backup program. It supports compression using various codecs as well.<br /> <br /> The borg backup software is installed on all xfer nodes. You can use this software to archive your files. If you have a large amount of data this could possibly reduce storage by deduplicating and compressing your data. This is especially true for large genomic datasets.<br /> <br /> == Example showing archiving Lustre data into your lab's project directory ==<br /> === Initializing a borg repository ===<br /> Borg uses a repository (a special directory in your filesystem) to store the backup data. You will have to initialize a repository before writing backup data to it.<br /> You can create the repository in any filesystem. In this example, I am storing the repository in my project filesystem.<br /> Run the following command to initialize the repository.<br /> &lt;pre&gt;<br /> $ borg init --encryption none /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> If successful, the command will not return/print anything.<br /> <br /> === Creating a backup ===<br /> The next step is to create a backup to the repository.<br /> Run the following command to create a backup with deduplication and fast compression.<br /> &lt;pre&gt;<br /> $ borg create -s --compression auto,lz4 /project/gclab/raj76/my_project::lustre1-{now} /lustre1/raj76/my_project<br /> &lt;/pre&gt;<br /> In the above command ::lustre1-{now} is the name of the archive that will be created by this backup. The {now} shorthand tells borg backup to use the current time stamp as part of the archive name. This will be useful later to identify archives.<br /> The above command should be run in a screen or tmux session as this will take a while for large datasets.<br /> === Checking the repository ===<br /> You can check the repository for consistency using the following command.<br /> &lt;pre&gt;<br /> $ borg check /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> You can list the contents of the repository using the following command. This will lists the archives in the repo.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project<br /> lustre-2018-09-01T23:26:59 Sat, 2018-09-01 23:27:00 [d2365ef51f205d20428c3df74bc9ae9ffadb779283f806722acc6e282b6abd27]<br /> &lt;/pre&gt;<br /> You can list the files in each archive using a similar command.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project::lustre-2018-09-01T23:26:59<br /> drwxrwx--- raj76 jlmlab 0 Wed, 2018-04-11 23:39:20 scratch/raj76/Dogwood<br /> drwx------ raj76 jlmlab 0 Wed, 2017-08-30 08:40:08 scratch/raj76/Dogwood/PASA_runs<br /> drwxr-xr-x raj76 jlmlab 0 Tue, 2017-09-05 01:37:31 scratch/raj76/Dogwood/PASA_runs/run_2<br /> drwxr-xr-x raj76 jlmlab 0 Mon, 2017-09-04 15:54:19 scratch/raj76/Dogwood/PASA_runs/run_2/compreh_init_build<br /> -rw-r--r-- raj76 jlmlab 141790367 Wed, 2017-08-30 22:53:47 scratch/raj76/Dogwood/PASA_runs/run_2/StringTie-Merged.gtf.fasta<br /> -rw-r--r-- raj76 jlmlab 80133357 Mon, 2017-09-04 17:18:08 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep<br /> -rw------- raj76 jlmlab 63993718 Tue, 2017-09-05 01:37:46 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep-longest-ORFs.fasta<br /> drwxr-xr-x raj76 jlmlab 0 Wed, 2017-08-30 21:44:27 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir<br /> -rw-r--r-- raj76 jlmlab 37565886 Wed, 2017-08-30 13:37:15 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 51667326 Wed, 2017-08-30 21:36:05 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:36:48 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1.completed<br /> -rw-r--r-- raj76 jlmlab 36687377 Wed, 2017-08-30 13:37:55 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 49636612 Wed, 2017-08-30 21:36:01 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.top_1<br /> &lt;/pre&gt;<br /> === Accessing the data in the backup archives ===<br /> One of the nice features of borg backup is the ability to mount a backup archive as a FUSE filesystem and access the files in the backup as if they are in a real directory tree.<br /> Create a mount point in your home directory and mount the borg backup repo using the following commands.<br /> &lt;pre&gt;<br /> $ mkdir /home/raj76/backup_mount<br /> $ borg mount /project/gclab/raj76/my_project /home/raj76/backup_mount<br /> $ cd /home/raj76/backup_mount<br /> $ ls -l<br /> total 0<br /> drwxr-xr-x. 1 raj76 rccstaff 0 Sep 1 23:27 lustre-2018-09-01T23:26:59<br /> &lt;/pre&gt;<br /> You can browse the archive directories and access the files in the backup and if need be copy the files to an area outside of the backup.<br /> The borg backup mount is a read-only mount and files and directories cannot be changed or deleted from the archive.<br /> You can unmount the backup using the following command.<br /> &lt;pre&gt;<br /> $ cd<br /> $ borg umount /home/raj76/backup_mount<br /> &lt;/pre&gt;<br /> <br /> === More information ===<br /> Please refer to the Borg backup manual for more information and detailed explanation of the available options. <br /> https://borgbackup.readthedocs.io/en/stable/index.html</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Borg_backup&diff=14111 2018-09-17T19:19:05Z

<p>Gcormier: /* Initializing a borg repository */</p> <hr /> <div>= Introduction =<br /> The [https://borgbackup.readthedocs.io/en/stable/index.html Borg backup software] is a deduplicating backup program. It supports compression using various codecs as well.<br /> <br /> The borg backup software is installed on all xfer nodes. You can use this software to archive your files. If you have a large amount of data this could possibly reduce storage by deduplicating and compressing your data. This is especially true for large genomic datasets.<br /> <br /> == Example showing archiving Lustre data into your lab's project directory ==<br /> === Initializing a borg repository ===<br /> Borg uses a repository (a special directory in your filesystem) to store the backup data. You will have to initialize a repository before writing backup data to it.<br /> You can create the repository in any filesystem. In this example, I am storing the repository in my project filesystem.<br /> Run the following command to initialize the repository.<br /> &lt;pre&gt;<br /> $ borg init --encryption none /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> If successful, the command will not return/print anything.<br /> <br /> === Creating a backup ===<br /> The next step is to create a backup to the repository.<br /> Run the following command to create a backup with deduplication and fast compression.<br /> &lt;pre&gt;<br /> $ borg create -s --compression auto,lz4 /project/gclab/raj76/my_project::lustre1-{now} /lustre1/raj76/my_project<br /> &lt;/pre&gt;<br /> In the above command ::lustre1-{now} is the name of the archive that will be created by this backup. The {now} shorthand tells borg backup to use the current time stamp as part of the archive name. This will be useful later to identify archives.<br /> The above command should be run in a screen or tmux session as this will take a while for large datasets.<br /> === Checking the repository ===<br /> You can check the repository for consistency using the following command.<br /> &lt;pre&gt;<br /> $ borg check /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> You can list the contents of the repository using the following command. This will lists the archives in the repo.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project<br /> lustre-2018-09-01T23:26:59 Sat, 2018-09-01 23:27:00 [d2365ef51f205d20428c3df74bc9ae9ffadb779283f806722acc6e282b6abd27]<br /> &lt;/pre&gt;<br /> You can list the files in each archive using a similar command.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project::lustre-2018-09-01T23:26:59<br /> drwxrwx--- raj76 jlmlab 0 Wed, 2018-04-11 23:39:20 scratch/raj76/Dogwood<br /> drwx------ raj76 jlmlab 0 Wed, 2017-08-30 08:40:08 scratch/raj76/Dogwood/PASA_runs<br /> drwxr-xr-x raj76 jlmlab 0 Tue, 2017-09-05 01:37:31 scratch/raj76/Dogwood/PASA_runs/run_2<br /> drwxr-xr-x raj76 jlmlab 0 Mon, 2017-09-04 15:54:19 scratch/raj76/Dogwood/PASA_runs/run_2/compreh_init_build<br /> -rw-r--r-- raj76 jlmlab 141790367 Wed, 2017-08-30 22:53:47 scratch/raj76/Dogwood/PASA_runs/run_2/StringTie-Merged.gtf.fasta<br /> -rw-r--r-- raj76 jlmlab 80133357 Mon, 2017-09-04 17:18:08 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep<br /> -rw------- raj76 jlmlab 63993718 Tue, 2017-09-05 01:37:46 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep-longest-ORFs.fasta<br /> drwxr-xr-x raj76 jlmlab 0 Wed, 2017-08-30 21:44:27 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir<br /> -rw-r--r-- raj76 jlmlab 37565886 Wed, 2017-08-30 13:37:15 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 51667326 Wed, 2017-08-30 21:36:05 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:36:48 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1.completed<br /> -rw-r--r-- raj76 jlmlab 36687377 Wed, 2017-08-30 13:37:55 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 49636612 Wed, 2017-08-30 21:36:01 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.top_1<br /> &lt;/pre&gt;<br /> === Accessing the data in the backup archives ===<br /> One of the nice feature of borg backup is the ability to mount a backup archive as a FUSE filesystem and access the files in the backup as if they are in a real directory tree.<br /> Create a mount point in your home directory and mount the borg backup repo using the following commands.<br /> &lt;pre&gt;<br /> $ mkdir /home/raj76/backup_mount<br /> $ borg mount /project/gclab/raj76/my_project /home/raj76/backup_mount<br /> $ cd /home/raj76/backup_mount<br /> $ ls -l<br /> total 0<br /> drwxr-xr-x. 1 raj76 rccstaff 0 Sep 1 23:27 lustre-2018-09-01T23:26:59<br /> &lt;/pre&gt;<br /> You can browse the archive directories and access the files in the backup and if need be copy the files to an area outside of the backup.<br /> The borg backup mount is a read-only mount and files and directories cannot be changed or deleted from the archive.<br /> You can unmount the backup using the following command.<br /> &lt;pre&gt;<br /> $ cd<br /> $ borg umount /home/raj76/backup_mount<br /> &lt;/pre&gt;<br /> <br /> === More information ===<br /> Please refer to the Borg backup manual for more information and detailed explanation of the available options. <br /> https://borgbackup.readthedocs.io/en/stable/index.html</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Borg_backup&diff=14110 2018-09-17T19:17:53Z

<p>Gcormier: /* Example showing archiving lustre project directory */</p> <hr /> <div>= Introduction =<br /> The [https://borgbackup.readthedocs.io/en/stable/index.html Borg backup software] is a deduplicating backup program. It supports compression using various codecs as well.<br /> <br /> The borg backup software is installed on all xfer nodes. You can use this software to archive your files. If you have a large amount of data this could possibly reduce storage by deduplicating and compressing your data. This is especially true for large genomic datasets.<br /> <br /> == Example showing archiving Lustre data into your lab's project directory ==<br /> === Initializing a borg repository ===<br /> Borg uses a repository (a special directory in your filesystem) to store the backup data. You will have to initialize a repository before writing backup data to it.<br /> You can create the repository in any filesystem. In this example I am storing the repository in my project filesystem.<br /> Run the following command to initialize the repository.<br /> &lt;pre&gt;<br /> $ borg init --encryption none /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> If successful the command will not return/print anything.<br /> === Creating a backup ===<br /> The next step is to create a backup to the repository.<br /> Run the following command to create a backup with deduplication and fast compression.<br /> &lt;pre&gt;<br /> $ borg create -s --compression auto,lz4 /project/gclab/raj76/my_project::lustre1-{now} /lustre1/raj76/my_project<br /> &lt;/pre&gt;<br /> In the above command ::lustre1-{now} is the name of the archive that will be created by this backup. The {now} shorthand tells borg backup to use the current time stamp as part of the archive name. This will be useful later to identify archives.<br /> The above command should be run in a screen or tmux session as this will take a while for large datasets.<br /> === Checking the repository ===<br /> You can check the repository for consistency using the following command.<br /> &lt;pre&gt;<br /> $ borg check /project/gclab/raj76/my_project<br /> &lt;/pre&gt;<br /> You can list the contents of the repository using the following command. This will lists the archives in the repo.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project<br /> lustre-2018-09-01T23:26:59 Sat, 2018-09-01 23:27:00 [d2365ef51f205d20428c3df74bc9ae9ffadb779283f806722acc6e282b6abd27]<br /> &lt;/pre&gt;<br /> You can list the files in each archive using a similar command.<br /> &lt;pre&gt;<br /> $ borg list /project/gclab/raj76/my_project::lustre-2018-09-01T23:26:59<br /> drwxrwx--- raj76 jlmlab 0 Wed, 2018-04-11 23:39:20 scratch/raj76/Dogwood<br /> drwx------ raj76 jlmlab 0 Wed, 2017-08-30 08:40:08 scratch/raj76/Dogwood/PASA_runs<br /> drwxr-xr-x raj76 jlmlab 0 Tue, 2017-09-05 01:37:31 scratch/raj76/Dogwood/PASA_runs/run_2<br /> drwxr-xr-x raj76 jlmlab 0 Mon, 2017-09-04 15:54:19 scratch/raj76/Dogwood/PASA_runs/run_2/compreh_init_build<br /> -rw-r--r-- raj76 jlmlab 141790367 Wed, 2017-08-30 22:53:47 scratch/raj76/Dogwood/PASA_runs/run_2/StringTie-Merged.gtf.fasta<br /> -rw-r--r-- raj76 jlmlab 80133357 Mon, 2017-09-04 17:18:08 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep<br /> -rw------- raj76 jlmlab 63993718 Tue, 2017-09-05 01:37:46 scratch/raj76/Dogwood/PASA_runs/run_2/pasa_spakala_201.assemblies.fasta.transdecoder.pep-longest-ORFs.fasta<br /> drwxr-xr-x raj76 jlmlab 0 Wed, 2017-08-30 21:44:27 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir<br /> -rw-r--r-- raj76 jlmlab 37565886 Wed, 2017-08-30 13:37:15 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 51667326 Wed, 2017-08-30 21:36:05 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:36:48 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.0.fa.pslx.top_1.completed<br /> -rw-r--r-- raj76 jlmlab 36687377 Wed, 2017-08-30 13:37:55 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa<br /> -rw-r--r-- raj76 jlmlab 0 Wed, 2017-08-30 21:29:35 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.completed<br /> -rw-r--r-- raj76 jlmlab 49636612 Wed, 2017-08-30 21:36:01 scratch/raj76/Dogwood/PASA_runs/run_2/blat_out_dir/partition.111180.fa.pslx.top_1<br /> &lt;/pre&gt;<br /> === Accessing the data in the backup archives ===<br /> One of the nice feature of borg backup is the ability to mount a backup archive as a FUSE filesystem and access the files in the backup as if they are in a real directory tree.<br /> Create a mount point in your home directory and mount the borg backup repo using the following commands.<br /> &lt;pre&gt;<br /> $ mkdir /home/raj76/backup_mount<br /> $ borg mount /project/gclab/raj76/my_project /home/raj76/backup_mount<br /> $ cd /home/raj76/backup_mount<br /> $ ls -l<br /> total 0<br /> drwxr-xr-x. 1 raj76 rccstaff 0 Sep 1 23:27 lustre-2018-09-01T23:26:59<br /> &lt;/pre&gt;<br /> You can browse the archive directories and access the files in the backup and if need be copy the files to an area outside of the backup.<br /> The borg backup mount is a read-only mount and files and directories cannot be changed or deleted from the archive.<br /> You can unmount the backup using the following command.<br /> &lt;pre&gt;<br /> $ cd<br /> $ borg umount /home/raj76/backup_mount<br /> &lt;/pre&gt;<br /> <br /> === More information ===<br /> Please refer to the Borg backup manual for more information and detailed explanation of the available options. <br /> https://borgbackup.readthedocs.io/en/stable/index.html</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=9984 2018-01-18T18:00:05Z

<p>Gcormier: Reverted edits by Gcormier (talk) to last revision by Shtsai</p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current zcluster users.<br /> * [[zcluster Decommissioning]]<br /> <br /> * [[The Sapelo2 Project]]<br /> <br /> * [[Sapelo2 Frequently Asked Questions]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Sapelo and Sapelo2 comparison]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> * [[Build Applications]]<br /> <br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=9983 2018-01-18T17:59:20Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current zcluster users.<br /> * [[zcluster Decommissioning]]<br /> <br /> * [[The Sapelo2 Project]]<br /> <br /> * [[Sapelo2 Frequently Asked Questions]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Sapelo and Sapelo2 comparison]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> * [[How To Build Applications]]<br /> <br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Sapelo2_Frequently_Asked_Questions&diff=9808 2017-12-12T20:57:04Z

<p>Gcormier: </p> <hr /> <div><br /> ===When can I get access to Sapelo2?===<br /> <br /> We are still configuring and testing Sapelo2 and it is not yet available for users. Sapelo users will be notified before we start migrating accounts from Sapelo to Sapelo2. If necessary, e.g. if you have jobs running on Sapelo, we will coordinate with you before migrating your account. <br /> <br /> ===How do I connect to Sapelo2===<br /> <br /> Once we migrate your account from Sapelo to Sapelo2, you will be able to connect to Sapelo2 using Secure Shell (ssh). The hostname will be made available when Sapelo2 is ready for users. You will need to authenticate using your UGA MyID.<br /> <br /> We are currently evaluating the use of two-factor authentication for logging into Sapelo2 sometime in the near future. We will communicate any related changes at an appropriate time. <br /> <br /> <br /> ===Will I have to transfer data between Sapelo and Sapelo2?===<br /> <br /> No. Your home directory on Sapelo2 will be the same as on Sapelo. The Lustre file system will also be available on Sapelo2 and it will be mounted with the same path, i.e. /lustre1. Therefore, Sapelo users will not have to transfer data to Sapelo2. <br /> <br /> ===Can I use the xfer nodes to transfer data to/from Sapelo2?===<br /> <br /> Yes. You can continue to use the file transfer nodes (xfer nodes) to transfer data between your local machine and Sapelo2 and to transfer data between your Sapelo2 home and /lustre1 directories, and to access data in your lab's project area (/project).<br /> <br /> ===What operating system does Sapelo2 use?===<br /> <br /> The operating system (OS) on Sapelo2 is CentOS Linux release 7.1. Note that Sapelo uses CentOS Linux 6.5. Therefore, if you will use any applications installed in your home directory or code that you previously compiled, we'd suggest that you recompile and reinstall them on Sapelo2. <br /> <br /> ===What queueing system does Sapelo2 run?===<br /> <br /> Sapelo2 uses the same queueing system that is used on Sapelo, namely Torque/Moab. However, it is likely that there will be some small configuration changes on Sapelo2 and you might have to make some (mostly minor) changes to your job submission scripts. One significant change is that users will be required to request memory for their jobs and memory usage will be enforced. We suggest that current Sapelo users monitor memory usage of their current jobs, if needed, to glean a better understanding of memory consumption by their different types of jobs.<br /> <br /> ===What software packages are available on Sapelo2?=== <br /> <br /> We are still working on installing applications on Sapelo2. There are over 500 software packages installed centrally on Sapelo and it is our plan to migrate those that users still need to Sapelo2. While we do not have resources to migrate all needed packages to Sapelo2 before its go-live date, we will continue to add packages after Sapelo2 is in production. Our intention is to install first those applications that are needed by most users or that are dependencies for other applications. <br /> <br /> A preliminary list of applications that have already been installed on Sapelo2 is available at [[Software installed on Sapelo2]].</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Sapelo2_Frequently_Asked_Questions&diff=9807 2017-12-12T20:39:59Z

