Training: Difference between revisions

From Research Computing Center Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
 
(719 intermediate revisions by 8 users not shown)
Line 4: Line 4:
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.  
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 an introductory training session and information about that will be sent once an account is requested.'''
'''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==
==Regular Training Announcement==


The GACRC is going to host '''seventeen''' regular training sessions and '''three''' interactive Question-and-Answer sessions in '''August''' 2017. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, Python language basics, Perl language basics, and NCBI Blast application on Sapelo.
In '''June 2025''', the GACRC is hosting 9 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 offer:
We will offer:


1. Four Sapelo cluster new user training sessions (mandatory for new user account creation)
1. Linux training for Linux-inexperienced cluster new users (3 sessions)


2. Three Linux-I introductory sessions and Three Linux-II introductory sessions (each combined with a Linux hands-on practice session)
2. Sapelo2 cluster new user training (3 sessions)


3. One Python language basics I session and One Python basics II session
3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)


4. One Perl language basics I session
4. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)  '''''NEW'''''


5. Four topical sessions on:
5. Job Parallelization with GNU Parallel and SLURM Arrays (1 session)  '''''NEW'''''
==Event Schedule==


(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)
This section describes the training workshops that we offer, along with the sessions that are currently scheduled.


(2) One session of NCBI Blast application on Sapelo
===Sapelo2 Cluster New User Training===


6. Three interactive Question-and-Answer sessions (Bring your questions to us for a discussion. No registration is needed. We are looking forward to seeing you in the classroom with your questions to us!)
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.


====Training Location:====
'''Workshop Training Goals:'''


Davison Life Sciences Complex (Life Science Building), Room C128
*Understand the layout of Sapelo2


120 East Green Street, Athens, GA 30602
*Understand the Sapelo2 file systems


*Understand the Sapelo2 partitions


*Understand the Sapelo2 software environment


==Event Schedule==
*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


===Sapelo New User Training===
'''Scheduled Sessions:'''


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" | Title
! scope="col" |Title
! scope="col" | Date/Time
! scope="col" |Date/Time  
|-
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 1st, Tuesday, 11:00 AM - 12:30 PM
|Using Sapelo2 Cluster at the GACRC
|May 15th, Thursday, 2:00 PM - 4:00 PM
|-
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 11th, Friday, 10:00 AM - 11:30 AM
|Using Sapelo2 Cluster at the GACRC
|May 21st, Wednesday, 2:00 PM - 4:00 PM
|-
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 15th, Tuesday, 11:00 AM - 12:30 PM
|Using Sapelo2 Cluster at the GACRC
|June 4th, Wednesday, 2:00 PM - 4:00 PM
|-
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 25th, Friday, 10:00 AM - 11:30 AM
|Using Sapelo2 Cluster at the GACRC
|June 12th, Thursday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC
|June 20th, Friday, 2:00 PM - 4:00 PM
|}
|}


===Linux Basics and Hands-on===


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
===Linux Training for Linux-inexperienced Cluster New Users===
The Sapelo2 High Performance Computing (HPC) cluster runs a headless Linux distribution as the operating system on each of its constituent nodes. The term headless refers to the fact that these nodes do not have a desktop graphical user interface (GUI) installed by default. Graphical desktop environments consume resources that analyses could otherwise use, so users employ a command-line interface (CLI) instead. To interact with these resources, users connect to a remote terminal via SSH and execute commands.
 
The Linux Training workshop provides hands-on practice of the fundamental Linux commands necessary to interact with HPC resources.
 
'''Prerequisite:'''
 
Please watch the introductory videos on Linux, basic Linux terms, and Linux Paths and Directories (total ~17 minutes) '''before attending the training workshop'''.
 
*[https://kaltura.uga.edu/media/t/1_81u2kfi2/176125031 Linux]
*[https://kaltura.uga.edu/media/t/1_ol51cuyn/176125031 basic Linux terms]
*[https://kaltura.uga.edu/media/t/1_wdyxhgdg/176125031 Linux Paths and Directories]
 
'''Training Goals:'''
 
1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.) 
 
