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==Training Sessions==
==GACRC Training==


The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.
'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''
==Regular Training Announcement==
In '''March 2025''', the GACRC is hosting 8 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.
We will offer:
1. Linux training for Linux-inexperienced cluster new users (3 sessions)
2. Sapelo2 cluster new user training (3 sessions)
3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)
4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)  '''''NEW'''''
==Event Schedule==
This section describes the training workshops that we offer, along with the sessions that are currently scheduled.
===Sapelo2 Cluster New User Training===
This mandatory training consists of an overview of the structure of Sapelo2 as well as hands-on practice submitting a job along with guidance and best practices when using the Sapelo2 cluster.
'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
'''Workshop Training Goals:'''
*Understand the layout of Sapelo2
*Understand the Sapelo2 file systems
*Understand the Sapelo2 partitions
*Understand the Sapelo2 software environment
*Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow
*Understand how to initiate an interactive job
*Understand how to transfer files to and from the cluster
*Understand how to get support from GACRC support team when you have any issues on cluster
'''Scheduled Sessions:'''
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC
|March 5th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 13th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|March 21st, Friday, 2:00 PM - 4:00 PM
|}
===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.
The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.
'''Prerequisite:'''
Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.
*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]
'''Training Goals:'''
1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.) 
2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)
3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment
'''Scheduled Sessions:'''
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster
|March 11th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|March 19th, Wednesday, 1:00 PM - 3:00 PM
|}
===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.
'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training.  Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.
'''Training Goals:'''
1. Learn about high-performance computing framework
2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?
3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?
4. How can I make my job run more efficiently (through the correct use of software and hardware)?
5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2
'''Scheduled Sessions:'''
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC, Part II
| February 21st, Friday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|March 14th, Friday, 2:00 PM - 4:00 PM
|}
===Installing Software Packages in Virtual Environments on Sapelo2 ===
This workshop will cover the basics of virtual environments as well as provide practical guidance and best practices for using virtual environments on the Sapelo2 cluster. Participants will learn the basics of creating and configuring virtual environments, how to install software packages in both a Conda virtual environment and a Python virtual environment, and manage dependencies in their environments.
'''Prerequisite:'''
Must already have strong understanding of the Linux environment and Sapelo2.
'''Training Goals:'''
1. Learn how to create a virtual environment on Sapelo2 
2. Be able to install software packages into both Conda and Python virtual environments
3. Understand how to manage dependencies of their virtual environments
'''Scheduled Sessions:'''
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|March 18th, Tuesday, 2:00 PM - 3:00 PM
|}
<!--
===Python Basics===
'''Prerequisite:''' No prerequisites
'''Training Goals:'''
1. Understand Python scientific modules and distributions
2. Understand Python general lexical conventions; Python built-in data types, like string, list, tuple, dictionary, etc.
3. Understand Python programming structures and procedural programming using functions
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Python Basics I||Not scheduled
|-
| Python Basics II||Not scheduled
|-
|}
=== R Basics===
'''Prerequisite:''' No prerequisites
'''Training Goals:'''
1. Understand fundamentals of R language, e.g. R general lexical conventions, data types, functions, and packages. Part 2 will introduce loops and functions.
2. Be able to manipulate and create data frames using built in functions and the dplyr package.
3. Interact with your file system and submit R code as a batch job to Sapelo 2. 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|R Basics I||Not scheduled
|-
|R Basics II||Not scheduled
|-
|}
===Conda===
'''Prerequisite:''' No prerequisites
'''Training Goals:'''
1. Understand fundamentals of conda environment
2. Use conda to create and configure your own virtual environments


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.  
3. Activate your environments to run python apps from your home directory on Sapelo2
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Conda Basics ||Not scheduled
|-
|}
-->
 
==How to Register==
 
The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839|GACRC User Account Request Form].
If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''' and/or '''Installing Software Packages in Virtual Environments on Sapelo2''' training workshops, please send us a request using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852|GACRC Training Request Form]. In your request, please tell us which session(s) you would like to attend.
 
 
<!--
==Topic Introduction==


'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''
Title: '''Sap2test cluster migration training'''


Focus:  Slurm queueing system, including Slurm job commands, job environment variables, and job submission headers, etc.


==Event Announcement==
The new software environment on Sap2test


Dear GACRC user,
Other important topics related to Sap2test working environment


The GACRC is going to host '''seven''' training workshops in this '''November 2015''' at Life Sciences Building, room C128. The seven workshops will provide an introduction to the GACRC Linux high performance computing (HPC) clusters, GACRC storage environment, and the Linux basics and scripting.