<p>Gcormier: </p> <hr /> <div><br /> ===When can I get access to Sapelo2?===<br /> <br /> We are still configuring and testing Sapelo2 and it is not yet available for users. Sapelo users will be notified before we start migrating accounts from Sapelo to Sapelo2. If necessary, e.g. if you have jobs running on Sapelo, we will coordinate with you before migrating your account. <br /> <br /> ===How do I connect to Sapelo2===<br /> <br /> Once we migrate your account from Sapelo to Sapelo2, you will be able to connect to Sapelo2 using Secure Shell (ssh). The hostname will be made available when Sapelo2 is ready for users. You will need to authenticate using your UGA MyID and you will need to use the two-factor (Duo) authentication. <br /> <br /> When connecting to Sapelo2 from an off-campus location, users will need to use the UGA VPN. <br /> <br /> For more information on how to sign up for Duo, please use your MyID to log into https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo/<br /> <br /> How to use the UGA VPN is detailed at https://eits.uga.edu/access_and_security/infosec/tools/vpn/<br /> <br /> ===Will I have to transfer data between Sapelo and Sapelo2?===<br /> <br /> No. Your home directory on Sapelo2 will be the same as on Sapelo. The Lustre file system will also be available on Sapelo2 and it will be mounted with the same path, i.e. /lustre1. Therefore, Sapelo users will not have to transfer data to Sapelo2. <br /> <br /> ===Can I use the xfer nodes to transfer data to/from Sapelo2?===<br /> <br /> Yes. You can continue to use the file transfer nodes (xfer nodes) to transfer data between your local machine and Sapelo2 and to transfer data between your Sapelo2 home and /lustre1 directories, and to access data in your lab's project area (/project).<br /> <br /> ===What operating system does Sapelo2 use?===<br /> <br /> The operating system (OS) on Sapelo2 is CentOS Linux release 7.1. Note that Sapelo uses CentOS Linux 6.5. Therefore, if you will use any applications installed in your home directory or code that you previously compiled, we'd suggest that you recompile and reinstall them on Sapelo2. <br /> <br /> ===What queueing system does Sapelo2 run?===<br /> <br /> Sapelo2 uses the same queueing system that is used on Sapelo, namely Torque/Moab. However, it is likely that there will be some small configuration changes on Sapelo2 and you might have to make some (mostly minor) changes to your job submission scripts. One significant change is that users will be required to request memory for their jobs and memory usage will be enforced. We suggest that current Sapelo users monitor memory usage of their current jobs, if needed, to glean a better understanding of memory consumption by their different types of jobs.<br /> <br /> ===What software packages are available on Sapelo2?=== <br /> <br /> We are still working on installing applications on Sapelo2. There are over 500 software packages installed centrally on Sapelo and it is our plan to migrate those that users still need to Sapelo2. While we do not have resources to migrate all needed packages to Sapelo2 before its go-live date, we will continue to add packages after Sapelo2 is in production. Our intention is to install first those applications that are needed by most users or that are dependencies for other applications. <br /> <br /> A preliminary list of applications that have already been installed on Sapelo2 is available at [[Software installed on Sapelo2]].</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Sapelo2_Frequently_Asked_Questions&diff=9806 2017-12-12T20:35:06Z

<p>Gcormier: </p> <hr /> <div><br /> ===When can I get access to Sapelo2?===<br /> <br /> We are still configuring and testing Sapelo2 and it is not yet available for users. Sapelo users will be notified before we start migrating accounts from Sapelo to Sapelo2. If necessary, e.g. if you have jobs running on Sapelo, we will coordinate with you before migrating your account. <br /> <br /> ===How do I connect to Sapelo2===<br /> <br /> Once we migrate your account from Sapelo to Sapelo2, you will be able to connect to Sapelo2 using Secure Shell (ssh). The hostname will be made available when Sapelo2 is ready for users. You will need to authenticate using your UGA MyID and you will need to use the two-factor (Duo) authentication. <br /> <br /> When connecting to Sapelo2 from an off-campus location, users will need to use the UGA VPN. <br /> <br /> For more information on how to sign up for Duo, please use your MyID to log into [[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo/]]<br /> <br /> How to use the UGA VPN is detailed at [[https://eits.uga.edu/access_and_security/infosec/tools/vpn/]] <br /> <br /> ===Will I have to transfer data between Sapelo and Sapelo2?===<br /> <br /> No. Your home directory on Sapelo2 will be the same as on Sapelo. The Lustre file system will also be available on Sapelo2 and it will be mounted with the same path, i.e. /lustre1. Therefore, Sapelo users will not have to transfer data to Sapelo2. <br /> <br /> ===Can I use the xfer nodes to transfer data to/from Sapelo2?===<br /> <br /> Yes. You can continue to use the file transfer nodes (xfer nodes) to transfer data between your local machine and Sapelo2 and to transfer data between your Sapelo2 home and /lustre1 directories, and to access data in your lab's project area (/project).<br /> <br /> ===What operating system does Sapelo2 use?===<br /> <br /> The operating system (OS) on Sapelo2 is CentOS Linux release 7.1. Note that Sapelo uses CentOS Linux 6.5. Therefore, if you will use any applications installed in your home directory or code that you previously compiled, we'd suggest that you recompile and reinstall them on Sapelo2. <br /> <br /> ===What queueing system does Sapelo2 run?===<br /> <br /> Sapelo2 uses the same queueing system that is used on Sapelo, namely Torque/Moab. However, it is likely that there will be some small configuration changes on Sapelo2 and you might have to make some (mostly minor) changes to your job submission scripts. One significant change is that users will be required to request memory for their jobs and memory usage will be enforced. We suggest that current Sapelo users monitor memory usage of their current jobs, if needed, to glean a better understanding of memory consumption by their different types of jobs.<br /> <br /> ===What software packages are available on Sapelo2?=== <br /> <br /> We are still working on installing applications on Sapelo2. There are over 500 software packages installed centrally on Sapelo and it is our plan to migrate those that users still need to Sapelo2. While we do not have resources to migrate all needed packages to Sapelo2 before its go-live date, we will continue to add packages after Sapelo2 is in production. Our intention is to install first those applications that are needed by most users or that are dependencies for other applications. <br /> <br /> A preliminary list of applications that have already been installed on Sapelo2 is available at [[Software installed on Sapelo2]].</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Sapelo2_Frequently_Asked_Questions&diff=9805 2017-12-12T20:33:23Z

<p>Gcormier: </p> <hr /> <div><br /> ===When can I get access to Sapelo2?===<br /> <br /> We are still configuring and testing Sapelo2 and it is not yet available for users. Sapelo users will be notified before we start migrating accounts from Sapelo to Sapelo2. If necessary, e.g. if you have jobs running on Sapelo, we will coordinate with you before migrating your account. <br /> <br /> ===How do I connect to Sapelo2===<br /> <br /> Once we migrate your account from Sapelo to Sapelo2, you will be able to connect to Sapelo2 using Secure Shell (ssh). The hostname will be made available when Sapelo2 is ready for users. You will need to authenticate using your UGA MyID and you will need to use the two-factor (Duo) authentication. <br /> <br /> When connecting to Sapelo2 from an off-campus location, users will need to use the UGA VPN. <br /> <br /> For more information on how to sign up for Duo, please use your MyID to log into [https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo/]<br /> <br /> How to use the UGA VPN is detailed at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/] <br /> <br /> ===Will I have to transfer data between Sapelo and Sapelo2?===<br /> <br /> No. Your home directory on Sapelo2 will be the same as on Sapelo. The Lustre file system will also be available on Sapelo2 and it will be mounted with the same path, i.e. /lustre1. Therefore, Sapelo users will not have to transfer data to Sapelo2. <br /> <br /> ===Can I use the xfer nodes to transfer data to/from Sapelo2?===<br /> <br /> Yes. You can continue to use the file transfer nodes (xfer nodes) to transfer data between your local machine and Sapelo2 and to transfer data between your Sapelo2 home and /lustre1 directories, and to access data in your lab's project area (/project).<br /> <br /> ===What operating system does Sapelo2 use?===<br /> <br /> The operating system (OS) on Sapelo2 is CentOS Linux release 7.1. Note that Sapelo uses CentOS Linux 6.5. Therefore, if you will use any applications installed in your home directory or code that you previously compiled, we'd suggest that you recompile and reinstall them on Sapelo2. <br /> <br /> ===What queueing system does Sapelo2 run?===<br /> <br /> Sapelo2 uses the same queueing system that is used on Sapelo, namely Torque/Moab. However, it is likely that there will be some small configuration changes on Sapelo2 and you might have to make some (mostly minor) changes to your job submission scripts. One significant change is that users will be required to request memory for their jobs and memory usage will be enforced. We suggest that current Sapelo users monitor memory usage of their current jobs, if needed, to glean a better understanding of memory consumption by their different types of jobs.<br /> <br /> ===What software packages are available on Sapelo2?=== <br /> <br /> We are still working on installing applications on Sapelo2. There are over 500 software packages installed centrally on Sapelo and it is our plan to migrate those that users still need to Sapelo2. While we do not have resources to migrate all needed packages to Sapelo2 before its go-live date, we will continue to add packages after Sapelo2 is in production. Our intention is to install first those applications that are needed by most users or that are dependencies for other applications. <br /> <br /> A preliminary list of applications that have already been installed on Sapelo2 is available at [[Software installed on Sapelo2]].</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=The_Sapelo2_Project&diff=9783 2017-11-29T15:16:50Z

<p>Gcormier: </p> <hr /> <div>==Overview – “Sapelo” to “Sapelo2” Migration Project==<br /> <br /> '''Rationale'''<br /> <br /> With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in impactful issues which seem inherent to the design of the cluster management stack that currently runs Sapelo. We propose replacing the legacy deployment with a more flexible, robust set of components.<br /> <br /> '''Goals'''<br /> <br /> - Remove problems experienced with Sapelo’s cluster management stack. While the vendor has addressed some issues, other issues are a result of design choices and they are unable to address them. <br /> <br /> - Replicate a user environment that will not be different from the current user experience available on Sapelo. This will enable a transparent migration from one platform to another. <br /> <br /> - Considerably increase resiliency to faults. <br /> <br /> <br /> '''Proposed Approach <br /> '''<br /> <br /> Sapelo2 is essentially a transformation of Sapelo. The compute layer, storage devices and network fabrics (InfiniBand and Ethernet) will remain physically in place. A new management layer will be built on hardware currently installed in the GACRC’s development environment. Login and queueing/scheduling services will now be provided through physical servers and not lightweight virtual servers. <br /> <br /> Once all management components are deployed, tested and integrated, then we will proceed to create a first version of the new cluster through the integration of a set of initial compute nodes. <br /> <br /> All relevant filesystems will be mounted per Sapelo standards. As a parallel effort by the GACRC support team, an initial set of scientific software, compilers, libraries will be installed on a separate robust filesystem that will be accessible to all compute nodes of Sapelo2. <br /> <br /> These efforts would result in a cluster ready for pre-production testing and acceptance. Acceptance will be performed both by the GACRC support team as well as by selected users with a wide variety of requirements and experience. <br /> <br /> Acceptance tests will cover the usual performance and stress suites, but will also examine issues of usability/functionality, accuracy of monitoring mechanisms, network connectivity and performance across the Ethernet and InfiniBand fabrics, appropriate access to filesystems, queueing system, system management software, program development environment and various O/S functionality. <br /> <br /> Bringing Sapelo2 into full production would consist of draining and logically migrating the current set of Sapelo compute nodes onto the Sapelo2 environment, till Sapelo does not exist as a cluster and Sapelo2 is fully populated. <br /> <br /> The expected end-result is that one day users will be asked to not login onto sapelo1.gacrc.uga.edu, but rather onto another location, and their whole user environment will be there, with a significantly enhanced cluster to work with. <br /> <br /> <br /> <br /> '''A few technical issues experienced on Sapelo, tackled with Sapelo2<br /> '''<br /> <br /> • Over quite a long period of time, ssh sessions to the Sapelo login node would freeze when idle for around 30 minutes. This issue has been resolved, but it contributed to many user's experience on Sapelo.<br /> <br /> • Users cannot access the scratch area (/lustre1) from the login node. They need to use qlogin to get to an interactive node to submit jobs from /lustre1. This might give them a sense of inconvenience.<br /> <br /> • Interactive nodes are slow and/or freeze from time to time.<br /> <br /> • Until recently, the Sapelo login node only had 1 core and 500MB of RAM. So even a simple text editing process on the login node would sometimes get killed due to lack of RAM. Commands like showjobs sometimes did not work on the login node, also due to lack of memory.<br /> <br /> • Text editors such as vi and nano don't work well on the Sapelo interactive nodes. Editing files on the login node was problematic due to its low RAM. So users sometimes ended up editing their files on the xfer nodes, but had to go back to submit jobs from the interactive node (i.e. from a qlogin session).<br /> <br /> • Code compilation on the compute nodes, including qlogin sessions, don't work using higher versions of gcc (e.g. gcc 4.7.4 and 5.3.0). These compilations just hang on compute nodes.<br /> <br /> • Because Sapelo only has one batch queue, users are required to include many PBS header lines in the job submission scripts. This might be seen as an inconvenience. Multiple queues and advanced scheduling mechanisms will be implemented on Sapelo2.<br /> <br /> • Users cannot ssh into compute nodes to check on their jobs on Sapelo or to copy and delete files from /lscratch on the compute nodes when a job crashes.<br /> <br /> • Some users were affected by the issue whereby home dirs did not get mounted on the login or xfer nodes when they logged into these systems. This issue was common over a period of some 9 months.<br /> <br /> • When a user accidentally fills up his home dir, he cannot delete any files.<br /> <br /> • Users cannot use ‘control-z’ to stop a process on an interactive node. If a control-z is used, the interactive session starts giving &quot;bash fork&quot; errors.<br /> <br /> • Several users experienced issues with small MPI jobs crashing due to the lack of PSM contexts. There has also been confusion on how to request an appropriate number of nodes/cores for hybrid MPI/threaded jobs and how it relates to PSM contexts. For small MPI jobs users also are asked to request multiple of 3 cores per job.<br /> <br /> • Issues with nodes crashing randomly, or processes hanging on the compute nodes.<br /> <br /> • Some applications are extremely complex to install due to dependencies that are not properly addressed by the version of the O/S that we currently run on Sapelo. Sapelo2 will be running an updated O/S version that will address many of these issues.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=The_Sapelo2_Project&diff=9782 2017-11-29T15:15:31Z

<p>Gcormier: </p> <hr /> <div>==Overview – “Sapelo” to “Sapelo2” Migration Project==<br /> <br /> '''Rationale'''<br /> <br /> With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in impactful issues which seem inherent to the design of the cluster management stack that currently runs Sapelo. We propose replacing the legacy deployment with a more flexible, robust set of components.<br /> <br /> '''Goals'''<br /> <br /> - Remove problems experienced with Sapelo’s cluster management stack. While the vendor has addressed some issues, other issues are a result of design choices and they are unable to address them. <br /> - Replicate a user environment that will not be different from the current user experience available on Sapelo. This will enable a transparent migration from one platform to another. <br /> - Considerably increase resiliency to faults. <br /> <br /> <br /> '''Proposed Approach <br /> '''<br /> <br /> Sapelo2 is essentially a transformation of Sapelo. The compute layer, storage devices and network fabrics (InfiniBand and Ethernet) will remain physically in place. A new management layer will be built on hardware currently installed in the GACRC’s development environment. Login and queueing/scheduling services will now be provided through physical servers and not lightweight virtual servers. <br /> <br /> Once all management components are deployed, tested and integrated, then we will proceed to create a first version of the new cluster through the integration of a set of initial compute nodes. <br /> <br /> All relevant filesystems will be mounted per Sapelo standards. As a parallel effort by the GACRC support team, an initial set of scientific software, compilers, libraries will be installed on a separate robust filesystem that will be accessible to all compute nodes of Sapelo2. <br /> <br /> These efforts would result in a cluster ready for pre-production testing and acceptance. Acceptance will be performed both by the GACRC support team as well as by selected users with a wide variety of requirements and experience. <br /> <br /> Acceptance tests will cover the usual performance and stress suites, but will also examine issues of usability/functionality, accuracy of monitoring mechanisms, network connectivity and performance across the Ethernet and InfiniBand fabrics, appropriate access to filesystems, queueing system, system management software, program development environment and various O/S functionality. <br /> <br /> Brining Sapelo2 into full production would consist of draining and logically migrating the current set of Sapelo compute nodes onto the Sapelo2 environment, till Sapelo does not exist as a cluster and Sapelo2 is fully populated. <br /> <br /> The expected end-result is that one day users will be asked to not login onto sapelo1.gacrc.uga.edu, but rather onto another location, and their whole user environment will be there, with a significantly enhanced cluster to work with. <br /> <br /> <br /> <br /> '''A few technical issues experienced on Sapelo, tackled with Sapelo2<br /> '''<br /> <br /> • Over quite a long period of time, ssh sessions to the Sapelo login node would freeze when idle for around 30 minutes. This issue has been resolved, but it contributed to many user's experience on Sapelo.<br /> <br /> • Users cannot access the scratch area (/lustre1) from the login node. They need to use qlogin to get to an interactive node to submit jobs from /lustre1. This might give them a sense of inconvenience.<br /> <br /> • Interactive nodes are slow and/or freeze from time to time.<br /> <br /> • Until recently, the Sapelo login node only had 1 core and 500MB of RAM. So even a simple text editing process on the login node would sometimes get killed due to lack of RAM. Commands like showjobs sometimes did not work on the login node, also due to lack of memory.<br /> <br /> • Text editors such as vi and nano don't work well on the Sapelo interactive nodes. Editing files on the login node was problematic due to its low RAM. So users sometimes ended up editing their files on the xfer nodes, but had to go back to submit jobs from the interactive node (i.e. from a qlogin session).<br /> <br /> • Code compilation on the compute nodes, including qlogin sessions, don't work using higher versions of gcc (e.g. gcc 4.7.4 and 5.3.0). These compilations just hang on compute nodes.<br /> <br /> • Because Sapelo only has one batch queue, users are required to include many PBS header lines in the job submission scripts. This might be seen as an inconvenience. Multiple queues and advanced scheduling mechanisms will be implemented on Sapelo2.<br /> <br /> • Users cannot ssh into compute nodes to check on their jobs on Sapelo or to copy and delete files from /lscratch on the compute nodes when a job crashes.<br /> <br /> • Some users were affected by the issue whereby home dirs did not get mounted on the login or xfer nodes when they logged into these systems. This issue was common over a period of some 9 months.<br /> <br /> • When a user accidentally fills up his home dir, he cannot delete any files.<br /> <br /> • Users cannot use ‘control-z’ to stop a process on an interactive node. If a control-z is used, the interactive session starts giving &quot;bash fork&quot; errors.<br /> <br /> • Several users experienced issues with small MPI jobs crashing due to the lack of PSM contexts. There has also been confusion on how to request an appropriate number of nodes/cores for hybrid MPI/threaded jobs and how it relates to PSM contexts. For small MPI jobs users also are asked to request multiple of 3 cores per job.<br /> <br /> • Issues with nodes crashing randomly, or processes hanging on the compute nodes.<br /> <br /> • Some applications are extremely complex to install due to dependencies that are not properly addressed by the version of the O/S that we currently run on Sapelo. Sapelo2 will be running an updated O/S version that will address many of these issues.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=9781 2017-11-29T02:30:27Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current zcluster users.<br /> * [[zcluster Decommissioning]]<br /> <br /> * [[The Sapelo2 Project]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Build Applications]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> <br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=The_Sapelo2_Project&diff=9780 2017-11-29T02:20:06Z

