Training: Difference between revisions

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==Regular Training Announcement==
==Regular Training Announcement==


 
In '''February 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.
In '''January 2025''', the GACRC is hosting 7 training sessions (3 Linux basics and 3 Sapelo2 cluster new user trainings and 1 Using Sapelo2 Cluster at the GACRC, Part II training).


We will offer:
We will offer:
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3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)
3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)


In '''February 2025''', the GACRC is hosting 7 training sessions (3 Linux basics and 3 Sapelo2 cluster new user trainings and 1 Using Sapelo2 Cluster at the GACRC, Part II training).
4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)  '''''NEW'''''


We will offer:


1. Linux training for Linux-inexperienced cluster new users (3 sessions)
==Event Schedule==
 
2. Sapelo2 cluster new user training (3 sessions)
 
3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)
 
 
 
'''Please Note:''' The training workshops will be offered remotely via Zoom Meeting. Detailed information on how to join the Zoom meeting will be sent to your UGA email account prior to each training session.


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


===Sapelo2 Cluster New User Training===
===Sapelo2 Cluster New User Training===


Our Sapelo2 training consists of 1 hr 30 mins of instructional videos, followed by a 1 hr 30 min workshop.  
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:'''  
'''Prerequisites:'''  


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


'''Workshop Training Goals:'''  
'''Workshop Training Goals:'''  


* Understand the layout of Sapelo2
*Understand the layout of Sapelo2


* Understand the Sapelo2 file systems
*Understand the Sapelo2 file systems


* Understand the Sapelo2 partitions
*Understand the Sapelo2 partitions


* Understand the Sapelo2 software environment
*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 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 initiate an interactive job


* Understand how to transfer files to and from the cluster
*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
*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"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" |Title
! scope="col" |Title
! scope="col" |Date/Time
! scope="col" |Date/Time  
|-
|Using Sapelo2 Cluster at the GACRC
|January 8th, Wednesday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 16th, Thursday, 2:00 PM - 4:00 PM
|-
|Using Sapelo2 Cluster at the GACRC
|January 24th, Friday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC
|Using Sapelo2 Cluster at the GACRC
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|February 12th, Wednesday, 2:00 PM - 4:00 PM
|February 12th, Wednesday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC
| Using Sapelo2 Cluster at the GACRC  
|February 20th, Thursday, 2:00 PM - 4:00 PM
|February 20th, Thursday, 2:00 PM - 4:00 PM
|}
|}


===Linux Training for Linux-inexperienced Cluster New Users===
===Linux Training for Linux-inexperienced Cluster New Users===
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The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.
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'''.
'''Prerequisite:'''  


* [https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
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_ol51cuyn/176125031 basic Linux terms]
 
* [https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]
*[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:'''
'''Training Goals:'''
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3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment
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"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
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|-
|-
|Use Linux on Cluster
|Use Linux on Cluster
|January 14th, Tuesday, 1:00 PM - 3:00 PM
|February 5th, Wednesday, 1:00 PM - 3:00 PM  
|-
|Use Linux on Cluster
|January 22nd, Wednesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|February 3rd, Wednesday, 1:00 PM - 3:00 PM
|-
|-
|Use Linux on Cluster
|Use Linux on Cluster
|February 10th, Monday, 1:00 PM - 3:00 PM
|February 10th, Monday, 1:00 PM - 3:00 PM
|-
|-
|Use Linux on Cluster
|Use Linux on Cluster  
|February 18th, Tuesday, 1:00 PM - 3:00 PM
|February 18th, Tuesday, 1:00 PM - 3:00 PM
|}
|}


===Using Sapelo2 Cluster at the GACRC, Part II===
 
===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:'''
'''Prerequisites:'''
* Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*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.
*Sapelo2 cluster new user training.  Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.