Title: '''Using Sapelo2 Cluster at the GACRC'''


'''Who Should Attend:'''
Focus: Sapelo2 HPC cluster and computational batch job submission workflow


New HPC cluster and zcluster users, or researchers who are interested in learning about the GACRC computing resources and Linux basics (Linux OS, Linux shell and shell scripting. etc.).
Cluster's storage environment


Computational queues on cluster


'''Details:'''
Software environment


Title: '''Introduction to HPC Using zcluster at GACRC'''
How to submit computational batch jobs


Date: November 2nd, 2015, Monday
Other tips and guidelines for users


Time: 2:00 PM - 3:30 PM
Title: '''Using Sapelo2 Cluster at the GACRC, Part II'''


Location: Life Sciences Building, room C128
Focus: More topics on how to use Sapelo2 cluster


Focus:
Learn about high-performance computing framework


What's zcluster at GACRC
Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?


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


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


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




Title: '''Introduction to HPC Using the New Cluster at GACRC'''
Title: '''Use Linux on Cluster'''


Date: November 6th, 2015, Friday
Focus: Linux OS fundamentals


Time: 10:00 AM - 11:30 AM
Linux common commands, filesystem, and shell


Location: Life Sciences Building, room C128
Linux shell scripting basics


Focus:
Common Linux utilities, e.g., grep, sed, find, sort, and awk, etc.


What's the new cluster at GACRC
Linux Hands-on practice


New cluster's current computing resources


New cluster software environment
Title: '''Python Basics I, II'''


How to operate with the new cluster
Focus of I: Python language overview, scientific modules and distributions


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.
Python general lexical conventions


Basic built-in data types, like string, list, tuple, dictionary, etc.


Title: '''Introduction to GACRC Storage Environment'''
Focus of II: Programming structures: control flow and loop


Date: November 9th, 2015, Monday
Function: procedural programming with examples, lambda expression, factory function and generator


Time: 2:00 PM - 3:30 PM


Location: Life Sciences Building, room C128
Title: '''R Basics I, II'''


Focus:
Focus of I: R language overview,general lexical conventions, data types, functions, and packages.


Overview of Linux common commands related to file and folder operations
Basic built-in data types, like string, numeric, list, dataframe etc. Using the dplyr package.


Overview of the storage enviornment of zcluster and the new cluster at GACRC
Focus of II: Programming structures: control flow, loops and functions


How to transfer data between local and GACRC storage


New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster
Title: '''Python on GACRC Sapelo2 Cluster'''


GACRC suggestions on good practices on GACRC storage, etc;
Focus: Install Python packages/modules in a user's home directory on Sapelo2 cluster


Python versions installed on Sapelo2


Title: '''Introduction to Linux Basics Part-I'''
Python environment details on Sapelo2


Date: November 13th, 2015, Friday
How to know a Python package is installed or not on Sapelo2


Time: 10:00 AM - 11:30 AM
How to install a Python package in user's home directory on Sapelo2


Location: Life Sciences Building, room C128


Focus:
Title: '''Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly!'''


Linux OS and brief history
Focus: Use conda to create and configure your own python virtual environments; Activate your environments to run python apps from your home directory on Sapelo2


Linux command, filesystem, and shell
What is Conda and its environment


Linux common commands, etc.
Conda on Sapelo2


Use conda to create and configure your own python virtual environments


Title: '''Introduction to HPC Using the New Cluster at GACRC'''
Activate your environments to run python apps from your home directory on Sapelo2


Date: November 16th, 2015, Monday


Time: 2:00 PM - 3:30 PM
Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''


Location: Life Sciences Building, room C128
Focus: Sapelo2 cluster general workflow and correct computing resource requesting


Focus:
Overview of Sapelo2 cluster with reference tables and operational diagrams


What's the new cluster at GACRC
Sapelo2 batch job submission workflow taking global scratch as job working space


New cluster's current computing resources
How to request computing resources correctly


New cluster software environment
How to run pipeline tasks and what are advantages/disadvantages of different options


How to operate with the new cluster
Sapelo2 cluster guideline and practical tips


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.