<p>Gcormier: </p> <hr /> <div>==Overview – “Sapelo” to “Sapelo2” Migration Project==<br /> <br /> '''Rationale'''<br /> <br /> With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in impactful issues which seem inherent to the design of the Scyld cluster management stack. We propose replacing the OpenStack-based Scyld deployment with a more flexible, robust set of components.<br /> <br /> '''Goals'''<br /> <br /> - Remove problems experienced with Sapelo’s cluster management stack, namely Penguin’s Scyld Cloud Manager Suite based on OpenStack. While Penguin has addressed some issues, other issues are a result of design choices and they are unable to address them. <br /> - Replicate a user environment that will not be different from the current user experience available on Sapelo. This will enable a transparent migration from one platform to another. <br /> - Considerably increase resiliency to faults. <br /> <br /> <br /> '''Proposed Approach <br /> '''<br /> <br /> Sapelo2 is essentially a transformation of Sapelo. The compute layer, storage devices and network fabrics (InfiniBand and Ethernet) will remain physically in place. A new management layer will be built on hardware currently installed in the GACRC’s development environment. Login and queueing/scheduling services will now be provided through physical servers and not lightweight virtual servers. <br /> <br /> Once all management components are deployed, tested and integrated, then we will proceed to create a first version of the new cluster through the integration of a set of initial compute nodes. <br /> <br /> All relevant filesystems will be mounted per Sapelo standards. As a parallel effort by the GACRC support team, an initial set of scientific software, compilers, libraries will be installed on a separate robust filesystem that will be accessible to all compute nodes of Sapelo2. <br /> <br /> These efforts would result in a cluster ready for pre-production testing and acceptance. Acceptance will be performed both by the GACRC support team as well as by selected users with a wide variety of requirements and experience. <br /> <br /> Acceptance tests will cover the usual performance and stress suites, but will also examine issues of usability/functionality, accuracy of monitoring mechanisms, network connectivity and performance across the Ethernet and InfiniBand fabrics, appropriate access to filesystems, queueing system, system management software, program development environment and various O/S functionality. <br /> <br /> Brining Sapelo2 into full production would consist of draining and logically migrating the current set of Sapelo compute nodes onto the Sapelo2 environment, till Sapelo does not exist as a cluster and Sapelo2 is fully populated. <br /> <br /> The expected end-result is that one day users will be asked to not login onto sapelo1.gacrc.uga.edu, but rather onto another location, and their whole user environment will be there, with a significantly enhanced cluster to work with. <br /> <br /> <br /> <br /> '''A few technical issues experienced on Sapelo, tackled with Sapelo2<br /> '''<br /> <br /> • Over quite a long period of time, ssh sessions to the Sapelo login node would freeze when idle for around 30 minutes. This issue has been resolved, but it contributed to many user's experience on Sapelo.<br /> <br /> • Users cannot access the scratch area (/lustre1) from the login node. They need to use qlogin to get to an interactive node to submit jobs from /lustre1. This might give them a sense of inconvenience.<br /> <br /> • Interactive nodes are slow and/or freeze from time to time.<br /> <br /> • Until recently, the Sapelo login node only had 1 core and 500MB of RAM. So even a simple text editing process on the login node would sometimes get killed due to lack of RAM. Commands like showjobs sometimes did not work on the login node, also due to lack of memory.<br /> <br /> • Text editors such as vi and nano don't work well on the Sapelo interactive nodes. Editing files on the login node was problematic due to its low RAM. So users sometimes ended up editing their files on the xfer nodes, but had to go back to submit jobs from the interactive node (i.e. from a qlogin session).<br /> <br /> • Code compilation on the compute nodes, including qlogin sessions, don't work using higher versions of gcc (e.g. gcc 4.7.4 and 5.3.0). These compilations just hang on compute nodes.<br /> <br /> • Because Sapelo only has one batch queue, users are required to include many PBS header lines in the job submission scripts. This might be seen as an inconvenience. Multiple queues and advanced scheduling mechanisms will be implemented on Sapelo2.<br /> <br /> • Users cannot ssh into compute nodes to check on their jobs on Sapelo or to copy and delete files from /lscratch on the compute nodes when a job crashes.<br /> <br /> • Some users were affected by the issue whereby home dirs did not get mounted on the login or xfer nodes when they logged into these systems. This issue was common over a period of some 9 months.<br /> <br /> • When a user accidentally fills up his home dir, he cannot delete any files.<br /> <br /> • Users cannot use ‘control-z’ to stop a process on an interactive node. If a control-z is used, the interactive session starts giving &quot;bash fork&quot; errors.<br /> <br /> • Several users experienced issues with small MPI jobs crashing due to the lack of PSM contexts. There has also been confusion on how to request an appropriate number of nodes/cores for hybrid MPI/threaded jobs and how it relates to PSM contexts. For small MPI jobs users also are asked to request multiple of 3 cores per job.<br /> <br /> • Issues with nodes crashing randomly, or processes hanging on the compute nodes.<br /> <br /> • Some applications are extremely complex to install due to dependencies that are not properly addressed by the version of the O/S that we currently run on Sapelo. Sapelo2 will be running an updated O/S version that will address many of these issues.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=The_Sapelo2_Project&diff=9779 2017-11-29T02:18:16Z

<p>Gcormier: </p> <hr /> <div>==Overview – “Sapelo” to “Sapelo2” Migration Project==<br /> <br /> '''Rationale'''<br /> <br /> With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in impactful issues which seem inherent to the design of the Scyld cluster management stack. We propose replacing the OpenStack-based Scyld deployment with a more flexible, robust set of components.<br /> <br /> '''Goals'''<br /> <br /> - Remove problems experienced with Sapelo’s cluster management stack, namely Penguin’s Scyld Cloud Manager Suite based on OpenStack. While Penguin has addressed some issues, other issues are a result of design choices and they are unable to address them. <br /> - Replicate a user environment that will not be different from the current user experience available on Sapelo. This will enable a transparent migration from one platform to another. <br /> - Considerably increase resiliency to faults. <br /> <br /> <br /> '''Proposed Approach <br /> '''<br /> Sapelo2 is essentially a transformation of Sapelo. The compute layer, storage devices and network fabrics (InfiniBand and Ethernet) will remain physically in place. A new management layer will be built on hardware currently installed in the GACRC’s development environment. Login and queueing/scheduling services will now be provided through physical servers and not lightweight virtual servers. <br /> <br /> Once all management components are deployed, tested and integrated, then we will proceed to create a first version of the new cluster through the integration of a set of initial compute nodes. <br /> <br /> All relevant filesystems will be mounted per Sapelo standards. As a parallel effort by the GACRC support team, an initial set of scientific software, compilers, libraries will be installed on a separate robust filesystem that will be accessible to all compute nodes of Sapelo2. <br /> <br /> These efforts would result in a cluster ready for pre-production testing and acceptance. Acceptance will be performed both by the GACRC support team as well as by selected users with a wide variety of requirements and experience. <br /> <br /> Acceptance tests will cover the usual performance and stress suites, but will also examine issues of usability/functionality, accuracy of monitoring mechanisms, network connectivity and performance across the Ethernet and InfiniBand fabrics, appropriate access to filesystems, queueing system, system management software, program development environment and various O/S functionality. <br /> <br /> Brining Sapelo2 into full production would consist of draining and logically migrating the current set of Sapelo compute nodes onto the Sapelo2 environment, till Sapelo does not exist as a cluster and Sapelo2 is fully populated. <br /> <br /> The expected end-result is that one day users will be asked to not login onto sapelo1.gacrc.uga.edu, but rather onto another location, and their whole user environment will be there, with a significantly enhanced cluster to work with. <br /> <br /> <br /> <br /> '''A few technical issues experienced on Sapelo, tackled with Sapelo2<br /> '''<br /> <br /> • Over quite a long period of time, ssh sessions to the Sapelo login node would freeze when idle for around 30 minutes. This issue has been resolved, but it contributed to many user's experience on Sapelo.<br /> <br /> • Users cannot access the scratch area (/lustre1) from the login node. They need to use qlogin to get to an interactive node to submit jobs from /lustre1. This might give them a sense of inconvenience.<br /> <br /> • Interactive nodes are slow and/or freeze from time to time.<br /> <br /> • Until recently, the Sapelo login node only had 1 core and 500MB of RAM. So even a simple text editing process on the login node would sometimes get killed due to lack of RAM. Commands like showjobs sometimes did not work on the login node, also due to lack of memory.<br /> <br /> • Text editors such as vi and nano don't work well on the Sapelo interactive nodes. Editing files on the login node was problematic due to its low RAM. So users sometimes ended up editing their files on the xfer nodes, but had to go back to submit jobs from the interactive node (i.e. from a qlogin session).<br /> <br /> • Code compilation on the compute nodes, including qlogin sessions, don't work using higher versions of gcc (e.g. gcc 4.7.4 and 5.3.0). These compilations just hang on compute nodes.<br /> <br /> • Because Sapelo only has one batch queue, users are required to include many PBS header lines in the job submission scripts. This might be seen as an inconvenience. Multiple queues and advanced scheduling mechanisms will be implemented on Sapelo2.<br /> <br /> • Users cannot ssh into compute nodes to check on their jobs on Sapelo or to copy and delete files from /lscratch on the compute nodes when a job crashes.<br /> <br /> • Some users were affected by the issue whereby home dirs did not get mounted on the login or xfer nodes when they logged into these systems. This issue was common over a period of some 9 months.<br /> <br /> • When a user accidentally fills up his home dir, he cannot delete any files.<br /> <br /> • Users cannot use ‘control-z’ to stop a process on an interactive node. If a control-z is used, the interactive session starts giving &quot;bash fork&quot; errors.<br /> <br /> • Several users experienced issues with small MPI jobs crashing due to the lack of PSM contexts. There has also been confusion on how to request an appropriate number of nodes/cores for hybrid MPI/threaded jobs and how it relates to PSM contexts. For small MPI jobs users also are asked to request multiple of 3 cores per job.<br /> <br /> • Issues with nodes crashing randomly, or processes hanging on the compute nodes.<br /> <br /> • Some applications are extremely complex to install due to dependencies that are not properly addressed by the version of the O/S that we currently run on Sapelo. Sapelo2 will be running an updated O/S version that will address many of these issues.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=The_Sapelo2_Project&diff=9778 2017-11-29T02:15:17Z

<p>Gcormier: </p> <hr /> <div>Overview – “Sapelo” to “Sapelo2” Migration Project<br /> <br /> '''Rationale'''<br /> <br /> With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in impactful issues which seem inherent to the design of the Scyld cluster management stack. We propose replacing the OpenStack-based Scyld deployment with a more flexible, robust set of components.<br /> <br /> '''Goals'''<br /> <br /> - Remove problems experienced with Sapelo’s cluster management stack, namely Penguin’s Scyld Cloud Manager Suite based on OpenStack. While Penguin has addressed some issues, other issues are a result of design choices and they are unable to address them. <br /> - Replicate a user environment that will not be different from the current user experience available on Sapelo. This will enable a transparent migration from one platform to another. <br /> - Considerably increase resiliency to faults. <br /> <br /> <br /> '''Proposed Approach <br /> '''<br /> Sapelo2 is essentially a transformation of Sapelo. The compute layer, storage devices and network fabrics (InfiniBand and Ethernet) will remain physically in place. A new management layer will be built on hardware currently installed in the GACRC’s development environment. Login and queueing/scheduling services will now be provided through physical servers and not lightweight virtual servers. <br /> <br /> Once all management components are deployed, tested and integrated, then we will proceed to create a first version of the new cluster through the integration of a set of initial compute nodes. <br /> <br /> All relevant filesystems will be mounted per Sapelo standards. As a parallel effort by the GACRC support team, an initial set of scientific software, compilers, libraries will be installed on a separate robust filesystem that will be accessible to all compute nodes of Sapelo2. <br /> <br /> These efforts would result in a cluster ready for pre-production testing and acceptance. Acceptance will be performed both by the GACRC support team as well as by selected users with a wide variety of requirements and experience. <br /> <br /> Acceptance tests will cover the usual performance and stress suites, but will also examine issues of usability/functionality, accuracy of monitoring mechanisms, network connectivity and performance across the Ethernet and InfiniBand fabrics, appropriate access to filesystems, queueing system, system management software, program development environment and various O/S functionality. <br /> <br /> Brining Sapelo2 into full production would consist of draining and logically migrating the current set of Sapelo compute nodes onto the Sapelo2 environment, till Sapelo does not exist as a cluster and Sapelo2 is fully populated. <br /> <br /> The expected end-result is that one day users will be asked to not login onto sapelo1.gacrc.uga.edu, but rather onto another location, and their whole user environment will be there, with a significantly enhanced cluster to work with. <br /> <br /> <br /> <br /> '''A few technical issues experienced on Sapelo, tackled with Sapelo2<br /> '''<br /> <br /> • Over quite a long period of time, ssh sessions to the Sapelo login node would freeze when idle for around 30 minutes. This issue has been resolved, but it contributed to many user's experience on Sapelo.<br /> <br /> • Users cannot access the scratch area (/lustre1) from the login node. They need to use qlogin to get to an interactive node to submit jobs from /lustre1. This might give them a sense of inconvenience.<br /> <br /> • Interactive nodes are slow and/or freeze from time to time.<br /> <br /> • Until recently, the Sapelo login node only had 1 core and 500MB of RAM. So even a simple text editing process on the login node would sometimes get killed due to lack of RAM. Commands like showjobs sometimes did not work on the login node, also due to lack of memory.<br /> <br /> • Text editors such as vi and nano don't work well on the Sapelo interactive nodes. Editing files on the login node was problematic due to its low RAM. So users sometimes ended up editing their files on the xfer nodes, but had to go back to submit jobs from the interactive node (i.e. from a qlogin session).<br /> <br /> • Code compilation on the compute nodes, including qlogin sessions, don't work using higher versions of gcc (e.g. gcc 4.7.4 and 5.3.0). These compilations just hang on compute nodes.<br /> <br /> • Because Sapelo only has one batch queue, users are required to include many PBS header lines in the job submission scripts. This might be seen as an inconvenience. Multiple queues and advanced scheduling mechanisms will be implemented on Sapelo2.<br /> <br /> • Users cannot ssh into compute nodes to check on their jobs on Sapelo or to copy and delete files from /lscratch on the compute nodes when a job crashes.<br /> <br /> • Some users were affected by the issue whereby home dirs did not get mounted on the login or xfer nodes when they logged into these systems. This issue was common over a period of some 9 months.<br /> <br /> • When a user accidentally fills up his home dir, he cannot delete any files.<br /> <br /> • Users cannot use ‘control-z’ to stop a process on an interactive node. If a control-z is used, the interactive session starts giving &quot;bash fork&quot; errors.<br /> <br /> • Several users experienced issues with small MPI jobs crashing due to the lack of PSM contexts. There has also been confusion on how to request an appropriate number of nodes/cores for hybrid MPI/threaded jobs and how it relates to PSM contexts. For small MPI jobs users also are asked to request multiple of 3 cores per job.<br /> <br /> • Issues with nodes crashing randomly, or processes hanging on the compute nodes.<br /> <br /> • Some applications are extremely complex to install due to dependencies that are not properly addressed by the version of the O/S that we currently run on Sapelo. Sapelo2 will be running an updated O/S version that will address many of these issues.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=The_Sapelo2_Project&diff=9777 2017-11-29T02:14:51Z