2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)
 
3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment
 
'''Scheduled Sessions:'''
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" | Title
! scope="col" | Title
! scope="col" | Date/Time
! scope="col" |Date/Time
|-
|-
| Introduction to Linux Basics I and Hands-on || August 4th, Friday, 10:00 AM - 11:30 AM
|Use Linux on Cluster
|May 19th, Monday, 1:00 PM - 3:00 PM
|-
|-
| Introduction to Linux Basics II and Hands-on || August 4th, Friday, 11:30 AM - 1:00 PM
|Use Linux on Cluster
|June 2nd, Monday, 1:00 PM - 3:00 PM
|-
|-
| Introduction to Linux Basics I and Hands-on || August 10th, Thursday, 11:00 AM - 12:30 PM  
|Use Linux on Cluster
|June 10th, Tuesday, 1:00 PM - 3:00 PM
|-
|-
| Introduction to Linux Basics II and Hands-on || August 17th, Thursday, 11:00 AM - 12:30 PM  
|Use Linux on Cluster
|June 18th, Wednesday, 1:00 PM - 3:00 PM
|}
 
 
===Using Sapelo2 Cluster at the GACRC, Part II ===
This workshop will cover high-performance computing on Sapelo2, including job scheduling, resource requests (CPU, memory, GPU), and techniques for optimizing job performance.
 
'''Prerequisites:'''
*Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
*Sapelo2 cluster new user training.  Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.
 
'''Training Goals:'''
 
1. Learn about high-performance computing framework
 
2. Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?
 
3. How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?
 
4. How can I make my job run more efficiently (through the correct use of software and hardware)?
 
5. A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2
 
'''Scheduled Sessions:'''
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| Introduction to Linux Basics I and Hands-on || August 22nd, Tuesday, 11:00 AM - 12:30 PM
! scope="col" |Title
! scope="col" |Date/Time
|-
|-
| Introduction to Linux Basics II and Hands-on || August 24th, Thursday, 11:00 AM - 12:30 PM  
|Using Sapelo2 Cluster at the GACRC, Part II
|May 16th, Friday, 2:00 PM - 4:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|June 27th, Friday, 2:00 PM - 4:00 PM
|}
|}


===Python Basics===


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
===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.
! scope="col" | Title
 
! scope="col" | Date/Time
'''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"
|-
|-
| Python Language Basics I || August 18th, Friday, 10:00 AM - 11:30 AM
! scope="col" |Title
! scope="col" |Date/Time
|-
|-
| Python Language Basics II || August 18th, Friday, 11:30 AM - 1:00 PM
|Installing Software Packages in Virtual Environments on Sapelo2
|May 26th, Monday, 2:00 PM - 3:00 PM
|-
|-
|Installing Software Packages in Virtual Environments on Sapelo2
|June 17th, Tuesday, 2:00 PM - 3:00 PM
|}
|}


===Perl Basics===


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
===Job Parallelization with GNU Parallel and Slurm Arrays ===
Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.
 
'''Prerequisite:'''
 
Must already have strong understanding of the Linux environment and Sapelo2.
 
'''Training Goals:'''
 
1. Understand which jobs benefit from GNU Parallel and Slurm Arrays
 
2. Use GNU Parallel and Slurm Arrays to parallelize jobs
 
3. Understand the differences and similarities between GNU Parallel and Slurm Arrays
 
'''Scheduled Sessions:'''
 
{| 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
|-
|-
| Perl Language Basics I || August 31st, Thursday, 11:00 AM - 12:30 PM
|Job Parallelization with GNU Parallel and Slurm Arrays
|May 29th, Thursday, 1:00 PM - 2:30 PM
|-
|-
|Job Parallelization with GNU Parallel and Slurm Arrays
|June 26th, Thursday, 1:00 PM - 2:30 PM
|}
|}


===Topical Sessions===


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
<!--
===Python Basics===
'''Prerequisite:''' No prerequisites
 
'''Training Goals:'''
 
1. Understand Python scientific modules and distributions
 
2. Understand Python general lexical conventions; Python built-in data types, like string, list, tuple, dictionary, etc.
 
3. Understand Python programming structures and procedural programming using functions
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" | Title
! scope="col" | Title
! scope="col" | Date/Time
! scope="col" |Date/Time
|-
|-
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 3rd, Thursday, 11:00 AM - 12:30 PM
|Python Basics I||Not scheduled
|-
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 11th, Friday, 11:30 AM - 1:00 PM
| Python Basics II||Not scheduled
|-
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 25th, Friday, 11:30 AM - 1:00 PM
|-
| NCBI Blast application on Sapelo cluster || August 29th, Tuesday, 11:00 AM - 12:30 PM
|}
|}


===Interactive Question-and-Answer Sessions===
=== R Basics===
'''Prerequisite:''' No prerequisites


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
'''Training Goals:'''
 
1. Understand fundamentals of R language, e.g. R general lexical conventions, data types, functions, and packages. Part 2 will introduce loops and functions.
 