Title: '''GACRC Storage Environment'''


Title: '''Introduction to HPC Using zcluster at GACRC'''
Focus: Overview of Linux common commands related to file and folder operations


Date: November 20th, 2015, Friday
Overview of the storage environment of zcluster and Sapelo cluster at GACRC


Time: 10:00 AM - 11:30 AM
How to transfer data between local and GACRC storage


Location: Life Sciences Building, room C128
New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster


Focus:
GACRC suggestions on good practices on GACRC storage, etc;


What's zcluster at GACRC


zcluster current computing resources
Title: '''NCBI Blast application on sapelo'''


zcluster software environment
Focus: Introduction to BLAST


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.
BLAST job submission to sapelo


Advantages & Disadvantages: NCBI website vs run at sapelo.


Title: '''Introduction to Linux Basics Part-II''' (Basic Linux knowledge required)
Understand BLAST output


Date: November 30th, 2015, Monday
Troubleshooting the BLAST results


Time: 2:00 PM - 3:30 PM


Location: Life Sciences Building, room C128
Title: '''NGS application overview at GACRC'''


Focus:
Focus: Overview of Bioinformatics software available on HPC clusters at GACRC


Linux shell
It’s a brave new world – NGS and its Applications 


Common practices on Linux shell scripting
Hardware, Software, Databases available at GACRC


Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.
NGS project: Logistics and resource considerations


Best practices, common mistakes, troubleshooting and getting help from GACRC


If you would like to attend, please respond by email to: '''zhuofei@uga.edu'''. Also please tell us which session you want to attend.


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.
Title: '''Perl Language Basics I, II'''


The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC introduction, Linux working environment (Linux Basics, Part III), scientific programming languages, etc., in the near future. We will announce those events when they are scheduled.
Focus of I: Overview of Perl language,  


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.
Perl general scripting style


Perl fundamental data types


Sincerely,
Focus of II: Program structure: control flow and loop


GACRC Staff
Perl subroutine


Perl I/O
-->


==Upcoming Sessions==
== Download==


The GACRC is going to host '''seven''' training workshops in this '''November''' at '''Life Sciences Building, room C128'''. The workshops will provide an introduction to the Linux basics and GACRC Linux high performance computing (HPC) clusters and other computing resources.
This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.
====Sapelo2 Cluster Training====


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|-
! scope="col" | Presentation Date/Time
|}
! scope="col" | Location
 
! scope="col" | Title
====Teaching Cluster Training====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| November 6th, 2015, Friday, 10:00 AM - 11:30 AM || Davison Life Sciences Complex C128 || Introduction to HPC Using the New Cluster at GACRC
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2025.pdf]]
|-
|-
| November 9th, 2015, Monday, 2:00 PM - 3:30 PM || Davison Life Sciences Complex C128 || Introduction to GACRC Storage Environment
|}
 
====Linux Training for New Cluster Users====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| November 13th, 2015, Friday, 10:00 AM - 11:30 AM || Davison Life Sciences Complex C128 || Introduction to Linux Basics Part-I
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|-
| November 16th, 2015, Monday, 2:00 PM - 3:30 PM || Davison Life Sciences Complex C128 || Introduction to HPC Using the New Cluster at GACRC
|-
| November 20th, 2015, Friday, 10:00 AM - 11:30 AM || Davison Life Sciences Complex C128 || Introduction to HPC Using zcluster at GACRC
|-
| November 30th, 2015, Monday, 2:00 PM - 3:30 PM || Davison Life Sciences Complex C128 || Introduction to Linux Basics Part-II (Basic Linux knowledge required)
|}
|}


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


==Past Sessions==
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
 
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
|-
! scope="col" | Presentation Date/Time
|[[Media:GACRC_virtual_environments_training_v1.1.pdf]]
! scope="col" | Location
! scope="col" | Title
|-
| November 2nd, 2015, Monday, 2:00 PM - 3:30 PM || Davison Life Sciences Complex C128 || Introduction to HPC Using zcluster at GACRC
|}
|}


[[Past Sessions in 2015]]
====Python Basics====


{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|}


==Presentation Slides Download==
====R Basics====


 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
===GACRC Computing Resources===
 
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
|-
! scope="col" | Workshop PDF
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|-
| [[media: Introduction to HPC Using the New Cluster at GACRC Workshop20151106 v6.pdf]]
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|-
| [[media: Introduction to HPC Using zcluster at GACRC Workshop20151105 v4.pdf]]
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|-
| [[media: Introduction to GACRC Storage Environment Workshop20150928 v1.pdf]]
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|-
|}
|}


===Linux Basics===
====Perl Basics====


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" | Workshop PDF
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|-
| [[media: Introduction to Linux Basics Part-I Workshop20150915 v2.pdf]]
|}
|-
 
| [[media: Introduction to Linux Basics Part-II Workshop20151023 v1.pdf]]
====Sap2test Migration Training====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}
|}