<p>Gcormier: </p> <hr /> <div>Overview – “Sapelo” to “Sapelo2” Migration Project<br /> <br /> '''Rationale'''<br /> <br /> With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in impactful issues which seem inherent to the design of the Scyld cluster management stack. We propose replacing the OpenStack-based Scyld deployment with a more flexible, robust set of components.<br /> <br /> '''Goals'''<br /> <br /> - Remove problems experienced with Sapelo’s cluster management stack, namely Penguin’s Scyld Cloud Manager Suite based on OpenStack. While Penguin has addressed some issues, other issues are a result of design choices and they are unable to address them. <br /> - Replicate a user environment that will not be different from the current user experience available on Sapelo. This will enable a transparent migration from one platform to another. <br /> - Considerably increase resiliency to faults. <br /> <br /> <br /> '''Proposed Approach <br /> '''<br /> Sapelo2 is essentially a transformation of Sapelo. The compute layer, storage devices and network fabrics (InfiniBand and Ethernet) will remain physically in place. A new management layer will be built on hardware currently installed in the GACRC’s development environment. Login and queueing/scheduling services will now be provided through physical servers and not lightweight virtual servers. <br /> <br /> Once all management components are deployed, tested and integrated, then we will proceed to create a first version of the new cluster through the integration of a set of initial compute nodes. <br /> <br /> All relevant filesystems will be mounted per Sapelo standards. As a parallel effort by the GACRC support team, an initial set of scientific software, compilers, libraries will be installed on a separate robust filesystem that will be accessible to all compute nodes of Sapelo2. <br /> <br /> These efforts would result in a cluster ready for pre-production testing and acceptance. Acceptance will be performed both by the GACRC support team as well as by selected users with a wide variety of requirements and experience. <br /> <br /> Acceptance tests will cover the usual performance and stress suites, but will also examine issues of usability/functionality, accuracy of monitoring mechanisms, network connectivity and performance across the Ethernet and InfiniBand fabrics, appropriate access to filesystems, queueing system, system management software, program development environment and various O/S functionality. <br /> <br /> Brining Sapelo2 into full production would consist of draining and logically migrating the current set of Sapelo compute nodes onto the Sapelo2 environment, till Sapelo does not exist as a cluster and Sapelo2 is fully populated. <br /> <br /> The expected end-result is that one day users will be asked to not login onto sapelo1.gacrc.uga.edu, but rather onto another location, and their whole user environment will be there, with a significantly enhanced cluster to work with. <br /> <br /> <br /> <br /> '''A few technical issues experienced on Sapelo, tackled with Sapelo2<br /> '''<br /> • Over quite a long period of time, ssh sessions to the Sapelo login node would freeze when idle for around 30 minutes. This issue has been resolved, but it contributed to many user's experience on Sapelo.<br /> <br /> • Users cannot access the scratch area (/lustre1) from the login node. They need to use qlogin to get to an interactive node to submit jobs from /lustre1. This might give them a sense of inconvenience.<br /> <br /> • Interactive nodes are slow and/or freeze from time to time.<br /> <br /> • Until recently, the Sapelo login node only had 1 core and 500MB of RAM. So even a simple text editing process on the login node would sometimes get killed due to lack of RAM. Commands like showjobs sometimes did not work on the login node, also due to lack of memory.<br /> <br /> • Text editors such as vi and nano don't work well on the Sapelo interactive nodes. Editing files on the login node was problematic due to its low RAM. So users sometimes ended up editing their files on the xfer nodes, but had to go back to submit jobs from the interactive node (i.e. from a qlogin session).<br /> <br /> • Code compilation on the compute nodes, including qlogin sessions, don't work using higher versions of gcc (e.g. gcc 4.7.4 and 5.3.0). These compilations just hang on compute nodes.<br /> <br /> • Because Sapelo only has one batch queue, users are required to include many PBS header lines in the job submission scripts. This might be seen as an inconvenience. Multiple queues and advanced scheduling mechanisms will be implemented on Sapelo2.<br /> <br /> • Users cannot ssh into compute nodes to check on their jobs on Sapelo or to copy and delete files from /lscratch on the compute nodes when a job crashes.<br /> <br /> • Some users were affected by the issue whereby home dirs did not get mounted on the login or xfer nodes when they logged into these systems. This issue was common over a period of some 9 months.<br /> <br /> • When a user accidentally fills up his home dir, he cannot delete any files.<br /> <br /> • Users cannot use ‘control-z’ to stop a process on an interactive node. If a control-z is used, the interactive session starts giving &quot;bash fork&quot; errors.<br /> <br /> • Several users experienced issues with small MPI jobs crashing due to the lack of PSM contexts. There has also been confusion on how to request an appropriate number of nodes/cores for hybrid MPI/threaded jobs and how it relates to PSM contexts. For small MPI jobs users also are asked to request multiple of 3 cores per job.<br /> <br /> • Issues with nodes crashing randomly, or processes hanging on the compute nodes.<br /> <br /> • Some applications are extremely complex to install due to dependencies that are not properly addressed by the version of the O/S that we currently run on Sapelo. Sapelo2 will be running an updated O/S version that will address many of these issues.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=The_Sapelo2_Project&diff=9776 2017-11-29T02:12:19Z

<p>Gcormier: Created page with &quot;Overview – “Sapelo” to “Sapelo2” Migration Project Rationale With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in...&quot;</p> <hr /> <div>Overview – “Sapelo” to “Sapelo2” Migration Project<br /> <br /> Rationale<br /> <br /> With the rapid rise of the number of users on the Sapelo cluster, we have noted the concurrent rise in impactful issues which seem inherent to the design of the Scyld cluster management stack. We propose replacing the OpenStack-based Scyld deployment with a more flexible, robust set of components.<br /> <br /> Goals<br /> <br /> - Remove problems experienced with Sapelo’s cluster management stack, namely Penguin’s Scyld Cloud Manager Suite based on OpenStack. While Penguin has addressed some issues, other issues are a result of design choices and they are unable to address them. <br /> - Replicate a user environment that will not be different from the current user experience available on Sapelo. This will enable a transparent migration from one platform to another. <br /> - Considerably increase resiliency to faults. <br /> <br /> <br /> Proposed Approach <br /> <br /> Sapelo2 is essentially a transformation of Sapelo. The compute layer, storage devices and network fabrics (InfiniBand and Ethernet) will remain physically in place. A new management layer will be built on hardware currently installed in the GACRC’s development environment. Login and queueing/scheduling services will now be provided through physical servers and not lightweight virtual servers. <br /> <br /> Once all management components are deployed, tested and integrated, then we will proceed to create a first version of the new cluster through the integration of a set of initial compute nodes. <br /> <br /> All relevant filesystems will be mounted per Sapelo standards. As a parallel effort by the GACRC support team, an initial set of scientific software, compilers, libraries will be installed on a separate robust filesystem that will be accessible to all compute nodes of Sapelo2. <br /> <br /> These efforts would result in a cluster ready for pre-production testing and acceptance. Acceptance will be performed both by the GACRC support team as well as by selected users with a wide variety of requirements and experience. <br /> <br /> Acceptance tests will cover the usual performance and stress suites, but will also examine issues of usability/functionality, accuracy of monitoring mechanisms, network connectivity and performance across the Ethernet and InfiniBand fabrics, appropriate access to filesystems, queueing system, system management software, program development environment and various O/S functionality. <br /> <br /> Brining Sapelo2 into full production would consist of draining and logically migrating the current set of Sapelo compute nodes onto the Sapelo2 environment, till Sapelo does not exist as a cluster and Sapelo2 is fully populated. <br /> <br /> The expected end-result is that one day users will be asked to not login onto sapelo1.gacrc.uga.edu, but rather onto another location, and their whole user environment will be there, with a significantly enhanced cluster to work with. <br /> <br /> <br /> <br /> A few technical issues experienced on Sapelo, tackled with Sapelo2<br /> <br /> • Over quite a long period of time, ssh sessions to the Sapelo login node would freeze when idle for around 30 minutes. This issue has been resolved, but it contributed to many user's experience on Sapelo.<br /> <br /> • Users cannot access the scratch area (/lustre1) from the login node. They need to use qlogin to get to an interactive node to submit jobs from /lustre1. This might give them a sense of inconvenience.<br /> <br /> • Interactive nodes are slow and/or freeze from time to time.<br /> <br /> • Until recently, the Sapelo login node only had 1 core and 500MB of RAM. So even a simple text editing process on the login node would sometimes get killed due to lack of RAM. Commands like showjobs sometimes did not work on the login node, also due to lack of memory.<br /> <br /> • Text editors such as vi and nano don't work well on the Sapelo interactive nodes. Editing files on the login node was problematic due to its low RAM. So users sometimes ended up editing their files on the xfer nodes, but had to go back to submit jobs from the interactive node (i.e. from a qlogin session).<br /> <br /> • Code compilation on the compute nodes, including qlogin sessions, don't work using higher versions of gcc (e.g. gcc 4.7.4 and 5.3.0). These compilations just hang on compute nodes.<br /> <br /> • Because Sapelo only has one batch queue, users are required to include many PBS header lines in the job submission scripts. This might be seen as an inconvenience. Multiple queues and advanced scheduling mechanisms will be implemented on Sapelo2.<br /> <br /> • Users cannot ssh into compute nodes to check on their jobs on Sapelo or to copy and delete files from /lscratch on the compute nodes when a job crashes.<br /> <br /> • Some users were affected by the issue whereby home dirs did not get mounted on the login or xfer nodes when they logged into these systems. This issue was common over a period of some 9 months.<br /> <br /> • When a user accidentally fills up his home dir, he cannot delete any files.<br /> <br /> • Users cannot use ‘control-z’ to stop a process on an interactive node. If a control-z is used, the interactive session starts giving &quot;bash fork&quot; errors.<br /> <br /> • Several users experienced issues with small MPI jobs crashing due to the lack of PSM contexts. There has also been confusion on how to request an appropriate number of nodes/cores for hybrid MPI/threaded jobs and how it relates to PSM contexts. For small MPI jobs users also are asked to request multiple of 3 cores per job.<br /> <br /> • Issues with nodes crashing randomly, or processes hanging on the compute nodes.<br /> <br /> • Some applications are extremely complex to install due to dependencies that are not properly addressed by the version of the O/S that we currently run on Sapelo. Sapelo2 will be running an updated O/S version that will address many of these issues.</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=9775 2017-11-29T02:11:16Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current zcluster users.<br /> * [[zcluster Decommissioning]]<br /> <br /> * [[The Sapelo2 Project]]<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Build Applications]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Job and Data Management &lt;/div&gt;<br /> Information on how to run jobs and data management.<br /> * [[Running Jobs]]<br /> * [[Monitoring Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> * [[Best Practices]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> <br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Training&diff=9221 2017-08-07T21:41:09Z

<p>Gcormier: </p> <hr /> <div><br /> ==GACRC Training==<br /> <br /> 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. <br /> <br /> '''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''<br /> <br /> <br /> ==Regular Training Announcement==<br /> <br /> The GACRC is going to host '''seventeen''' regular training sessions and '''three''' interactive Question-and-Answer sessions in '''August''' 2017. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, Python language basics, Perl language basics, and NCBI Blast application on Sapelo.<br /> <br /> We offer:<br /> <br /> 1. Four Sapelo cluster new user training sessions (mandatory for new user account creation)<br /> <br /> 2. Three Linux-I introductory sessions and Three Linux-II introductory sessions (each combined with a Linux hands-on practice session)<br /> <br /> 3. One Python language basics I session and One Python basics II session<br /> <br /> 4. One Perl language basics I session<br /> <br /> 5. Four topical sessions on:<br /> <br /> (1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users) <br /> <br /> (2) One session of NCBI Blast application on Sapelo<br /> <br /> 6. Three interactive Question-and-Answer sessions (Bring your questions to us for a discussion. No registration is needed. We are looking forward to seeing you in the classroom with your questions to us!)<br /> <br /> <br /> <br /> ====Training Location:====<br /> <br /> Davison Life Sciences Complex (Life Science Building), Room C128<br /> <br /> 120 East Green Street, Athens, GA 30602<br /> <br /> <br /> <br /> ==Event Schedule==<br /> <br /> ===Sapelo New User Training===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 1st, Tuesday, 11:00 AM - 12:30 PM<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 11th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 15th, Tuesday, 11:00 AM - 12:30 PM<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 25th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> |}<br /> <br /> ===Linux Basics and Hands-on===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to Linux Basics I and Hands-on || August 4th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> | Introduction to Linux Basics II and Hands-on || August 4th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> | Introduction to Linux Basics I and Hands-on || August 10th, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> | Introduction to Linux Basics II and Hands-on || August 17th, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> | Introduction to Linux Basics I and Hands-on || August 22nd, Tuesday, 11:00 AM - 12:30 PM <br /> |-<br /> | Introduction to Linux Basics II and Hands-on || August 24th, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> |}<br /> <br /> ===Python Basics===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Python Language Basics I || August 18th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> | Python Language Basics II || August 18th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> |}<br /> <br /> ===Perl Basics===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Perl Language Basics I || August 31st, Thursday, 11:00 AM - 12:30 PM<br /> |-<br /> |}<br /> <br /> ===Topical Sessions===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> |-<br /> | How to submit and run jobs efficiently and correctly on Sapelo || August 3rd, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> | How to submit and run jobs efficiently and correctly on Sapelo || August 11th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> | How to submit and run jobs efficiently and correctly on Sapelo || August 25th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> | NCBI Blast application on Sapelo cluster || August 29th, Tuesday, 11:00 AM - 12:30 PM <br /> |}<br /> <br /> ===Interactive Question-and-Answer Sessions===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Question-and-Answer || August 1st, Tuesday, 14:00 PM - 15:30 PM<br /> |-<br /> | Question-and-Answer || August 3rd, Thursday, 14:00 PM - 15:30 PM<br /> |-<br /> | Question-and-Answer || August 10th, Thursday, 14:00 PM - 15:30 PM<br /> |-<br /> |}<br /> <br /> ===Zcluster Decommissioning Awareness Sessions===<br /> <br /> The GACRC will host '''three''' awareness sessions in '''August'''. We will help to answer your questions related to the zcluster decommissioning. <br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Session 1 || August 15th, Tuesday, 14:00 PM - 15:30 PM<br /> |-<br /> | Session 2 || August 17th, Thursday, 14:00 PM - 15:30 PM<br /> |-<br /> | Session 3 || August 22nd, Tuesday, 14:00 PM - 15:30 PM<br /> |-<br /> |}<br /> <br /> '''Please Note:''' [[A Sapelo user account will not be granted by only attending awareness sessions.]] To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session to be scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly. <br /> <br /> More information about these training sessions will be posted on the GACRC’s training web page, at gacrc.uga.edu/training as well as on the GACRC's wiki, at wiki.gacrc.uga.edu/wiki/Training .<br /> <br /> <br /> ==How to Register==<br /> <br /> If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.<br /> <br /> We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.<br /> <br /> <br /> The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.<br /> <br /> The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.<br /> <br /> <br /> <br /> ==Topic Introduction==<br /> <br /> Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''<br /> <br /> Focus: What's the Sapelo cluster at GACRC<br /> <br /> Sapelo cluster's computing resources<br /> <br /> Sapelo cluster's software environment<br /> <br /> How to operate with Sapelo cluster and batch job submission workflows<br /> <br /> How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.<br /> <br /> <br /> Title: '''Introduction to HPC Using zcluster at GACRC'''<br /> <br /> Focus: What's zcluster at GACRC<br /> <br /> zcluster current computing resources<br /> <br /> zcluster software environment<br /> <br /> How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.<br /> <br /> <br /> Title: '''Introduction to Linux Basics I and II'''<br /> <br /> Focus of I: Linux OS and brief history<br /> <br /> Linux command, filesystem, and shell<br /> <br /> Linux common commands, etc.<br /> <br /> Focus of II: Linux shell<br /> <br /> Common practices on Linux shell scripting<br /> <br /> Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.<br /> <br /> <br /> Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''<br /> <br /> Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.<br /> <br /> Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.<br /> <br /> <br /> Title: '''Python Language Basics I, II, and III'''<br /> <br /> Focus of I: Overview of Python language, scientific modules and distributions<br /> <br /> General Lexical conventions<br /> <br /> Basic built-in data types<br /> <br /> Focus of II: Program structure: control flow and loop<br /> <br /> Function: procedural and functional programming with examples<br /> <br /> Python Class<br /> <br /> Focus of III: Python modules and importing<br /> <br /> Python Package and usage<br /> <br /> <br /> Title: '''Python on GACRC Computing Resources'''<br /> <br /> Focus: Python and Python packages/modules installed on zcluster and Sapelo<br /> <br /> Python Overview<br /> <br /> Python on Clusters<br /> <br /> Python Packages on Clusters<br /> <br /> Run Python Interactively on Clusters<br /> <br /> Run Python Batch Job on Clusters<br /> <br /> <br /> Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''<br /> <br /> Focus: Sapelo general workflow and correct computing resource requesting<br /> <br /> Overview of Sapelo cluster with reference tables and operational diagrams<br /> <br /> Sapelo batch job submission workflow taking global scratch as job working space<br /> <br /> How to request computing resources correctly <br /> <br /> How to run pipeline tasks and what are advantages/disadvantages of different options<br /> <br /> Sapelo guideline and practical tips<br /> <br /> <br /> Title: '''GACRC Storage Environment'''<br /> <br /> Focus: Overview of Linux common commands related to file and folder operations<br /> <br /> Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC<br /> <br /> How to transfer data between local and GACRC storage<br /> <br /> New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster<br /> <br /> GACRC suggestions on good practices on GACRC storage, etc;<br /> <br /> <br /> Title: '''Software installation on zcluster'''<br /> <br /> Focus: Current status of software on zcluster; What GACRC have now and what should users install<br /> <br /> How to obtain, install, organize software by users; What about databases<br /> <br /> How to validate the software installation<br /> <br /> How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.<br /> <br /> How to get help from GACRC and Common problems/mistakes<br /> <br /> <br /> Title: '''NCBI Blast application on sapelo'''<br /> <br /> Focus: Introduction to BLAST<br /> <br /> BLAST job submission to sapelo<br /> <br /> Advantages &amp; Disadvantages: NCBI website vs run at sapelo.<br /> <br /> Understand BLAST output<br /> <br /> Troubleshooting the BLAST results<br /> <br /> <br /> Title: '''NGS application overview at GACRC'''<br /> <br /> Focus: Overview of Bioinformatics software available on HPC clusters at GACRC<br /> <br /> It’s a brave new world – NGS and its Applications <br /> <br /> Hardware, Software, Databases available at GACRC<br /> <br /> NGS project: Logistics and resource considerations<br /> <br /> Best practices, common mistakes, troubleshooting and getting help from GACRC<br /> <br /> <br /> Title: '''R Language Introduction'''<br /> <br /> Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)<br /> <br /> Focus: Common general topics about R language<br /> <br /> Description:This short course will introduce users to the program R and how to use it for data analysis.<br /> <br /> Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.<br /> <br /> Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.<br /> <br /> ==Download==<br /> <br /> <br /> ====Sapelo and zcluster New User Training====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02132017.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]<br /> |-<br /> |}<br /> <br /> ====Linux Basics and Hands-on====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]<br /> |-<br /> | [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]<br /> |-<br /> | [[media: Linux Hands-on Practice 20160120.pdf]]<br /> |-<br /> | [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]<br /> |-<br /> | [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]<br /> |-<br /> |}<br /> <br /> ====Python Basics====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Python Language Basics I Workshop20160328 v4.pdf]]<br /> |-<br /> | [[media: Python Language Basics II Workshop20160425 v1.pdf]]<br /> |-<br /> |}<br /> <br /> ====Topical Sessions====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Python on GACRC Computing Resources v1.pdf]]<br /> |-<br /> | [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]<br /> |-<br /> | [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]<br /> |-<br /> | [[media: High Performance Computing (HPC) on Cluster.pdf]]<br /> |-<br /> | [[media: Software installation on zcluster.pdf]]<br /> |-<br /> | [[media: Blast Workshop GACRC 02012017.pdf]]<br /> |-<br /> |-<br /> | [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]<br /> |-<br /> |}<br /> <br /> ====Out-Reach/On-Class Talk====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Dept./Center/Institute<br /> ! scope=&quot;col&quot; | Type<br /> ! scope=&quot;col&quot; | Workshop PDF<br /> |-<br /> | Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]<br /> |-<br /> | Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]<br /> |-<br /> | The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]<br /> |-<br /> | The Center for Simulational Physics || Out-Reach || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]<br /> |-<br /> | Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]<br /> |-<br /> | Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]<br /> |-<br /> | Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]<br /> |-<br /> | Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]<br /> |-<br /> | Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]<br /> |-<br /> | Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]<br /> |-<br /> | Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]<br /> |-<br /> | Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]<br /> |-<br /> | Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]<br /> |}<br /> <br /> '''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.<br /> <br /> ==Past Sessions==<br /> <br /> [[Past Sessions in 2017]]<br /> <br /> [[Past Sessions in 2016]]<br /> <br /> [[Past Sessions in 2015]]</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Training&diff=9217 2017-08-07T17:41:40Z

