Training: Difference between revisions

From Research Computing Center Wiki
Jump to navigation Jump to search
Tag: Reverted
No edit summary
 
(9 intermediate revisions by 3 users not shown)
Line 9: Line 9:
==Regular Training Announcement==
==Regular Training Announcement==


 
In '''February 2025''', the GACRC is hosting 8 training sessions (3 Linux basics and 3 Sapelo2 cluster new user trainings, 1 Using Sapelo2 Cluster at the GACRC Part II training, and 1 Installing Software Packages in Virtual Environments on Sapelo2 training).
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:
Line 20: Line 19:
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)  


We will offer:
'''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.


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


2. Sapelo2 cluster new user training (3 sessions)
==Event Schedule==


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==


===Sapelo2 Cluster New User Training===
===Sapelo2 Cluster New User Training===
Line 42: Line 33:
'''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


{| 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
Line 82: Line 64:
|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===
Line 93: Line 76:
'''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:''' 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_81u2kfi2/176125031 Linux]
* [https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[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_wdyxhgdg/176125031 Linux Paths and Directories]


'''Training Goals:'''
'''Training Goals:'''
Line 111: Line 94:
|-
|-
|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 ===
'''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:'''
Line 145: Line 123:
{| 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
|-
|-
Line 152: Line 130:
|-
|-
|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
 
{| 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
Line 173: Line 175:
|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


Line 191: Line 193:
{| 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
Line 216: Line 218:
! scope="col" |Date/Time
! scope="col" |Date/Time
|-
|-
|Conda Basics||Not scheduled
|Conda Basics ||Not scheduled
|-
|-
|}
|}
 
-->


==How to Register==
==How to Register==
Line 225: Line 227:
'''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
'''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
   
   
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 want 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 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.
 
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.
The GACRC is planning to host other training workshops and seminars covering various HPC topics; these will be announced when scheduled.


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


Title: '''Sap2test cluster migration training'''
Title: '''Sap2test cluster migration training'''
Line 270: Line 271:


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




Line 306: Line 306:


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'''
Line 352: Line 353:
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
Line 400: Line 401:


Perl I/O
Perl I/O
-->


==Download==
== Download==


====Sapelo2 Cluster Training====
====Sapelo2 Cluster Training====
Line 420: Line 422:
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).


==== Teaching Cluster Training====
====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"
Line 436: Line 438:
|}
|}


==== 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"
Line 466: Line 468:
{| 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]]
|-
|-
|}
|}
Line 475: Line 477:
|
|
|-
|-
| [[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]]
Line 487: Line 489:
|}
|}


==== Out-Reach/On-Class Talk====
====Out-Reach/On-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
|-
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop bcmb8330-spring2025.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]]
|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]]
Line 515: Line 517:
|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]]
Line 525: Line 527:
|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]]
Line 531: Line 533:
|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 579:
|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]]
Line 586: Line 588:
'''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 ==
<!--
==Past Sessions==


[[Pass Sessions in 2021]]
[[Pass Sessions in 2021]]
Line 601: Line 604:


[[Past Sessions in 2015]]
[[Past Sessions in 2015]]
-->

Latest revision as of 09:57, 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 (3 Linux basics and 3 Sapelo2 cluster new user trainings, 1 Using Sapelo2 Cluster at the GACRC Part II training, and 1 Installing Software Packages in Virtual Environments on Sapelo2 training).

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)

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

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.

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
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

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

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

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

Title Date/Time
Installing Software Packages in Virtual Environments on Sapelo2 February 19th, Wednesday, 2:00 PM - 3:00 PM


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

If you want 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 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.

The GACRC is planning to host other training workshops and seminars covering various HPC topics; these will be announced when scheduled.


Download

Sapelo2 Cluster Training

Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.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).

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

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/On-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=22226"