'''Please note:''' 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).
====Topical Sessions====


===Out-Reach Talk===
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|
|-
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|-
! scope="col" | Dept./Center/Institute
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
! scope="col" | Date
! scope="col" | Workshop PDF
|-
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || 2015-10-14 || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|-
| The Center for Simulational Physics || 2015-09-15 || [[media: Introduction to HPC Using the New Cluster at GACRC Workshop CSP20150915 v2.pdf]]
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|-
|}
|}


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


===On-Class Training===
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
 
|-
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
|-
! scope="col" | Course ID
|Bioinformatics - Essential Computing Skills for Biologists Fall2016||In-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
! scope="col" | Course Title
! scope="col" | Workshop PDF
|-
|-
| MIBO 8150 || Introduction to UGA Research Resources || [[media: Introduction to HPC Resources at GACRC MIBO8150 20151007.pdf]]
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|-
| STAT 8060 || Computing Techniques in Statistics I || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}
|}


'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.
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==Past Sessions==
[[Pass Sessions in 2021]]
[[Past Sessions in 2020]]
[[Past Sessions in 2019]]
[[Past Sessions in 2018]]
[[Past Sessions in 2017]]
[[Past Sessions in 2016]]


'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.
[[Past Sessions in 2015]]
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Latest revision as of 17:31, 28 February 2025

GACRC Training

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

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


Regular Training Announcement

In March 2025, the GACRC is hosting 8 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

We will offer:

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

2. Sapelo2 cluster new user training (3 sessions)

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

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

Event Schedule

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

Sapelo2 Cluster New User Training

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

Prerequisites:

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

Workshop Training Goals:

  • Understand the layout of Sapelo2
  • Understand the Sapelo2 file systems
  • Understand the Sapelo2 partitions
  • Understand the Sapelo2 software environment
  • Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow
  • Understand how to initiate an interactive job
  • Understand how to transfer files to and from the cluster
  • Understand how to get support from GACRC support team when you have any issues on cluster

Scheduled Sessions:

Title Date/Time
Using Sapelo2 Cluster at the GACRC March 5th, Wednesday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC March 13th, Thursday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC March 21st, Friday, 2:00 PM - 4:00 PM


Linux Training for Linux-inexperienced Cluster New Users

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

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

Prerequisite:

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

Training Goals:

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

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

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

Scheduled Sessions:

Title Date/Time
Use Linux on Cluster March 11th, Tuesday, 1:00 PM - 3:00 PM
Use Linux on Cluster March 19th, Wednesday, 1:00 PM - 3:00 PM


Using Sapelo2 Cluster at the GACRC, Part II

This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.

Prerequisites:

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

Training Goals:

1. Learn about high-performance computing framework

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

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

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

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

Scheduled Sessions:

Title Date/Time
Using Sapelo2 Cluster at the GACRC, Part II February 21st, Friday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC, Part II March 14th, Friday, 2:00 PM - 4:00 PM


Installing Software Packages in Virtual Environments on Sapelo2

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

Prerequisite:

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

Training Goals:

1. Learn how to create a virtual environment on Sapelo2

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

3. Understand how to manage dependencies of their virtual environments

Scheduled Sessions:

Title Date/Time
Installing Software Packages in Virtual Environments on Sapelo2 March 18th, Tuesday, 2:00 PM - 3:00 PM


How to Register

The training workshops Using Sapelo2 Cluster at the GACRC and Use Linux on Cluster are ONLY offered to new users who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the User Account Request Form.

If you would like to attend the Using Sapelo2 Cluster at the GACRC, Part II and/or Installing Software Packages in Virtual Environments on Sapelo2 training workshops, please send us a request using the Training Request Form. In your request, please tell us which session(s) you would like to attend.


Download

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

Sapelo2 Cluster Training

Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf

Teaching Cluster Training

Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2025.pdf

Linux Training for New Cluster Users

Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf

Installing Software Packages in Virtual Environments on Sapelo2

Media:GACRC_virtual_environments_training_v1.1.pdf

Python Basics

Media:Python_Language_Basics_I_v5.1.pdf
Media:Python_Language_Basics_II_v5.1.pdf
Media:Python_Basics_v6.1.pdf

R Basics

Media:R_Language_Basics_PowerPoint_v2.0.pdf
Media:R_Language_Basics_Document_v2.0.pdf
Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf
Media:R_Language_Basics_part_2_Document_v1.0.pdf

Perl Basics

Media:Perl_Language_Basics_I_Workshop_v1.pdf

Sap2test Migration Training

Media:Migrating_to_Slurm_and_new_software_environment.pdf

Please note: 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).