<p>Gcormier: </p> <hr /> <div><br /> ==GACRC Training==<br /> <br /> 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. <br /> <br /> '''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''<br /> <br /> <br /> ==Regular Training Announcement==<br /> <br /> The GACRC is going to host '''seventeen''' regular training sessions and '''three''' interactive Question-and-Answer sessions in '''August''' 2017. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, Python language basics, Perl language basics, and NCBI Blast application on Sapelo.<br /> <br /> We offer:<br /> <br /> 1. Four Sapelo cluster new user training sessions (mandatory for new user account creation)<br /> <br /> 2. Three Linux-I introductory sessions and Three Linux-II introductory sessions (each combined with a Linux hands-on practice session)<br /> <br /> 3. One Python language basics I session and One Python basics II session<br /> <br /> 4. One Perl language basics I session<br /> <br /> 5. Four topical sessions on:<br /> <br /> (1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users) <br /> <br /> (2) One session of NCBI Blast application on Sapelo<br /> <br /> 6. Three interactive Question-and-Answer sessions (Bring your questions to us for a discussion. No registration is needed. We are looking forward to seeing you in the classroom with your questions to us!)<br /> <br /> <br /> <br /> ====Training Location:====<br /> <br /> Davison Life Sciences Complex (Life Science Building), Room C128<br /> <br /> 120 East Green Street, Athens, GA 30602<br /> <br /> <br /> <br /> ==Event Schedule==<br /> <br /> ===Sapelo New User Training===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 1st, Tuesday, 11:00 AM - 12:30 PM<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 11th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 15th, Tuesday, 11:00 AM - 12:30 PM<br /> |-<br /> | Introduction to HPC Using Sapelo Cluster at GACRC || August 25th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> |}<br /> <br /> ===Linux Basics and Hands-on===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to Linux Basics I and Hands-on || August 4th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> | Introduction to Linux Basics II and Hands-on || August 4th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> | Introduction to Linux Basics I and Hands-on || August 10th, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> | Introduction to Linux Basics II and Hands-on || August 17th, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> | Introduction to Linux Basics I and Hands-on || August 22nd, Tuesday, 11:00 AM - 12:30 PM <br /> |-<br /> | Introduction to Linux Basics II and Hands-on || August 24th, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> |}<br /> <br /> ===Python Basics===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Python Language Basics I || August 18th, Friday, 10:00 AM - 11:30 AM<br /> |-<br /> | Python Language Basics II || August 18th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> |}<br /> <br /> ===Perl Basics===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Perl Language Basics I || August 31st, Thursday, 11:00 AM - 12:30 PM<br /> |-<br /> |}<br /> <br /> ===Topical Sessions===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> |-<br /> | How to submit and run jobs efficiently and correctly on Sapelo || August 3rd, Thursday, 11:00 AM - 12:30 PM <br /> |-<br /> | How to submit and run jobs efficiently and correctly on Sapelo || August 11th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> | How to submit and run jobs efficiently and correctly on Sapelo || August 25th, Friday, 11:30 AM - 1:00 PM<br /> |-<br /> | NCBI Blast application on Sapelo cluster || August 29th, Tuesday, 11:00 AM - 12:30 PM <br /> |}<br /> <br /> ===Interactive Question-and-Answer Sessions===<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Question-and-Answer || August 1st, Tuesday, 14:00 PM - 15:30 PM<br /> |-<br /> | Question-and-Answer || August 3rd, Thursday, 14:00 PM - 15:30 PM<br /> |-<br /> | Question-and-Answer || August 10th, Thursday, 14:00 PM - 15:30 PM<br /> |-<br /> |}<br /> <br /> ===Zcluster Decommissioning Awareness Sessions===<br /> <br /> The GACRC will host '''three''' awareness sessions in '''August'''. We will help to answer your questions related to the zcluster decommissioning. <br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Session 1 || August 15th, Tuesday, 14:00 PM - 15:30 PM<br /> |-<br /> | Session 2 || August 17th, Thursday, 14:00 PM - 15:30 PM<br /> |-<br /> | Session 3 || August 22nd, Tuesday, 14:00 PM - 15:30 PM<br /> |-<br /> |}<br /> <br /> '''Please Note:''' [[A Sapelo user account will not be granted by only attending awareness sessions.]] To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session to be scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, host weekly. <br /> <br /> More information about these training sessions will be posted on the GACRC’s training web page, at gacrc.uga.edu/training as well as on the GACRC's wiki, at wiki.gacrc.uga.edu/wiki/Training .<br /> <br /> <br /> ==How to Register==<br /> <br /> If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.<br /> <br /> We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.<br /> <br /> <br /> The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.<br /> <br /> The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.<br /> <br /> <br /> <br /> ==Topic Introduction==<br /> <br /> Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''<br /> <br /> Focus: What's the Sapelo cluster at GACRC<br /> <br /> Sapelo cluster's computing resources<br /> <br /> Sapelo cluster's software environment<br /> <br /> How to operate with Sapelo cluster and batch job submission workflows<br /> <br /> How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.<br /> <br /> <br /> Title: '''Introduction to HPC Using zcluster at GACRC'''<br /> <br /> Focus: What's zcluster at GACRC<br /> <br /> zcluster current computing resources<br /> <br /> zcluster software environment<br /> <br /> How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.<br /> <br /> <br /> Title: '''Introduction to Linux Basics I and II'''<br /> <br /> Focus of I: Linux OS and brief history<br /> <br /> Linux command, filesystem, and shell<br /> <br /> Linux common commands, etc.<br /> <br /> Focus of II: Linux shell<br /> <br /> Common practices on Linux shell scripting<br /> <br /> Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.<br /> <br /> <br /> Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''<br /> <br /> Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.<br /> <br /> Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.<br /> <br /> <br /> Title: '''Python Language Basics I, II, and III'''<br /> <br /> Focus of I: Overview of Python language, scientific modules and distributions<br /> <br /> General Lexical conventions<br /> <br /> Basic built-in data types<br /> <br /> Focus of II: Program structure: control flow and loop<br /> <br /> Function: procedural and functional programming with examples<br /> <br /> Python Class<br /> <br /> Focus of III: Python modules and importing<br /> <br /> Python Package and usage<br /> <br /> <br /> Title: '''Python on GACRC Computing Resources'''<br /> <br /> Focus: Python and Python packages/modules installed on zcluster and Sapelo<br /> <br /> Python Overview<br /> <br /> Python on Clusters<br /> <br /> Python Packages on Clusters<br /> <br /> Run Python Interactively on Clusters<br /> <br /> Run Python Batch Job on Clusters<br /> <br /> <br /> Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''<br /> <br /> Focus: Sapelo general workflow and correct computing resource requesting<br /> <br /> Overview of Sapelo cluster with reference tables and operational diagrams<br /> <br /> Sapelo batch job submission workflow taking global scratch as job working space<br /> <br /> How to request computing resources correctly <br /> <br /> How to run pipeline tasks and what are advantages/disadvantages of different options<br /> <br /> Sapelo guideline and practical tips<br /> <br /> <br /> Title: '''GACRC Storage Environment'''<br /> <br /> Focus: Overview of Linux common commands related to file and folder operations<br /> <br /> Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC<br /> <br /> How to transfer data between local and GACRC storage<br /> <br /> New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster<br /> <br /> GACRC suggestions on good practices on GACRC storage, etc;<br /> <br /> <br /> Title: '''Software installation on zcluster'''<br /> <br /> Focus: Current status of software on zcluster; What GACRC have now and what should users install<br /> <br /> How to obtain, install, organize software by users; What about databases<br /> <br /> How to validate the software installation<br /> <br /> How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.<br /> <br /> How to get help from GACRC and Common problems/mistakes<br /> <br /> <br /> Title: '''NCBI Blast application on zcluster'''<br /> <br /> Focus: Introduction to BLAST<br /> <br /> BLAST job submission to zcluster<br /> <br /> Advantages &amp; Disadvantages: NCBI website vs run at zcluster.<br /> <br /> Understand BLAST output<br /> <br /> Troubleshooting the BLAST results<br /> <br /> <br /> Title: '''NGS application overview at GACRC'''<br /> <br /> Focus: Overview of Bioinformatics software available on HPC clusters at GACRC<br /> <br /> It’s a brave new world – NGS and its Applications <br /> <br /> Hardware, Software, Databases available at GACRC<br /> <br /> NGS project: Logistics and resource considerations<br /> <br /> Best practices, common mistakes, troubleshooting and getting help from GACRC<br /> <br /> <br /> Title: '''R Language Introduction'''<br /> <br /> Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)<br /> <br /> Focus: Common general topics about R language<br /> <br /> Description:This short course will introduce users to the program R and how to use it for data analysis.<br /> <br /> Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.<br /> <br /> Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.<br /> <br /> <br /> ==Download==<br /> <br /> <br /> ====Sapelo and zcluster New User Training====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02132017.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]<br /> |-<br /> |}<br /> <br /> ====Linux Basics and Hands-on====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]<br /> |-<br /> | [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]<br /> |-<br /> | [[media: Linux Hands-on Practice 20160120.pdf]]<br /> |-<br /> | [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]<br /> |-<br /> | [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]<br /> |-<br /> |}<br /> <br /> ====Python Basics====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Python Language Basics I Workshop20160328 v4.pdf]]<br /> |-<br /> | [[media: Python Language Basics II Workshop20160425 v1.pdf]]<br /> |-<br /> |}<br /> <br /> ====Topical Sessions====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Python on GACRC Computing Resources v1.pdf]]<br /> |-<br /> | [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]<br /> |-<br /> | [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]<br /> |-<br /> | [[media: High Performance Computing (HPC) on Cluster.pdf]]<br /> |-<br /> | [[media: Software installation on zcluster.pdf]]<br /> |-<br /> | [[media: Blast Workshop GACRC 02012017.pdf]]<br /> |-<br /> |-<br /> | [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]<br /> |-<br /> |}<br /> <br /> ====Out-Reach/On-Class Talk====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Dept./Center/Institute<br /> ! scope=&quot;col&quot; | Type<br /> ! scope=&quot;col&quot; | Workshop PDF<br /> |-<br /> | Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]<br /> |-<br /> | Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]<br /> |-<br /> | The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]<br /> |-<br /> | The Center for Simulational Physics || Out-Reach || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]<br /> |-<br /> | Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]<br /> |-<br /> | Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]<br /> |-<br /> | Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]<br /> |-<br /> | Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]<br /> |-<br /> | Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]<br /> |-<br /> | Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]<br /> |-<br /> | Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]<br /> |-<br /> | Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]<br /> |-<br /> | Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]<br /> |}<br /> <br /> '''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.<br /> <br /> ==Past Sessions==<br /> <br /> [[Past Sessions in 2017]]<br /> <br /> [[Past Sessions in 2016]]<br /> <br /> [[Past Sessions in 2015]]</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=9189 2017-08-04T22:40:28Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current zcluster users.<br /> * [[zcluster Decommissioning]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Running Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> <br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Georgia_Advanced_Computing_Resource_Center&diff=9186 2017-08-04T22:05:44Z

<p>Gcormier: </p> <hr /> <div>__NOTOC__<br /> Welcome to the Georgia Advanced Computing Resource Center wiki. The information provided here is a supplement to the GACRC webpage. The GACRC online information resources include:<br /> <br /> *[http://gacrc.uga.edu/ Web Site] – general overview<br /> *[https://wiki.gacrc.uga.edu/ Wiki] – software docs and how-to’s - &quot;You Are Here&quot;<br /> &lt;!-- *[https://blog.gacrc.uga.edu/ Blog] – announcements --&gt;<br /> &lt;!-- *[https://forums.gacrc.uga.edu/ Forums] – user discussion area --&gt;<br /> <br /> &lt;!--Comments on color for the below --&gt;<br /> &lt;!-- green background = #00CC33 --&gt;<br /> &lt;!-- light orange background = #FF9F40 --&gt;<br /> &lt;!-- red background = red --&gt;<br /> &lt;!-- default text, at end of line, is: Online --&gt;<br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#00CC33; font-size:120%; font-weight:bold; border:1px solid #00CC33; text-align:left; color:white; padding:0.2em 0.4em;&quot;&gt; Current Status: &lt;span style=&quot;color:black&quot;&gt; Online &lt;/span&gt;&lt;/div&gt;<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; IMPORTANT NEWS &lt;/div&gt;<br /> The following is an important notice for all of our current zcluster users.<br /> * [[zcluster Decommisionning]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Getting Started &lt;/div&gt;<br /> Welcome to the Georgia Advanced Computing Resource Center at the University of Georgia. If you're new to the GACRC, start with these links to get acquainted with our resources.<br /> * [[User Accounts]]<br /> * [[Connecting]]<br /> * [[Transferring Files]]<br /> * [[Password | Changing your Password]]<br /> * [[Frequently Asked Questions]]<br /> * [[Command List]]<br /> * [[Getting Help]]<br /> * [[Policies]]<br /> * [[Consulting]]<br /> * [[Training]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Services &lt;/div&gt;<br /> Services and other resources.<br /> * [[Instructional Accounts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; System Information &lt;/div&gt;<br /> Hardware information and operational procedures are described below.<br /> * [[Systems]]<br /> * [[Disk Storage]]<br /> * [[Running Jobs]]<br /> * [[Job Submission Queues]]<br /> * [[Sample Scripts | Sample Job Scripts]]<br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#333333; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee; padding:0.2em 0.4em;&quot;&gt; Software and Libraries &lt;/div&gt;<br /> Documentation for software applications, programming tools, and usage.<br /> * [[Software]]<br /> * [[Bioinformatics Databases]]<br /> * [[OpenMP]]<br /> * [[MPI | Message Passing Interface (MPI)]]<br /> * [[Compilers]]<br /> * [[GPU|GPU and CUDA Programming]]<br /> * [[Galaxy]]<br /> <br /> <br /> <br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Knowledge Base]]&lt;/div&gt;<br /> &lt;br /&gt;<br /> &lt;div style=&quot;width=100%; margin:0; background:#eeeeee; font-size:120%; font-weight:bold; border:1px solid #f9f9f9; text-align:left; color:#eeeeee padding:0.2em 0.4em;&quot;&gt;<br /> [[GACRC Advisory Committee]]&lt;/div&gt;</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Running_Jobs&diff=9155 2017-07-21T23:38:08Z

<p>Gcormier: </p> <hr /> <div>[[Category:Zcluster]][[Category:Sapelo]]<br /> <br /> [[Running Jobs on Sapelo]]</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Systems&diff=9153 2017-07-21T23:15:15Z

<p>Gcormier: </p> <hr /> <div>[[Category:Zcluster]]<br /> [[Category:Sapelo]]<br /> <br /> === New cluster (temporarily called Sapelo) ===<br /> <br /> The new cluster (Sapelo) is a Linux cluster that runs a 64-bit CentOS 6.5 operating system<br /> and the login nodes has Intel Xeon processors. A QDR Infiniband network (40Gbps) provides internodal communication among <br /> compute nodes, and between the compute nodes and the storage systems serving the home directories and the <br /> scratch directories.<br /> <br /> The cluster is currently comprised of the following resources: <br /> <br /> * 112 compute nodes with AMD Opteron processors (48 cores and 128GB of RAM per node) <br /> * four 48-core 256GB RAM nodes with AMD Opteron processors (n16, n17, n18, n19)<br /> * six 48-core 512GB RAM nodes with AMD Opteron processors (n20, n21, n22, n23, n24, n25)<br /> * one 48-core 1TB RAM node with AMD Opteron processors (n26)<br /> * two 16-core 128GB RAM nodes with Intel Xeon processors and 8 NVIDIA K40m GPU cards each (n48, n49)<br /> <br /> ====[[Connecting]]====<br /> <br /> ====[[Code Compilation on Sapelo]]====<br /> <br /> ====[[Running Jobs on Sapelo]]====<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> ====[[Connecting]]====<br /> <br /> ====[[Transferring Files]]====<br /> <br /> ====[[Disk Storage]]====<br /> <br /> ====[[Code Compilation on zcluster]]====<br /> <br /> ====[[Running Jobs on zcluster]]====</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Disk_Storage&diff=7956 2016-06-29T00:51:59Z