'''Training Goals:'''
'''Training Goals:'''
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5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2
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"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" | Title
! scope="col" |Title
! scope="col" |Date/Time
! scope="col" |Date/Time
|-
|-
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|-
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|Using Sapelo2 Cluster at the GACRC, Part II
|February 21st, Friday, 2:00 PM - 4:00 PM
| February 21st, 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
|February 19th, Wednesday, 2:00 PM - 3:00 PM
|}
<!--
===Python Basics===
===Python Basics===
'''Prerequisite:''' No prerequisites
'''Prerequisite:''' No prerequisites
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|Python Basics I||Not scheduled
|Python Basics I||Not scheduled
|-
|-
|Python Basics II||Not scheduled
| Python Basics II||Not scheduled
|-
|-
|}
|}


===R Basics===
=== R Basics===
'''Prerequisite:''' No prerequisites
'''Prerequisite:''' No prerequisites


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{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" |Title
! scope="col" | Title
! scope="col" |Date/Time
! scope="col" |Date/Time  
|-
|-
| R Basics I||Not scheduled  
|R Basics I||Not scheduled
|-
|-
|R Basics II||Not scheduled
|R Basics II||Not scheduled
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! scope="col" |Date/Time
! scope="col" |Date/Time
|-
|-
|Conda Basics||Not scheduled
|Conda Basics ||Not scheduled
|-
|-
|}
|}
 
-->


==How to Register==
==How to Register==


'''Please Note''', the training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need computing user accounts on the GACRC Sapelo2 cluster, or any current users who have never attended the GACRC Sapelo2 cluster new user training before. Please ask your group PI/UGA faculty member to send us a request for you, using the GACRC User Account Request form at https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839
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 want to attend '''Python Basics''', '''R''', and '''Conda basics''' training sessions, please send us a request using the GACRC Training Request form at https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 . In your request, please tell us which session(s) you want to attend.
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.
 
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.


The GACRC Web Training page can be found at https://gacrc.uga.edu/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.


== Topic Introduction==
<!--
==Topic Introduction==


Title: '''Sap2test cluster migration training'''
Title: '''Sap2test cluster migration training'''
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A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2
A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2




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Focus of II: Programming structures: control flow, loops and functions
Focus of II: Programming structures: control flow, loops and functions


Title: '''Python on GACRC Sapelo2 Cluster'''
Title: '''Python on GACRC Sapelo2 Cluster'''
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Focus: Overview of Linux common commands related to file and folder operations
Focus: Overview of Linux common commands related to file and folder operations


Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC
Overview of the storage environment of zcluster and Sapelo cluster at GACRC


How to transfer data between local and GACRC storage
How to transfer data between local and GACRC storage
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Perl I/O
Perl I/O
-->


==Download==
== 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====
====Sapelo2 Cluster Training====


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|}
|}


====Sap2test Migration Training====
====Teaching Cluster 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).
 
==== Teaching Cluster Training====


{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
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|}
|}


==== Python Basics====
====Python Basics====


{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
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{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
|[[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
| [[Media:Perl_Language_Basics_I_Workshop_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====
====Topical Sessions====
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|
|
|-
|-
| [[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|-
| [[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|-
| [[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|[[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
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|}
|}


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


{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" | Dept./Center/Institute
! scope="col" |Dept./Center/Institute
! scope="col" | Type
! scope="col" |Type
! scope="col" |Workshop PDF
! scope="col" |Workshop PDF
|-
|-
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|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.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]]
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.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]]
|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]]
|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]]
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
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|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.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]]
|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]]
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
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|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.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]]
|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]]
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
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|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.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]]
|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]]
|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]]
|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]]
|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]]
|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 - 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 (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 (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]]
|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]]
|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]]
|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]]
|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]]
|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]]
|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 (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|-
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.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 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]]
|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]]
|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]]
|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]]
|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||In-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
Line 577: Line 593:
|Plant Biology - Bioinformatics Applications Fall2016||In-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.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]]
|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]]
|Computers in Experimental Genetics Fall2016||In-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
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'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.
'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.


== Past Sessions ==
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==Past Sessions==


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Latest revision as of 12:18, 31 January 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 February 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 February 7th, Friday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC February 12th, Wednesday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC February 20th, Thursday, 2:00 PM - 4:00 PM


Linux Training for Linux-inexperienced Cluster New Users

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

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

Prerequisite:

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

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 February 5th, Wednesday, 1:00 PM - 3:00 PM
Use Linux on Cluster February 10th, Monday, 1:00 PM - 3:00 PM
Use Linux on Cluster February 18th, Tuesday, 1:00 PM - 3:00 PM


Using Sapelo2 Cluster at the GACRC, Part II

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

Prerequisites:

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

Training Goals:

1. Learn about high-performance computing framework

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

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

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

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

Scheduled Sessions:

Title Date/Time
Using Sapelo2 Cluster at the GACRC, Part II January 17th, Friday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC, Part II February 21st, 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 February 19th, Wednesday, 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

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=22244"