Topical Sessions

Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf
Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf
Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf
Media:Blast_Workshop_GACRC_02012017.pdf
Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf

Out-Reach/In-Class Talk

Dept./Center/Institute Type Workshop PDF
BCMB8330 - Spring2025 In-Class Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf
PHYS8602 - Spring2025 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf ; Media:Gacrc_handout2025_phys8602.pdf
Engineering FYOS - Fall 2024 In-Class Media:GACRC_overview_20240920-FYOS.pdf
CSP seminar - Fall 2024 Out-Reach Media:GACRC_overview_20240820-CSP.pdf
BCMB8330 - Spring2024 In-Class Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf
PHYS4601/6601 - Spring2024 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf ; Media:Gacrc_handout2024_phys4601.pdf
PHYS8601 - Spring2024 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf ; Media:Gacrc_handout2024_phys8601.pdf
CSP seminar - Fall 2023 Out-Reach Media:GACRC_overview_20230822-CSP.pdf
BCMB8330 - Spring2023 In-Class Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf
PHYS4601/6601 - Spring2023 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf ; Media:Gacrc_handout2023_phys4601.pdf
PHYS8602 - Spring2023 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf ; Media:Gacrc_handout2023_phys8602.pdf
ILS GradFIRST course - Fall 2022 Out-Reach Media:GACRC_overview_20220901-ILS.pdf
FYOS1001 - Fall 2022 Out-Reach Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf
CSP seminar - Fall 2022 Out-Reach Media:GACRC_overview_20220830-CSP.pdf
CSP seminar - Fall 2022 Out-Reach Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf
Terry College IT - Spring2022 Out-Reach Media:GACRC_overview_20220506-Terry.pdf
PHYS8601 - Spring2022 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf
PHYS4601/6601 - Spring2022 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf ; Media:Gacrc_handout2021_phys4601.pdf
PHYS8602 - Spring2021 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf ; Media:Gacrc_handout2021_phys8602.pdf
GENE4220 - Fall2020 In-Class Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf
College of Veterinary Medicine - Spring2020 Out-Reach (jlslab) Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf
Byod Data Center - Fall2019 In-Class (FYOS1001) Media:High_Performance_Computing_(HPC)_on_Cluster.pdf
Department of Linguistics - Fall2019 In-class (LING6570) Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf
The Center for Simulational Physics - Fall2019 Out-Reach (Seminar Talk 20190820) Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf
The Center for Simulational Physics In-Class (PHYS4601/6601) Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf Media:Gacrc_handout2019_phys4601.pdf
The Center for Simulational Physics In-Class (PHYS8601) Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf Media:Gacrc_handout2020_phys8601.pdf
The Center for Simulational Physics In-Class (PHYS8602) Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf Media:Gacrc_handout2019_phys8602.pdf
Food Science - Fall2018 In-Class (FYOS1001) Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf
The Center for Simulational Physics - Summer2018 Out-Reach (Seminar Talk 20180821) Media:Introduction_to_GACRC_Sapelo2_cluster.pdf
Miller plant science - Summer2018 Out-Reach (jlmlab) Media:Introduction_to_GACRC_Sapelo2_cluster.pdf
Biochemistry and Molecular Biology - Spring2018 In-Class (BCMB8330) Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf
The Center for Simulational Physics - Summer2017 Out-Reach (Seminar Talk 20170831) Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf
Computational Physics - Spring2017 In-class (PHYS4601/6601) Media:Phys4601.pdf
Computational Physics - Spring2017 In-class (PHYS8602) Media:Phys8602.pdf
The Institute of Bioinformatics and the Quantitative Biology Consulting Group Out-Reach Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf
The Center for Simulational Physics Out-Reach (Seminar Talk 20160906) Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf
Microbiology In-Class (MIBO8150) Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf
Statistics In-Class (STAT8060) Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf
Biochemistry and Molecular Biology In-Class (BCMB8211) Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf
Plant Biology In-Class (PBIO/BINF8350) Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf
Plant Biology - Bioinformatics Applications Fall2016 In-Class (PBIO4550) Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf
Bioinformatics - Essential Computing Skills for Biologists Fall2016 In-Class (BINF4005) Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf
Computers in Experimental Genetics Fall2016 In-Class (GENE4220) Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf
Statistics - Advanced Applications and Computing in R Fall2016 In-Class (STAT8330) Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf

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


Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=Training&oldid=22296"