<p>Gcormier: </p> <hr /> <div>[[Category:Zcluster]][[Category:Storage]]<br /> <br /> <br /> == Storage Overview ==<br /> <br /> Network attached storage systems at the GACRC are tiered in three levels based on speed and capacity. Ranked in order of decreasing speed, the file systems are &quot;scratch&quot;, &quot;home&quot;, and &quot;offline&quot; storage. The home filesystem is the &quot;landing zone&quot; when users login, and the scratch filesystem is where jobs should be run. Scratch is considered temporary and files are not to be left on it long-term. The offline storage filesystem is where data that is currently being used should be stored when it is not being used on scratch.<br /> <br /> For home and scratch directories, users are assigned the following quotas (maximum space allowed):<br /> <br /> zcluster<br /> home= 100GB<br /> scratch= 4TB<br /> <br /> sapelo <br /> home= 100GB<br /> scratch= Currently none<br /> <br /> The offline storage filesystem is named &quot;project&quot; and is configured for use by lab groups, and by default, each lab group has a 1TB quota. Individual members of a lab group can create subdirectories under their lab's project directory. PI's of lab groups can request additional storage on project as needed. Please note that this storage is not meant for long-term (e.g., archive) storage of data. That type of storage is the responsibility of the user.<br /> <br /> <br /> === Storage Architecture ===<br /> <br /> The home and scratch filesystems are mounted on the zcluster and the sapelo cluster as follows, using an example user 'jsmith' in a lab group 'abclab':<br /> <br /> zcluster-<br /> <br /> home= /home/abclab/jsmith<br /> scratch= /escratch4/jsmith/jsmith_Month_Day<br /> <br /> sapelo-<br /> <br /> home= /home/jsmith<br /> scratch= /lustre1/jsmith<br /> <br /> Note that sapelo users already have a scratch directory. Users of the zcluster need to type <br /> <br /> make_escratch<br /> <br /> while on the login node (not interactive nodes) to create a scratch directory - the command will return the name of the directory. <br /> <br /> The project filesystem is not mounted on the compute nodes and cannot be accessed by running jobs. It is mounted on the zcluster login node, and on the file &quot;copy&quot; and &quot;xfer&quot; nodes. The copy and xfer nodes (discussed under [[Transferring Files | Transferring Files]]) are the preferred servers to use for copying and moving files between all of the filesystems, and to and from the outside world.<br /> <br /> The project filesystem has a consistent mount point of:<br /> <br /> /project/abclab<br /> <br /> === Auto Mounting Filesystems ===<br /> <br /> Some filesystems are &quot;auto mounted&quot; when they are first accessed on a server. For the xfer nodes, this includes Sapelo home directories and the project filesystems. For the zcluster copy nodes, this includes the project filesystems. Sapelo interactive (&quot;qlogin&quot;) nodes will mount a user's home directory when the qlogin happens.<br /> <br /> <br /> === Snapshots ===<br /> <br /> Home directories are snapshotted. Snapshots are like backups in that they are read-only moment-in-time captures of files and directories which can be used to restore files that may have been accidentally deleted or overwritten.<br /> <br /> Home directories on sapelo have snapshots taken once a day and maintained for 4 days, giving the user the ability to retrieve old files for up to 4 days after they have deleted them. On the zcluster, some home directories have snapshots taken once a day, and some have snapshots taken once every 2 days; these are maintained for 4 days.<br /> <br /> Any directory on the /home filesystem contains a completely invisible directory named &quot;.snapshot&quot;. This directory cannot be listed with ls or viewed by any program at all. Only the &quot;cd&quot; command can be used to enter this directory. Users of /home directories may retrieve files from these snapshots by using the &quot;cd&quot; command and copying files from the appropriate snapshot to any location they would like.<br /> <br /> '''Note: ANY user, from any HOME directory can access the snapshots *from that directory* to restore files'''<br /> <br /> Here is the example for zcluster:<br /> <br /> &lt;pre&gt;<br /> [cecombs@sites test]$ cd .snapshot<br /> [cecombs@sites .snapshot]$ ls<br /> 2013.04.16.00.00.01.daily 2013.04.17.00.00.01.daily 2013.04.18.00.00.01.daily<br /> [cecombs@sites .snapshot]$ cd 2013.04.18.00.00.01.daily/<br /> [cecombs@sites 2013.04.18.00.00.01.daily]$ cp my-to-restore-file /home/rccstaff/cecombs/test<br /> &lt;/pre&gt;<br /> <br /> For Sapelo, please send in a ticket for such request. It is a different procedure at backend.<br /> <br /> === Current Storage Systems ===<br /> <br /> (1) Panasas ActiveStor 12 storage cluster with 133TB usable capacity, running PanFS parallel file system. Currently supporting the home filesystem on the zcluster<br /> <br /> (1) Seagate (Xyratex) Lustre appliance with 480TB usable capacity. Currently supporting the scratch filesystem on sapelo<br /> <br /> (3) Penguin IceBreakers storage chains running ZFS mounted through NFS for a total of 84TB usable capacity. Currently supporting home directories on sapelo<br /> <br /> (2) Penguin IceBreakers storage chains running ZFS mounted through NFS for a total of 374TB usable capacity. This storage is used as an active project repository<br /> <br /> (1) Penguin IceBreaker storage chains running ZFS mounted through NFS for a total of 142TB usable capacity. This storage is used as a backup resource for the home and project filesystems</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Frequently_Asked_Questions&diff=7844 2016-05-20T20:52:38Z

<p>Gcormier: /* How do I forward X Window applications running on GACRC machines to my Mac? */</p> <hr /> <div>===How do I find out which compute platforms and software are available at GACRC?===<br /> <br /> A list of GACRC systems, including a brief description of the compute platforms, is available at the [[Systems]] page. <br /> <br /> Applications and software available on GACRC machines are grouped by category. <br /> For an alphabetical list of all software installed please refer to the [[Software]] page. You can sort by Category or by software Name.<br /> <br /> ===How do I apply for accounts on GACRC machines?===<br /> <br /> User accounts are created as part of a &quot;lab group&quot; which has been registered by a Principal Investigator (PI), i.e. a UGA faculty. Once the group is registered, the PI will receive an email stating that he/she can request individual accounts for members of his/her group. For more information, please see http://gacrc.uga.edu/accounts<br /> <br /> ===How do I connect to a GACRC machine?===<br /> <br /> Users can access GACRC machines using secure shell (ssh) from their local machines either on-campus or off-campus. To connect via ssh, you must have an ssh software on your local machine and a connection to the UGA campus network. ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OSX). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software). Note that connection via telnet is not allowed .<br /> <br /> For more detailed information on how to connect to a specific GACRC machine, please see the [[Connecting]] page.<br /> <br /> ===How do I copy files to/from a GACRC machine?===<br /> <br /> Users can transfer files between their local machines and GACRC machines using FTP with explicit SSL encryption, a secure copy (scp), or an SSH secure File Transfer software (SSH file transfer). 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). An SSH Secure File Transfer Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).<br /> <br /> Users are encouraged to use FTP with explicit SSL encryption for file transfer to zcluster. Two file transfer software that support FTP with explicit SSL encryption are the open source software [http://filezilla-project.org/ FileZilla] (available for Windows, Mac OS X, and Linux) and [http://winscp.net/ WinSCP] (available for Windows machines).<br /> <br /> For more detailed information on how to copy files to/from a specific GACRC machine, please see the [[Transferring Files]] page.<br /> <br /> ===How do I print files that are on a GACRC machine?===<br /> <br /> Files on any GACRC machine cannot be directly printed on your local printer. Please transfer the files from the GACRC machine to your local machine (see question above) and print them from your local machine.<br /> <br /> ===How do I run jobs on a GACRC machine?===<br /> <br /> Jobs should not be run on the login node of GACRC machines. <br /> <br /> The zcluster uses a variant of the Sun Grid Engine queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on zcluster]] page.<br /> <br /> The New Cluster (Sapelo) uses the Torque queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on Sapelo]] page.<br /> <br /> ===How do I change my default shell on a given machine?===<br /> <br /> When you login to an GACRC machine, the environment on your terminal and the commands that you type at the prompt are defined/interpreted by a program called shell. Examples of shell are bash, csh, ksh, tcsh. The syntax for setting environment variables and some of the functionality of your keyboard depend on the shell that you are running. For example, with bash and tcsh it is straightforward to use up arrows to recover previous commands. All users have a default shell defined at account creation time. Users can change their default shell by typing '''chsh''' at the command prompt. Note that this command needs to the run on the login node and on the interactive nodes (if you want the shell changed on them as well).<br /> <br /> ===Can I use text files (programs, scripts, etc) created on a Windows machine on the GACRC Unix/Linux machines?===<br /> <br /> Text (ascii) files created on Windows machines might have Windows newlines that are not interpreted correctly by a Unix/Linux system. However, you can convert a Windows text file to the Unix/Linux format with the dos2unix command available on the GACRC's Sapelo and zcluster. The syntax is<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> dos2unix filename<br /> &lt;/pre&gt;<br /> <br /> where ''filename'' is the name of the ascii file (such as program.c, program.f, run.sh, input.txt, etc) created on a Windows machine.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Windows desktop?===<br /> <br /> A number of software installed on GACRC machines have X Window (GUI) front ends. Examples of such applications are Matlab, Maple, some text editors and debuggers, etc. In order to export such X Window applications to your Windows desktop, your desktop needs to have an X Window client (or server) running on it. A free X Window server for Microsoft Windows (8/7/Vista/XP) is [http://sourceforge.net/projects/xming/ Xming]. You can download it from [http://sourceforge.net/projects/xming/ Sourceforge] and make a default installation. You will need to install the Xming server and the Xming-fonts package. Some applications also require having Xming-mesa installed. During the installation of Xming, you might want to select the option to create a desktop icon for Xming. When the installation of these two packages is complete, double click on the Xming icon to start the X Window server (a capital X will appear on your task bar). Now you need to configure your SSH client to allow tunneling of X11 connections. For example, if you use the SSH client provided at the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page you need to open the SSH client, then click on<br /> <br /> Edit -&gt; Settings -&gt; Tunneling (under Profile Settings)<br /> <br /> and check the box for &quot;Tunnel X11 connections&quot;, and then save the settings. Once that is done, you can SSH into your GACRC account (zcluster, Sapelo) and run X Window applications. The application should appear on your local Windows desktop. Each time you logout and log back into your Windows desktop, you might need to start the Xming Server manually before using SSH to connect to your GACRC accounts.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Mac?===<br /> For Apple's OSX v10.6.3 and beyond, users have to manually install XQuartz to enable the X11 features according to [http://support.apple.com/kb/HT5293 Apple]. It is free and available at [https://www.xquartz.org/ XQuartz]. <br /> <br /> Then connect to zcluster as:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh -X username@zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> Then connect to Sapelo as:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh -X myid@sapelo1.gacrc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> ===How to retrieve data from NCBI?===<br /> <br /> Please contact us to get permission if you need to connect to NCBI on GACRC clusters. Please specify your path of scripts, the block of code on how to connect to NCBI and command to test your script in the request. <br /> <br /> NCBI offers e-utilities to fetch data from their website: [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework&amp;part=eutils NCBI Eutility]<br /> <br /> Detailed information on how to connect to NCBI is at [[NCBI Connection]] <br /> <br /> ===How do I acknowledge the GACRC in my publication?===<br /> <br /> A sample acknowledgment statement is provided at http://gacrc.uga.edu/about/acknowledgment-statement</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Frequently_Asked_Questions&diff=7843 2016-05-20T20:44:28Z

<p>Gcormier: /* How do I forward X Window applications running on GACRC machines to my Windows desktop? */</p> <hr /> <div>===How do I find out which compute platforms and software are available at GACRC?===<br /> <br /> A list of GACRC systems, including a brief description of the compute platforms, is available at the [[Systems]] page. <br /> <br /> Applications and software available on GACRC machines are grouped by category. <br /> For an alphabetical list of all software installed please refer to the [[Software]] page. You can sort by Category or by software Name.<br /> <br /> ===How do I apply for accounts on GACRC machines?===<br /> <br /> User accounts are created as part of a &quot;lab group&quot; which has been registered by a Principal Investigator (PI), i.e. a UGA faculty. Once the group is registered, the PI will receive an email stating that he/she can request individual accounts for members of his/her group. For more information, please see http://gacrc.uga.edu/accounts<br /> <br /> ===How do I connect to a GACRC machine?===<br /> <br /> Users can access GACRC machines using secure shell (ssh) from their local machines either on-campus or off-campus. To connect via ssh, you must have an ssh software on your local machine and a connection to the UGA campus network. ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OSX). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software). Note that connection via telnet is not allowed .<br /> <br /> For more detailed information on how to connect to a specific GACRC machine, please see the [[Connecting]] page.<br /> <br /> ===How do I copy files to/from a GACRC machine?===<br /> <br /> Users can transfer files between their local machines and GACRC machines using FTP with explicit SSL encryption, a secure copy (scp), or an SSH secure File Transfer software (SSH file transfer). 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). An SSH Secure File Transfer Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).<br /> <br /> Users are encouraged to use FTP with explicit SSL encryption for file transfer to zcluster. Two file transfer software that support FTP with explicit SSL encryption are the open source software [http://filezilla-project.org/ FileZilla] (available for Windows, Mac OS X, and Linux) and [http://winscp.net/ WinSCP] (available for Windows machines).<br /> <br /> For more detailed information on how to copy files to/from a specific GACRC machine, please see the [[Transferring Files]] page.<br /> <br /> ===How do I print files that are on a GACRC machine?===<br /> <br /> Files on any GACRC machine cannot be directly printed on your local printer. Please transfer the files from the GACRC machine to your local machine (see question above) and print them from your local machine.<br /> <br /> ===How do I run jobs on a GACRC machine?===<br /> <br /> Jobs should not be run on the login node of GACRC machines. <br /> <br /> The zcluster uses a variant of the Sun Grid Engine queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on zcluster]] page.<br /> <br /> The New Cluster (Sapelo) uses the Torque queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on Sapelo]] page.<br /> <br /> ===How do I change my default shell on a given machine?===<br /> <br /> When you login to an GACRC machine, the environment on your terminal and the commands that you type at the prompt are defined/interpreted by a program called shell. Examples of shell are bash, csh, ksh, tcsh. The syntax for setting environment variables and some of the functionality of your keyboard depend on the shell that you are running. For example, with bash and tcsh it is straightforward to use up arrows to recover previous commands. All users have a default shell defined at account creation time. Users can change their default shell by typing '''chsh''' at the command prompt. Note that this command needs to the run on the login node and on the interactive nodes (if you want the shell changed on them as well).<br /> <br /> ===Can I use text files (programs, scripts, etc) created on a Windows machine on the GACRC Unix/Linux machines?===<br /> <br /> Text (ascii) files created on Windows machines might have Windows newlines that are not interpreted correctly by a Unix/Linux system. However, you can convert a Windows text file to the Unix/Linux format with the dos2unix command available on the GACRC's Sapelo and zcluster. The syntax is<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> dos2unix filename<br /> &lt;/pre&gt;<br /> <br /> where ''filename'' is the name of the ascii file (such as program.c, program.f, run.sh, input.txt, etc) created on a Windows machine.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Windows desktop?===<br /> <br /> A number of software installed on GACRC machines have X Window (GUI) front ends. Examples of such applications are Matlab, Maple, some text editors and debuggers, etc. In order to export such X Window applications to your Windows desktop, your desktop needs to have an X Window client (or server) running on it. A free X Window server for Microsoft Windows (8/7/Vista/XP) is [http://sourceforge.net/projects/xming/ Xming]. You can download it from [http://sourceforge.net/projects/xming/ Sourceforge] and make a default installation. You will need to install the Xming server and the Xming-fonts package. Some applications also require having Xming-mesa installed. During the installation of Xming, you might want to select the option to create a desktop icon for Xming. When the installation of these two packages is complete, double click on the Xming icon to start the X Window server (a capital X will appear on your task bar). Now you need to configure your SSH client to allow tunneling of X11 connections. For example, if you use the SSH client provided at the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page you need to open the SSH client, then click on<br /> <br /> Edit -&gt; Settings -&gt; Tunneling (under Profile Settings)<br /> <br /> and check the box for &quot;Tunnel X11 connections&quot;, and then save the settings. Once that is done, you can SSH into your GACRC account (zcluster, Sapelo) and run X Window applications. The application should appear on your local Windows desktop. Each time you logout and log back into your Windows desktop, you might need to start the Xming Server manually before using SSH to connect to your GACRC accounts.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Mac?===<br /> For Mac Mountain Lion (v10.8 so far), user has to manually one-time install XQuartz to enable X11 feature according to [http://support.apple.com/kb/HT5293 Mac]. It is free and available at [http://xquartz.macosforge.org/landing/ XQuartz]. <br /> <br /> For other version lower than 10.8 (non Mountain), X11 is built in with OS, no need to install extra component. <br /> <br /> Then connect to zcluster as:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh -X username@zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> ===How to retrieve data from NCBI?===<br /> <br /> Please contact us to get permission if you need to connect to NCBI on GACRC clusters. Please specify your path of scripts, the block of code on how to connect to NCBI and command to test your script in the request. <br /> <br /> NCBI offers e-utilities to fetch data from their website: [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework&amp;part=eutils NCBI Eutility]<br /> <br /> Detailed information on how to connect to NCBI is at [[NCBI Connection]] <br /> <br /> ===How do I acknowledge the GACRC in my publication?===<br /> <br /> A sample acknowledgment statement is provided at http://gacrc.uga.edu/about/acknowledgment-statement</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Frequently_Asked_Questions&diff=7842 2016-05-20T20:40:39Z