2. Be able to manipulate and create data frames using built in functions and the dplyr package.
 
3. Interact with your file system and submit R code as a batch job to Sapelo 2. 
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
! scope="col" | Title
! scope="col" | Title
! scope="col" | Date/Time
! scope="col" |Date/Time  
|-
|-
| Question-and-Answer || August 1st, Tuesday, 14:00 PM - 15:30 PM
|R Basics I||Not scheduled
|-
|-
| Question-and-Answer || August 3rd, Thursday, 14:00 PM - 15:30 PM
|R Basics II||Not scheduled
|-
| Question-and-Answer || August 10th, Thursday, 14:00 PM - 15:30 PM
|-
|-
|}
|}


===Zcluster Decommissioning Awareness Sessions===
===Conda===
'''Prerequisite:''' No prerequisites
 
'''Training Goals:'''
 
1. Understand fundamentals of conda environment
 
2. Use conda to create and configure your own virtual environments


The GACRC will host '''three''' awareness sessions in '''August'''. We will help to answer your questions related to the zcluster decommissioning.
3. Activate your environments to run python apps from your home directory on Sapelo2


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
|-
| Session 1 || August 15th, Tuesday, 14:00 PM - 15:30 PM
! scope="col" |Title
! scope="col" |Date/Time
|-
|-
| Session 2 || August 17th, Thursday, 14:00 PM - 15:30 PM
|Conda Basics ||Not scheduled
|-
| Session 3 || August 22nd, Tuesday, 14:00 PM - 15:30 PM
|-
|-
|}
|}
-->


'''Please Note:''' [[A Sapelo user account will not be granted by only attending awareness sessions.]] To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session to be scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.
==How to Register==


More information about these training sessions will be posted on the GACRC’s training web page, at gacrc.uga.edu/training as well as on the GACRC's wiki, at wiki.gacrc.uga.edu/wiki/Training .
The training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need user accounts on the GACRC Sapelo2 cluster or current Sapelo2 users seeking a refresher. If you would like to use the cluster, please ask your group PI/UGA faculty member to send us an account creation request for you, using the  [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839|GACRC User Account Request Form].
If you would like to attend the '''Using Sapelo2 Cluster at the GACRC, Part II''', the '''Installing Software Packages in Virtual Environments on Sapelo2''', and/or the '''Job Parallelization with GNU Parallel and Slurm Arrays''' 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.




==How to Register==
<!--
==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


If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.
Other important topics related to Sap2test working environment


We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.


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


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.
Focus: Sapelo2 HPC cluster and computational batch job submission workflow


The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.
Cluster's storage environment


Computational queues on cluster


Software environment


==Topic Introduction==
How to submit computational batch jobs


Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''
Other tips and guidelines for users


Focus: What's the Sapelo cluster at GACRC
Title: '''Using Sapelo2 Cluster at the GACRC, Part II'''


Sapelo cluster's computing resources
Focus: More topics on how to use Sapelo2 cluster


Sapelo cluster's software environment
Learn about high-performance computing framework


How to operate with Sapelo cluster and batch job submission workflows
Why is my job pending? How can I get my job to start sooner? How to find available computing resources on Sapelo2?


How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.
How to request computing resources such as nodes, CPU cores, memory, GPU device, etc. to run serial, threaded, MPI, and GPU jobs on Sapelo2?


Title: '''Introduction to HPC Using zcluster at GACRC'''
How can I make my job run more efficiently (through the correct use of software and hardware)?


Focus: What's zcluster at GACRC
A quick intro to MPI library and how to compile/run MPI jobs on Sapelo2


zcluster current computing resources


zcluster software environment
Title: '''Use Linux on Cluster'''


How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.
Focus: Linux OS fundamentals


Linux common commands, filesystem, and shell


Title: '''Introduction to Linux Basics I and II'''
Linux shell scripting basics


Focus of I: Linux OS and brief history
Common Linux utilities, e.g., grep, sed, find, sort, and awk, etc.


Linux command, filesystem, and shell
Linux Hands-on practice


Linux common commands, etc.


Focus of II: Linux shell
Title: '''Python Basics I, II'''


Common practices on Linux shell scripting
Focus of I: Python language overview, scientific modules and distributions


Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.
Python general lexical conventions


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


Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''
Focus of II: Programming structures: control flow and loop


Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.
Function: procedural programming with examples, lambda expression, factory function and generator


Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.


