Training: Difference between revisions

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==Regular Training Announcement==
==Regular Training Announcement==
In '''March''' 2022, the GACRC is hosting 7 training sessions (Linux basics, Sapelo2 cluster new user training, and Using Sapelo2 Cluster at the GACRC, Part II).
In '''November 2024''', 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 17: Line 17:


3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)
3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)
In '''December 2024''', 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:
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)




'''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.
'''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==
==Event Schedule==
Line 26: Line 40:
===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. '''The instructional videos are required to be viewed prior to the training workshop, and they can be found [https://kaltura.uga.edu/playlist/dedicated/176125031/1_4o12v8b4/1_9zi68rgi here]'''
Our Sapelo2 training consists of 1 hr 30 mins of instructional videos, followed by a 1 hr 30 min workshop.  


'''Prerequisites:'''  
'''Prerequisites:'''  
Line 32: Line 46:
* 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.


'''Video Playlist Training Goals:'''  
'''Workshop Training Goals:'''  


* Understand the layout of Sapelo2
* Understand the layout of Sapelo2
Line 41: Line 55:


* Understand the Sapelo2 software environment
* Understand the Sapelo2 software environment
'''Workshop Training Goals:'''


* 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
Line 58: Line 70:
|-
|-
|Using Sapelo2 Cluster at the GACRC
|Using Sapelo2 Cluster at the GACRC
|March 30th, Thursday, 1:00 PM - 3:00 PM
|November 14th, Thursday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC
|Using Sapelo2 Cluster at the GACRC
|April 7th, Friday, 1:00 PM - 3:00 PM
|November 20th, Wednesday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC
|Using Sapelo2 Cluster at the GACRC
|April 19th, Wednesday, 1:00 PM - 3:00 PM
|December 5th, Thursday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC
|Using Sapelo2 Cluster at the GACRC
|April 27th, Thursday, 1:00 PM - 3:00 PM
|December 11th, Wednesday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC
|December 19th, Thursday, 2:00 PM - 4:00 PM
|}
|}


===Linux Training for Linux-inexperienced Cluster New Users===
===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites
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:'''
'''Training Goals:'''
Line 88: Line 110:
|-
|-
|Use Linux on Cluster
|Use Linux on Cluster
|March 28th, Tuesday, 1:00 PM - 3:00 PM
|December 3rd, Tuesday, 1:00 PM - 3:00 PM
|-
|-
|Use Linux on Cluster
|Use Linux on Cluster
|April 5th, Wednesday, 1:00 PM - 3:00 PM
|December 9th, Monday, 1:00 PM - 3:00 PM
|-
|-
|Use Linux on Cluster
|Use Linux on Cluster
|April 17th, Monday, 1:00 PM - 3:00 PM
|December 17th, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster
|April 25th, Tuesday, 1:00 PM - 3:00 PM
|-
|}
|}


Line 123: Line 141:
! scope="col" |Date/Time
! scope="col" |Date/Time
|-
|-
|Using Sapelo2 Cluster at the GACRC, Part II||March 24th, Friday, 1:00 PM - 3:00 PM
|Using Sapelo2 Cluster at the GACRC, Part II
|November 15th, Friday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|Using Sapelo2 Cluster at the GACRC, Part II
|April 14th, Friday, 1:00 PM - 3:00 PM
|December 13th, Friday, 2:00 PM - 4:00 PM
|-
|}
|}


Line 146: Line 164:
! scope="col" |Date/Time
! scope="col" |Date/Time
|-
|-
|Python Basics I||Not scheduled in March
|Python Basics I||Not scheduled
|-
|-
|Python Basics II||Not scheduled in March
|Python Basics II||Not scheduled
|-
|-
|}
|}
Line 169: Line 187:
! scope="col" |Date/Time
! scope="col" |Date/Time
|-
|-
| R Basics I||Not scheduled in March
| R Basics I||Not scheduled  
|-
|-
|R Basics II||Not scheduled in March
|R Basics II||Not scheduled
|-
|-
|}
|}
Line 191: Line 209:
! scope="col" |Date/Time
! scope="col" |Date/Time
|-
|-
|Conda Basics||Not scheduled in March
|Conda Basics||Not scheduled
|-
|-
|}
|}
Line 381: Line 399:


{| 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:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.7.pdf]]
|-
|-
|}
|}
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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:GACRC-Teaching-cluster-new-user-training-workshop.pdf]]
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop_Fall2024.pdf]]
|-
|-
|}
|}
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|
|
|-
|-
| [[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II.pdf]]
| [[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:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
Line 469: Line 488:
! scope="col" |Workshop PDF
! scope="col" |Workshop PDF
|-
|-
|BCMB8330 - Spring2023||On-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.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||On-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||On-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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|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||On-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]]
|-
|-
|PHYS4601/6601 - Spring2022||On-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||On-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||On-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||On-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||On-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||On-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||On-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 ||On-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 ||On-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]]
Line 513: Line 544:
| 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||On-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||On-class (PHYS4601/6601) ||[[Media:Phys4601.pdf]]
|Computational Physics - Spring2017||In-class (PHYS4601/6601) ||[[Media:Phys4601.pdf]]
|-
|-
|Computational Physics - Spring2017||On-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]]
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|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||On-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||On-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||On-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||On-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]]
|-
|-
|Plant Biology - Bioinformatics Applications Fall2016||On-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||On-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||On-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]]
|-
|-
|Statistics - Advanced Applications and Computing in R Fall2016||On-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|Statistics - Advanced Applications and Computing in R Fall2016||In-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}
|}


Latest revision as of 10:45, 13 November 2024

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 November 2024, 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:

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)


In December 2024, 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:

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)



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 November 14th, Thursday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC November 20th, Wednesday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC December 5th, Thursday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC December 11th, Wednesday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC December 19th, 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 December 3rd, Tuesday, 1:00 PM - 3:00 PM
Use Linux on Cluster December 9th, Monday, 1:00 PM - 3:00 PM
Use Linux on Cluster December 17th, 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 November 15th, Friday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC, Part II December 13th, Friday, 2:00 PM - 4:00 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

Title 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.


Title 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

3. Activate your environments to run python apps from your home directory on Sapelo2

Title Date/Time
Conda Basics Not scheduled


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 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.

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

Title: Sap2test cluster migration training

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

The new software environment on Sap2test

Other important topics related to Sap2test working environment


Title: Using Sapelo2 Cluster at the GACRC

Focus: Sapelo2 HPC cluster and computational batch job submission workflow

Cluster's storage environment

Computational queues on cluster

Software environment

How to submit computational batch jobs

Other tips and guidelines for users


Title: Using Sapelo2 Cluster at the GACRC, Part II

Focus: More topics on how to use Sapelo2 cluster

Learn about high-performance computing framework

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

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

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

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


Title: Use Linux on Cluster

Focus: Linux OS fundamentals

Linux common commands, filesystem, and shell

Linux shell scripting basics

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

Linux Hands-on practice


Title: Python Basics I, II

Focus of I: Python language overview, scientific modules and distributions

Python general lexical conventions

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

Focus of II: Programming structures: control flow and loop

Function: procedural programming with examples, lambda expression, factory function and generator


Title: R Basics I, II

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

Basic built-in data types, like string, numeric, list, dataframe etc. Using the dplyr package.

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

Title: Python on GACRC Sapelo2 Cluster

Focus: Install Python packages/modules in a user's home directory on Sapelo2 cluster

Python versions installed on Sapelo2

Python environment details on Sapelo2

How to know a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2


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

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

What is Conda and its environment

Conda on Sapelo2

Use conda to create and configure your own python virtual environments

Activate your environments to run python apps from your home directory on Sapelo2


Title: How to submit and run jobs efficiently and correctly on Sapelo2

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips


Title: GACRC Storage Environment

Focus: Overview of Linux common commands related to file and folder operations

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

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

GACRC suggestions on good practices on GACRC storage, etc;


Title: NCBI Blast application on sapelo

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results


Title: NGS application overview at GACRC

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

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

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

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


Title: Perl Language Basics I, II

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

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_Fall2024.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
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.

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

Past Sessions in 2015

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