<p>Gcormier: </p> <hr /> <div>===How do I find out which compute platforms and software are available at GACRC?===<br /> <br /> A list of GACRC systems, including a brief description of the compute platforms, is available at the [[Systems]] page. <br /> <br /> Applications and software available on GACRC machines are grouped by category. <br /> For an alphabetical list of all software installed please refer to the [[Software]] page. You can sort by Category or by software Name.<br /> <br /> ===How do I apply for accounts on GACRC machines?===<br /> <br /> User accounts are created as part of a &quot;lab group&quot; which has been registered by a Principal Investigator (PI), i.e. a UGA faculty. Once the group is registered, the PI will receive an email stating that he/she can request individual accounts for members of his/her group. For more information, please see http://gacrc.uga.edu/accounts<br /> <br /> ===How do I connect to a GACRC machine?===<br /> <br /> Users can access GACRC machines using secure shell (ssh) from their local machines either on-campus or off-campus. To connect via ssh, you must have an ssh software on your local machine and a connection to the UGA campus network. ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OSX). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software). Note that connection via telnet is not allowed .<br /> <br /> For more detailed information on how to connect to a specific GACRC machine, please see the [[Connecting]] page.<br /> <br /> ===How do I copy files to/from a GACRC machine?===<br /> <br /> Users can transfer files between their local machines and GACRC machines using FTP with explicit SSL encryption, a secure copy (scp), or an SSH secure File Transfer software (SSH file transfer). 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). An SSH Secure File Transfer Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).<br /> <br /> Users are encouraged to use FTP with explicit SSL encryption for file transfer to zcluster. Two file transfer software that support FTP with explicit SSL encryption are the open source software [http://filezilla-project.org/ FileZilla] (available for Windows, Mac OS X, and Linux) and [http://winscp.net/ WinSCP] (available for Windows machines).<br /> <br /> For more detailed information on how to copy files to/from a specific GACRC machine, please see the [[Transferring Files]] page.<br /> <br /> ===How do I print files that are on a GACRC machine?===<br /> <br /> Files on any GACRC machine cannot be directly printed on your local printer. Please transfer the files from the GACRC machine to your local machine (see question above) and print them from your local machine.<br /> <br /> ===How do I run jobs on a GACRC machine?===<br /> <br /> Jobs should not be run on the login node of GACRC machines. <br /> <br /> The zcluster uses a variant of the Sun Grid Engine queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on zcluster]] page.<br /> <br /> The New Cluster (Sapelo) uses the Torque queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on Sapelo]] page.<br /> <br /> ===How do I change my default shell on a given machine?===<br /> <br /> When you login to an GACRC machine, the environment on your terminal and the commands that you type at the prompt are defined/interpreted by a program called shell. Examples of shell are bash, csh, ksh, tcsh. The syntax for setting environment variables and some of the functionality of your keyboard depend on the shell that you are running. For example, with bash and tcsh it is straightforward to use up arrows to recover previous commands. All users have a default shell defined at account creation time. Users can change their default shell by typing '''chsh''' at the command prompt. Note that this command needs to the run on the login node and on the interactive nodes (if you want the shell changed on them as well).<br /> <br /> ===Can I use text files (programs, scripts, etc) created on a Windows machine on the GACRC Unix/Linux machines?===<br /> <br /> Text (ascii) files created on Windows machines might have Windows newlines that are not interpreted correctly by a Unix/Linux system. However, you can convert a Windows text file to the Unix/Linux format with the dos2unix command available on the GACRC's Sapelo and zcluster. The syntax is<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> dos2unix filename<br /> &lt;/pre&gt;<br /> <br /> where ''filename'' is the name of the ascii file (such as program.c, program.f, run.sh, input.txt, etc) created on a Windows machine.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Windows desktop?===<br /> <br /> A number of software installed on GACRC machines have X Window (GUI) front ends. Examples of such applications are Mathematica, Maple, some text editors and debuggers, etc. In order to export such X Window applications to your Windows desktop, your desktop needs to have an X Window client (or server) running on it. A free X Window server for Microsoft Windows (XP/2008/Windows7) is [http://sourceforge.net/projects/xming/ Xming]. You can download it from [http://sourceforge.net/projects/xming/ Sourceforge] and make a default installation. You will need to install the Xming server and the Xming-fonts package. Some applications also require having Xming-mesa installed. During the installation of Xming, you might want to select the option to create a desktop icon for Xming. When the installation of these two packages is complete, double click on the Xming icon to start the X Window server (a capital X will appear on your task bar). Now you need to configure your SSH client to allow tunneling of X11 connections. For example, if you use the SSH client provided at the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page you need to open the SSH client, then click on<br /> <br /> Edit -&gt; Settings -&gt; Tunneling (under Profile Settings)<br /> <br /> and check the box for &quot;Tunnel X11 connections&quot;, and then save the settings. Once that is done, you can SSH into your GACRC account (zcluster, stats) and run X Window applications. The application should appear on your local Windows desktop. Each time you logout and log back into your Windows desktop, you might need to start the Xming Server manually before using SSH to connect to your GACRC accounts.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Mac?===<br /> For Mac Mountain Lion (v10.8 so far), user has to manually one-time install XQuartz to enable X11 feature according to [http://support.apple.com/kb/HT5293 Mac]. It is free and available at [http://xquartz.macosforge.org/landing/ XQuartz]. <br /> <br /> For other version lower than 10.8 (non Mountain), X11 is built in with OS, no need to install extra component. <br /> <br /> Then connect to zcluster as:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh -X username@zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> ===How to retrieve data from NCBI?===<br /> <br /> Please contact us to get permission if you need to connect to NCBI on GACRC clusters. Please specify your path of scripts, the block of code on how to connect to NCBI and command to test your script in the request. <br /> <br /> NCBI offers e-utilities to fetch data from their website: [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework&amp;part=eutils NCBI Eutility]<br /> <br /> Detailed information on how to connect to NCBI is at [[NCBI Connection]] <br /> <br /> ===How do I acknowledge the GACRC in my publication?===<br /> <br /> A sample acknowledgment statement is provided at http://gacrc.uga.edu/about/acknowledgment-statement</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Frequently_Asked_Questions&diff=7841 2016-05-20T20:36:30Z

<p>Gcormier: /* Can I use text files (programs, scripts, etc) created on a Windows machine on the GACRC Unix/Linux machines? */</p> <hr /> <div>===How do I find out which compute platforms and software are available at GACRC?===<br /> <br /> A list of GACRC systems, including a brief description of the compute platforms, is available at the [[Systems]] page. <br /> <br /> Applications and software available on GACRC machines are grouped by category. <br /> For an alphabetical list of all software installed please refer to the [[Software]] page. You can sort by Category or by software Name.<br /> <br /> ===How do I apply for accounts on GACRC machines?===<br /> <br /> User accounts are created as part of a &quot;lab group&quot; which has been registered by a Principal Investigator (PI), i.e. a UGA faculty. Once the group is registered, the PI will receive an email stating that he/she can request individual accounts for members of his/her group. For more information, please see http://gacrc.uga.edu/accounts<br /> <br /> ===How do I connect to a GACRC machine?===<br /> <br /> Users can access GACRC machines using secure shell (ssh) from their local machines either on-campus or off-campus. To connect via ssh, you must have an ssh software on your local machine and a connection to the UGA campus network. ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OSX). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software). Note that connection via telnet is not allowed .<br /> <br /> For more detailed information on how to connect to a specific GACRC machine, please see the [[Connecting]] page.<br /> <br /> ===How do I copy files to/from a GACRC machine?===<br /> <br /> Users can transfer files between their local machines and GACRC machines using FTP with explicit SSL encryption, a secure copy (scp), or an SSH secure File Transfer software (SSH file transfer). 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). An SSH Secure File Transfer Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).<br /> <br /> Users are encouraged to use FTP with explicit SSL encryption for file transfer to zcluster. Two file transfer software that support FTP with explicit SSL encryption are the open source software [http://filezilla-project.org/ FileZilla] (available for Windows, Mac OS X, and Linux) and [http://winscp.net/ WinSCP] (available for Windows machines).<br /> <br /> For more detailed information on how to copy files to/from a specific GACRC machine, please see the [[Transferring Files]] page.<br /> <br /> ===How do I print files that are on a GACRC machine?===<br /> <br /> Files on any GACRC machine cannot be directly printed on your local printer. Please transfer the files from the GACRC machine to your local machine (see question above) and print them from your local machine.<br /> <br /> ===How do I run jobs on a GACRC machine?===<br /> <br /> Jobs should not be run on the login node of GACRC machines. <br /> <br /> The zcluster uses a variant of the Sun Grid Engine queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on zcluster]] page.<br /> <br /> The New Cluster (Sapelo) uses the Torque queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on Sapelo]] page.<br /> <br /> ===How do I change my default shell on a given machine?===<br /> <br /> When you login to an GACRC machine, the environment on your terminal and the commands that you type at the prompt are defined/interpreted by a program called shell. Examples of shell are bash, csh, ksh, tcsh. The syntax for setting environment variables and some of the functionality of your keyboard depend on the shell that you are running. For example, with bash and tcsh it is straightforward to use up arrows to recover previous commands. All users have a default shell defined at account creation time. Users can change their default shell by typing '''chsh''' at the command prompt. Note that this command needs to the run on the login node and on the interactive nodes (if you want the shell changed on them as well).<br /> <br /> ===Can I use text files (programs, scripts, etc) created on a Windows machine on the GACRC Unix/Linux machines?===<br /> <br /> Text (ascii) files created on Windows machines might have Windows newlines that are not interpreted correctly by a Unix/Linux system. However, you can convert a Windows text file to the Unix/Linux format with the dos2unix command available on the GACRC's Sapelo and zcluster. The syntax is<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> dos2unix filename<br /> &lt;/pre&gt;<br /> <br /> where ''filename'' is the name of the ascii file (such as program.c, program.f, run.sh, input.txt, etc) created on a Windows machine.<br /> <br /> ===Can I use text files (programs, scripts, etc) created on a Mac on the GACRC Unix/Linux machines?===<br /> <br /> Text (ascii) files created on computers running Mac OS might have Mac newlines that are not interpreted correctly by a Unix/Linux system. However, you can convert a Mac text file to the Unix/Linux format with the mac2unix command available on the GACRC altix and rcluster. The syntax is:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> mac2unix filename<br /> &lt;/pre&gt;<br /> <br /> where ''filename'' is the name of the ascii file (such as program.c, program.f, run.sh, input.txt, etc) created on a machine with Mac OS.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Windows desktop?===<br /> <br /> A number of software installed on GACRC machines have X Window (GUI) front ends. Examples of such applications are Mathematica, Maple, some text editors and debuggers, etc. In order to export such X Window applications to your Windows desktop, your desktop needs to have an X Window client (or server) running on it. A free X Window server for Microsoft Windows (XP/2008/Windows7) is [http://sourceforge.net/projects/xming/ Xming]. You can download it from [http://sourceforge.net/projects/xming/ Sourceforge] and make a default installation. You will need to install the Xming server and the Xming-fonts package. Some applications also require having Xming-mesa installed. During the installation of Xming, you might want to select the option to create a desktop icon for Xming. When the installation of these two packages is complete, double click on the Xming icon to start the X Window server (a capital X will appear on your task bar). Now you need to configure your SSH client to allow tunneling of X11 connections. For example, if you use the SSH client provided at the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page you need to open the SSH client, then click on<br /> <br /> Edit -&gt; Settings -&gt; Tunneling (under Profile Settings)<br /> <br /> and check the box for &quot;Tunnel X11 connections&quot;, and then save the settings. Once that is done, you can SSH into your GACRC account (zcluster, stats) and run X Window applications. The application should appear on your local Windows desktop. Each time you logout and log back into your Windows desktop, you might need to start the Xming Server manually before using SSH to connect to your GACRC accounts.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Mac?===<br /> For Mac Mountain Lion (v10.8 so far), user has to manually one-time install XQuartz to enable X11 feature according to [http://support.apple.com/kb/HT5293 Mac]. It is free and available at [http://xquartz.macosforge.org/landing/ XQuartz]. <br /> <br /> For other version lower than 10.8 (non Mountain), X11 is built in with OS, no need to install extra component. <br /> <br /> Then connect to zcluster as:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh -X username@zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> ===How to retrieve data from NCBI?===<br /> <br /> Please contact us to get permission if you need to connect to NCBI on GACRC clusters. Please specify your path of scripts, the block of code on how to connect to NCBI and command to test your script in the request. <br /> <br /> NCBI offers e-utilities to fetch data from their website: [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework&amp;part=eutils NCBI Eutility]<br /> <br /> Detailed information on how to connect to NCBI is at [[NCBI Connection]] <br /> <br /> ===How do I acknowledge the GACRC in my publication?===<br /> <br /> A sample acknowledgment statement is provided at http://gacrc.uga.edu/about/acknowledgment-statement</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Frequently_Asked_Questions&diff=7840 2016-05-20T20:32:53Z

<p>Gcormier: /* How do I run jobs on a GACRC machine? */</p> <hr /> <div>===How do I find out which compute platforms and software are available at GACRC?===<br /> <br /> A list of GACRC systems, including a brief description of the compute platforms, is available at the [[Systems]] page. <br /> <br /> Applications and software available on GACRC machines are grouped by category. <br /> For an alphabetical list of all software installed please refer to the [[Software]] page. You can sort by Category or by software Name.<br /> <br /> ===How do I apply for accounts on GACRC machines?===<br /> <br /> User accounts are created as part of a &quot;lab group&quot; which has been registered by a Principal Investigator (PI), i.e. a UGA faculty. Once the group is registered, the PI will receive an email stating that he/she can request individual accounts for members of his/her group. For more information, please see http://gacrc.uga.edu/accounts<br /> <br /> ===How do I connect to a GACRC machine?===<br /> <br /> Users can access GACRC machines using secure shell (ssh) from their local machines either on-campus or off-campus. To connect via ssh, you must have an ssh software on your local machine and a connection to the UGA campus network. ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OSX). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software). Note that connection via telnet is not allowed .<br /> <br /> For more detailed information on how to connect to a specific GACRC machine, please see the [[Connecting]] page.<br /> <br /> ===How do I copy files to/from a GACRC machine?===<br /> <br /> Users can transfer files between their local machines and GACRC machines using FTP with explicit SSL encryption, a secure copy (scp), or an SSH secure File Transfer software (SSH file transfer). 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). An SSH Secure File Transfer Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).<br /> <br /> Users are encouraged to use FTP with explicit SSL encryption for file transfer to zcluster. Two file transfer software that support FTP with explicit SSL encryption are the open source software [http://filezilla-project.org/ FileZilla] (available for Windows, Mac OS X, and Linux) and [http://winscp.net/ WinSCP] (available for Windows machines).<br /> <br /> For more detailed information on how to copy files to/from a specific GACRC machine, please see the [[Transferring Files]] page.<br /> <br /> ===How do I print files that are on a GACRC machine?===<br /> <br /> Files on any GACRC machine cannot be directly printed on your local printer. Please transfer the files from the GACRC machine to your local machine (see question above) and print them from your local machine.<br /> <br /> ===How do I run jobs on a GACRC machine?===<br /> <br /> Jobs should not be run on the login node of GACRC machines. <br /> <br /> The zcluster uses a variant of the Sun Grid Engine queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on zcluster]] page.<br /> <br /> The New Cluster (Sapelo) uses the Torque queueing system, which should be used for both interactive and batch jobs. For more information, please see the [[Running Jobs on Sapelo]] page.<br /> <br /> ===How do I change my default shell on a given machine?===<br /> <br /> When you login to an GACRC machine, the environment on your terminal and the commands that you type at the prompt are defined/interpreted by a program called shell. Examples of shell are bash, csh, ksh, tcsh. The syntax for setting environment variables and some of the functionality of your keyboard depend on the shell that you are running. For example, with bash and tcsh it is straightforward to use up arrows to recover previous commands. All users have a default shell defined at account creation time. Users can change their default shell by typing '''chsh''' at the command prompt. Note that this command needs to the run on the login node and on the interactive nodes (if you want the shell changed on them as well).<br /> <br /> ===Can I use text files (programs, scripts, etc) created on a Windows machine on the GACRC Unix/Linux machines?===<br /> <br /> Text (ascii) files created on Windows machines might have Windows newlines that are not interpreted correctly by a Unix/Linux system. However, you can convert a Windows text file to the Unix/Linux format with the dos2unix command available on the GACRC altix and rcluster. The syntax is<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> dos2unix filename<br /> &lt;/pre&gt;<br /> <br /> where ''filename'' is the name of the ascii file (such as program.c, program.f, run.sh, input.txt, etc) created on a Windows machine.<br /> <br /> ===Can I use text files (programs, scripts, etc) created on a Mac on the GACRC Unix/Linux machines?===<br /> <br /> Text (ascii) files created on computers running Mac OS might have Mac newlines that are not interpreted correctly by a Unix/Linux system. However, you can convert a Mac text file to the Unix/Linux format with the mac2unix command available on the GACRC altix and rcluster. The syntax is:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> mac2unix filename<br /> &lt;/pre&gt;<br /> <br /> where ''filename'' is the name of the ascii file (such as program.c, program.f, run.sh, input.txt, etc) created on a machine with Mac OS.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Windows desktop?===<br /> <br /> A number of software installed on GACRC machines have X Window (GUI) front ends. Examples of such applications are Mathematica, Maple, some text editors and debuggers, etc. In order to export such X Window applications to your Windows desktop, your desktop needs to have an X Window client (or server) running on it. A free X Window server for Microsoft Windows (XP/2008/Windows7) is [http://sourceforge.net/projects/xming/ Xming]. You can download it from [http://sourceforge.net/projects/xming/ Sourceforge] and make a default installation. You will need to install the Xming server and the Xming-fonts package. Some applications also require having Xming-mesa installed. During the installation of Xming, you might want to select the option to create a desktop icon for Xming. When the installation of these two packages is complete, double click on the Xming icon to start the X Window server (a capital X will appear on your task bar). Now you need to configure your SSH client to allow tunneling of X11 connections. For example, if you use the SSH client provided at the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page you need to open the SSH client, then click on<br /> <br /> Edit -&gt; Settings -&gt; Tunneling (under Profile Settings)<br /> <br /> and check the box for &quot;Tunnel X11 connections&quot;, and then save the settings. Once that is done, you can SSH into your GACRC account (zcluster, stats) and run X Window applications. The application should appear on your local Windows desktop. Each time you logout and log back into your Windows desktop, you might need to start the Xming Server manually before using SSH to connect to your GACRC accounts.<br /> <br /> ===How do I forward X Window applications running on GACRC machines to my Mac?===<br /> For Mac Mountain Lion (v10.8 so far), user has to manually one-time install XQuartz to enable X11 feature according to [http://support.apple.com/kb/HT5293 Mac]. It is free and available at [http://xquartz.macosforge.org/landing/ XQuartz]. <br /> <br /> For other version lower than 10.8 (non Mountain), X11 is built in with OS, no need to install extra component. <br /> <br /> Then connect to zcluster as:<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh -X username@zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> ===How to retrieve data from NCBI?===<br /> <br /> Please contact us to get permission if you need to connect to NCBI on GACRC clusters. Please specify your path of scripts, the block of code on how to connect to NCBI and command to test your script in the request. <br /> <br /> NCBI offers e-utilities to fetch data from their website: [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework&amp;part=eutils NCBI Eutility]<br /> <br /> Detailed information on how to connect to NCBI is at [[NCBI Connection]] <br /> <br /> ===How do I acknowledge the GACRC in my publication?===<br /> <br /> A sample acknowledgment statement is provided at http://gacrc.uga.edu/about/acknowledgment-statement</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Training&diff=7445 2016-02-15T23:40:54Z

<p>Gcormier: </p> <hr /> <div><br /> <br /> ==Training Sessions==<br /> <br /> <br /> 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. <br /> <br /> '''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''<br /> <br /> <br /> ==Event Announcement==<br /> <br /> <br /> The GACRC is going to host '''thirteen''' training workshop in '''February''' of '''2016'''. These workshops will provide an introduction to the GACRC Linux high performance computing (HPC) clusters and the Linux basics. We have '''three''' Linux practice sessions for GACRC users to obtain Linux hands-on working experiences. We have '''three''' topical sessions focusing on GACRC storage environment, software installation on zcluster, and the NCBI Blast software on zcluster.<br /> <br /> The GACRC is going to host '''ten''' training workshop in '''March''' of '''2016'''. These workshops will provide an introduction to the GACRC Linux high performance computing (HPC) clusters and the Linux basics. We have '''two''' Linux practice sessions for GACRC users to obtain Linux hands-on working experiences. We have '''two''' topical sessions focusing on the NCBI Blast software on zcluster and scientific Python basics. <br /> <br /> ====Training Location====<br /> <br /> Davison Life Sciences Complex (Life Science Building), Room C128, 120 East Green St, Athens, GA 30602<br /> <br /> ===Regular New User Training===<br /> <br /> =====February Schedule=====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to HPC Using the New Cluster at GACRC || February 8th, Monday, 10:00 AM - 11:30 AM<br /> |-<br /> | Introduction to HPC Using zcluster at GACRC || February 10th, Wednesday, 3:00 PM - 4:30 PM<br /> |-<br /> | Introduction to HPC Using zcluster at GACRC || February 22nd, Monday, 10:00 AM - 11:30 AM<br /> |-<br /> | Introduction to HPC Using the New Cluster at GACRC || February 24th, Wednesday, 3:00 PM - 4:30 PM<br /> |-<br /> | Introduction to HPC Using the New Cluster at GACRC || February 24th, Wednesday, 3:00 PM - 4:30 PM<br /> |}<br /> <br /> =====March Schedule=====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to HPC Using the New Cluster at GACRC || March 2nd, Wednesday, 3:00 PM - 4:30 PM <br /> |-<br /> | Introduction to HPC Using zcluster at GACRC || March 14th, Monday, 10:00 AM - 11:30 AM<br /> |-<br /> | Introduction to HPC Using the New Cluster at GACRC || March 21st, Monday, 10:00 AM - 11:30 AM <br /> |-<br /> | Introduction to HPC Using zcluster at GACRC || March 30th, Wednesday, 3:00 PM - 4:30 PM<br /> |-<br /> |}<br /> <br /> ===Linux Basics and Hands-on===<br /> <br /> =====February Schedule=====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Linux Hands-on Practice Session (Basic Linux knowledge required) || February 8th, Monday, 1:00 PM - 2:30 PM<br /> |-<br /> | Introduction to Linux Basics Part-I || February 15th, Monday, 10:00 AM - 11:30 AM<br /> |-<br /> | Linux Hands-on Practice Session (Basic Linux knowledge required) || February 17th, Wednesday, 3:00 PM - 4:30 PM<br /> |-<br /> | Introduction to Linux Basics Part-II || February 22nd, Monday, 1:00 PM - 2:30 PM<br /> |-<br /> | Linux Hands-on Practice Session (Basic Linux knowledge required) || February 29th, Monday, 1:00 PM - 2:30 PM<br /> |}<br /> <br /> =====March Schedule=====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to Linux Basics I || March 14th, Monday, 1:00 PM - 2:30 PM<br /> |-<br /> | Linux Hands-on Practice Session (Basic Linux knowledge required) || March 16th, Wednesday, 3:00 PM - 4:30 PM<br /> |-<br /> | Introduction to Linux Basics II || March 21st, Monday, 1:00 PM - 2:30 PM<br /> |-<br /> | Linux Hands-on Practice Session (Basic Linux knowledge required) || March 28th, Monday, 10:00 AM - 11:30 AM<br /> |}<br /> <br /> <br /> ===Topical Sessions===<br /> <br /> =====February Schedule=====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | Introduction to GACRC Storage Environment || February 3rd, 2016, Wednesday, 3:00 PM - 4:30 PM<br /> |-<br /> | How to Install Software on zcluster at GACRC || February 15th, 2016, Monday, 1:00 PM - 2:30 PM<br /> |-<br /> | How to run NCBI Blast on zcluster at GACRC || February 29th, 2016, Monday, 10:00 AM - 11:30 AM<br /> |-<br /> |}<br /> <br /> =====March Schedule=====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Title<br /> ! scope=&quot;col&quot; | Date/Time<br /> |-<br /> | How to run NCBI Blast on zcluster at GACRC || March 23rd, 2016, Wednesday, 3:00 PM - 4:30 PM<br /> |-<br /> | Scientific Python Basics I || March 28th, 2016, Monday, 1:00 PM - 2:30 PM<br /> |-<br /> |}<br /> <br /> '''Who Should Attend: ''' New HPC cluster and zcluster users, or researchers who are interested in learning about the GACRC computing resources and Linux basics (Linux OS, Linux filesystem, shell, and common commands, scripting, etc.).<br /> <br /> <br /> ==Topic Introduction==<br /> <br /> <br /> Title: '''Introduction to HPC Using the New Cluster at GACRC'''<br /> <br /> Focus:<br /> <br /> What's the new cluster at GACRC<br /> <br /> New cluster's current computing resources<br /> <br /> New cluster software environment<br /> <br /> How to operate with the new cluster<br /> <br /> How to work with the new cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.<br /> <br /> <br /> Title: '''Introduction to HPC Using zcluster at GACRC'''<br /> <br /> Focus:<br /> <br /> What's zcluster at GACRC<br /> <br /> zcluster current computing resources<br /> <br /> zcluster software environment<br /> <br /> How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.<br /> <br /> <br /> Title: '''Introduction to Linux Basics Part-I'''<br /> <br /> Focus:<br /> <br /> Linux OS and brief history<br /> <br /> Linux command, filesystem, and shell<br /> <br /> Linux common commands, etc.<br /> <br /> <br /> Title: '''Introduction to Linux Basics Part-II (Basic Linux knowledge required)'''<br /> <br /> Focus:<br /> <br /> Linux shell<br /> <br /> Common practices on Linux shell scripting<br /> <br /> Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.<br /> <br /> <br /> Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''<br /> <br /> Focus:<br /> <br /> Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.<br /> <br /> <br /> Title: '''Introduction to GACRC Storage Environment'''<br /> <br /> Focus:<br /> <br /> Overview of Linux common commands related to file and folder operations<br /> <br /> Overview of the storage enviornment of zcluster and the new cluster at GACRC<br /> <br /> How to transfer data between local and GACRC storage<br /> <br /> New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster<br /> <br /> GACRC suggestions on good practices on GACRC storage, etc;<br /> <br /> <br /> ==How to Register==<br /> <br /> <br /> If you would like to attend, please respond by email to: '''zhuofei@uga.edu''' or '''pakala@uga.edu'''. Also please tell us which session you want to attend.<br /> <br /> We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.<br /> <br /> <br /> The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC introduction, Linux working environment and utilities (Linux Part III), Bioinfomatics applications, scientific programming, etc., in the near future. We will announce those events when they are scheduled.<br /> <br /> The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.<br /> <br /> <br /> ==Download==<br /> <br /> <br /> ====Regular New User Training====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Introduction to HPC Using the New Cluster at GACRC Workshop20160202 v7.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using zcluster at GACRC Workshop20160201 v6.pdf]]<br /> |-<br /> | [[media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02102016.pdf]]<br /> |-<br /> |}<br /> <br /> ====Linux Basics and Hands-on====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]<br /> |-<br /> | [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]<br /> |-<br /> | [[media: Linux Hands-on Practice 20160120.pdf]]<br /> |-<br /> |}<br /> <br /> ====Topical Sessions====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> | [[media: Introduction to GACRC Storage Environment Workshop20151109 v2.pdf]]<br /> |-<br /> |}<br /> <br /> ====Out-Reach/On-Class Talk====<br /> <br /> {| width=&quot;100%&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;2&quot; align=&quot;center&quot; class=&quot;wikitable unsortable&quot;<br /> |-<br /> ! scope=&quot;col&quot; | Dept./Center/Institute<br /> ! scope=&quot;col&quot; | Type<br /> ! scope=&quot;col&quot; | Workshop PDF<br /> |-<br /> | The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]<br /> |-<br /> | The Center for Simulational Physics || Out-Reach || [[media: Introduction to HPC Using the New Cluster at GACRC Workshop CSP20150915 v2.pdf]]<br /> |-<br /> | Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20151007.pdf]]<br /> |-<br /> | Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]<br /> |-<br /> | Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]<br /> |-<br /> | Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]<br /> |-<br /> | Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]<br /> |-<br /> |-<br /> | Bioinformatics - Applied Genome Analysis || On-Class (BINF8940) ||[[media:Introduction to HPC Using zcluster at GACRC BINF8940 20160128.pdf]]<br /> |-<br /> |}<br /> <br /> '''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.<br /> <br /> <br /> ==Past Sessions==<br /> <br /> [[Past Sessions in 2016]]<br /> <br /> [[Past Sessions in 2015]]</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Systems&diff=6171 2015-06-11T21:39:33Z

<p>Gcormier: </p> <hr /> <div>[[Category:Zcluster]]<br /> [[Category:Sapelo]]<br /> <br /> === New Cluster ===<br /> <br /> New Cluster is a Linux cluster that runs a 64-bit CentOS 6.5 operating system<br /> and the login nodes has Intel Xeon processors. A QDR Infiniband network (40Gbps) provides internodal communication among <br /> compute nodes, and between the compute nodes and the storage systems serving the home directories and the <br /> scratch directories.<br /> <br /> The cluster is currently comprised of the following resources: <br /> <br /> * 120 compute nodes with AMD Opteron processors (48 cores and 128GB of RAM per node) <br /> * two 48-core 512GB RAM nodes with AMD Opteron processors (n24, n25)<br /> * two 16-core 128GB RAM nodes with Intel Xeon processors and 8 NVIDIA K40m GPU cards each (n48, n49)<br /> <br /> <br /> <br /> ====[[Code Compilation on New Cluster]]====<br /> <br /> ====[[Running Jobs on New Cluster]]====<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> === Zcluster ===<br /> <br /> The Linux cluster is comprised of compute nodes with 4-, 6-, 8-, and 12-core processors from both Intel and AMD. Subsets of nodes have &quot;large memory&quot; (e.g., 128, 256, or 512 GB of RAM), while others have InfiniBand connectivity or GPU capabilities. Total CPU compute power is 25.9 Tflops.<br /> <br /> The cluster is currently comprised of the following resources:<br /> <br /> *230 compute nodes (2600 compute cores), 32 with InfiniBand connectivity.<br /> *Four 8-core, 192GB high-memory compute nodes<br /> *Ten 12-core, 256GB high-memory compute nodes<br /> *Two 32-core, 512GB high-memory compute nodes<br /> *Six 32-core, 64GB high-memory compute nodes <br /> *One NVIDIA Tesla S1070 with four GPU cards (4 x 240 = 960 GPU cores) for programs written to use this architecture.<br /> *One NVIDIA Tesla (Fermi) C2075 GPU processor (448 GPU cores)<br /> *Nine NVIDIA Tesla (Fermi) M2070 GPU cards (9 x 448 = 4032 GPU cores). These cards are installed on 2 hosts each of which has dual 6-core Intel Xeon CPUs and 48GB of RAM; there are 6 GPU cards on one host and 3 on the other.<br /> *32 NVIDIA Tesla (Kepler) K20X GPU cards (32 x 2688 = 86016 GPU cores). These cards are installed on 4 hosts each of which has dual 6-core Intel Xeon CPUs and 96GB of RAM; there are 8 GPU cards per host.<br /> <br /> ====[[Connecting]]====<br /> <br /> ====[[Transferring Files]]====<br /> <br /> ====[[Disk Storage]]====<br /> <br /> ====[[Code Compilation on zcluster]]====<br /> <br /> ====[[Running Jobs on zcluster]]====</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Systems&diff=6170 2015-06-11T21:37:40Z

<p>Gcormier: </p> <hr /> <div>[[Category:Zcluster]]<br /> [[Category:Sapelo]]<br /> <br /> === Sapelo ===<br /> <br /> Sapelo is a Linux cluster that runs a 64-bit CentOS 6.5 operating system<br /> and the login node has Intel Xeon processors. A QDR Infiniband network (40Gbps) provides internodal communication among <br /> compute nodes, and between the compute nodes and the storage systems serving the home directories and the <br /> scratch directories.<br /> <br /> The cluster is currently comprised of the following resources: <br /> <br /> * 120 compute nodes with AMD Opteron processors (48 cores and 128GB of RAM per node) <br /> * two 48-core 512GB RAM nodes with AMD Opteron processors (n24, n25)<br /> * two 16-core 128GB RAM nodes with Intel Xeon processors and 8 NVIDIA K40m GPU cards each (n48, n49)<br /> <br /> <br /> <br /> ====[[Code Compilation on Sapelo]]====<br /> <br /> ====[[Running Jobs on Sapelo]]====<br /> <br /> ----<br /> [[#top|Back to Top]]<br /> <br /> === Zcluster ===<br /> <br /> The Linux cluster is comprised of compute nodes with 4-, 6-, 8-, and 12-core processors from both Intel and AMD. Subsets of nodes have &quot;large memory&quot; (e.g., 128, 256, or 512 GB of RAM), while others have InfiniBand connectivity or GPU capabilities. Total CPU compute power is 25.9 Tflops.<br /> <br /> The cluster is currently comprised of the following resources:<br /> <br /> *230 compute nodes (2600 compute cores), 32 with InfiniBand connectivity.<br /> *Four 8-core, 192GB high-memory compute nodes<br /> *Ten 12-core, 256GB high-memory compute nodes<br /> *Two 32-core, 512GB high-memory compute nodes<br /> *Six 32-core, 64GB high-memory compute nodes <br /> *One NVIDIA Tesla S1070 with four GPU cards (4 x 240 = 960 GPU cores) for programs written to use this architecture.<br /> *One NVIDIA Tesla (Fermi) C2075 GPU processor (448 GPU cores)<br /> *Nine NVIDIA Tesla (Fermi) M2070 GPU cards (9 x 448 = 4032 GPU cores). These cards are installed on 2 hosts each of which has dual 6-core Intel Xeon CPUs and 48GB of RAM; there are 6 GPU cards on one host and 3 on the other.<br /> *32 NVIDIA Tesla (Kepler) K20X GPU cards (32 x 2688 = 86016 GPU cores). These cards are installed on 4 hosts each of which has dual 6-core Intel Xeon CPUs and 96GB of RAM; there are 8 GPU cards per host.<br /> <br /> ====[[Connecting]]====<br /> <br /> ====[[Transferring Files]]====<br /> <br /> ====[[Disk Storage]]====<br /> <br /> ====[[Code Compilation on zcluster]]====<br /> <br /> ====[[Running Jobs on zcluster]]====</div>

Gcormier https://wiki.gacrc.uga.edu/index.php?title=Connecting&diff=6169 2015-06-11T18:12:17Z

<p>Gcormier: </p> <hr /> <div>[[Category:zcluster]]<br /> <br /> <br /> ===Connecting to zcluster===<br /> <br /> Access to the Linux cluster (zcluster) is through secure shell (ssh) to zcluster.rcc.uga.edu (note that connection via telnet is not safe and it is therefore disabled). If you have a local system that runs an X Window client or server, you can run X applications remotely.<br /> <br /> To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).<br /> <br /> Open a connection to host: zcluster.rcc.uga.edu<br /> <br /> '''Examples of usage on Unix/Linux/MacOSX'''<br /> <br /> To open a connection to zcluster.rcc.uga.edu, first open a terminal and at the command prompt type<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh username@zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> or<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh -X username@zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> where '''''username''''' is your username on zcluster. The -X option might be necessary to allow X windows applications running on zcluster to be forwarded to your local machine. If your username on your local system and on the zcluster are the same, you can simply type<br /> <br /> &lt;pre class=&quot;gcommand&quot;&gt;<br /> ssh zcluster.rcc.uga.edu<br /> &lt;/pre&gt;<br /> <br /> In order to enable X forwarding from zcluster to a local '''Mac OS X machine''', the ssh command given above (i.e. ssh -X username@zcluster.rcc.uga.edu) has to be issued from an '''X11 terminal''' (and not from a regular terminal).<br /> <br /> ===To run X Window applications remotely on your local machine===<br /> <br /> If you have a local machine that runs an X Window client or server, you can forward X Window applications running on zcluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.<br /> <br /> Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the zcluster (ssh -X username@zcluster.rcc.uga.edu). <br /> <br /> Now you can issue commands to start up X applications on zcluster.rcc.uga.edu, such as xterm.<br /> <br /> If you plan to run resource consuming X Window applications, such as Matlab, graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on zcluster is at the [[Running Jobs on zcluster]] page.<br /> <br /> ===Logging in===<br /> <br /> When your ssh connection is established, you will be prompted for your password. The first time you login to zcluster, please change your initial password with the '''passwd''' command. This command can be used afterwards as well, to change your password.<br /> <br /> ===Logging Out===<br /> <br /> To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:<br /> <br /> exit</div>

Gcormier