Title: '''R Basics I, II'''


Title: '''Python Language Basics I, II, and III'''
Focus of I: R language overview,general lexical conventions, data types, functions, and packages.


Focus of I: Overview of Python language, scientific modules and distributions
Basic built-in data types, like string, numeric, list, dataframe etc. Using the dplyr package.


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


Basic built-in data types


Focus of II: Program structure: control flow and loop
Title: '''Python on GACRC Sapelo2 Cluster'''


Function: procedural and functional programming with examples
Focus: Install Python packages/modules in a user's home directory on Sapelo2 cluster


Python Class
Python versions installed on Sapelo2


Focus of III: Python modules and importing
Python environment details on Sapelo2


Python Package and usage
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: '''Python on GACRC Computing Resources'''


Focus: Python and Python packages/modules installed on zcluster and Sapelo
Title: '''Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly!'''


Python Overview
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


Python on Clusters
What is Conda and its environment


Python Packages on Clusters
Conda on Sapelo2


Run Python Interactively on Clusters
Use conda to create and configure your own python virtual environments


Run Python Batch Job on Clusters
Activate your environments to run python apps from your home directory on Sapelo2




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


Focus: Sapelo general workflow and correct computing resource requesting
Focus: Sapelo2 cluster general workflow and correct computing resource requesting


Overview of Sapelo cluster with reference tables and operational diagrams
Overview of Sapelo2 cluster with reference tables and operational diagrams


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


How to request computing resources correctly  
How to request computing resources correctly  
Line 264: Line 401:
How to run pipeline tasks and what are advantages/disadvantages of different options
How to run pipeline tasks and what are advantages/disadvantages of different options


Sapelo guideline and practical tips
Sapelo2 cluster guideline and practical tips




Line 271: Line 408:
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 278: Line 415:


GACRC suggestions on good practices on GACRC storage, etc;
GACRC suggestions on good practices on GACRC storage, etc;
Title: '''Software installation on zcluster'''
Focus: Current status of software on zcluster; What GACRC have now and what should users install
How to obtain, install, organize software by users; What about databases
How to validate the software installation
How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.
How to get help from GACRC and Common problems/mistakes




Line 319: Line 443:




Title: '''R Language Introduction'''
Title: '''Perl Language Basics I, II'''


Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)
Focus of I: Overview of Perl language,  


Focus: Common general topics about R language
Perl general scripting style


Description:This short course will introduce users to the program R and how to use it for data analysis.
Perl fundamental data types


Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.
Focus of II: Program structure: control flow and loop


Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.
Perl subroutine


==Download==
Perl I/O
-->


== Download==


====Sapelo and zcluster New User Training====
This section provides the slides that we use for our current workshops and material used for several of our past training events and presentations.
====Sapelo2 Cluster Training====


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|}
 
====Teaching Cluster Training====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf]]
|[[Media:GACRC-Teaching-cluster-new-user-training-workshop-Spring2025.pdf]]
|-
|-
| [[media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02132017.pdf]]
|}
 
====Linux Training for New Cluster Users====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|-
|}
|}


====Linux Basics and Hands-on====
====Installing Software Packages in Virtual Environments on Sapelo2====


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|[[Media:GACRC_virtual_environments_training_v1.1.pdf]]
|}
 
====Job Parallelization with GNU Parallel and Slurm Arrays====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|[[Media:GNU_Parallel_and_SLURM_Arrays_v1.pdf]]
|}
 
====Python Basics====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|[[Media:Python_Basics_v6.1.pdf]]
|-
|-
|}
|}


====Python Basics====
====R Basics====


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|-
|}
|}


====Topical Sessions====
====Perl Basics====


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
| [[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|}
 
====Sap2test Migration Training====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|[[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====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|[[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|-
| [[media: Software installation on zcluster.pdf]]
|[[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|-
| [[media: Blast Workshop GACRC 02012017.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 ]]
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|-
|}
|}


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


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Dept./Center/Institute
! scope="col" |Type
! scope="col" |Workshop PDF
|-
|BCMB8330 - Spring2025||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330-Spring2025.pdf]]
|-
|PHYS8602 - Spring2025||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-Spring2025.pdf]] ; [[Media:Gacrc_handout2025_phys8602.pdf]]
|-
|Engineering FYOS - Fall 2024|| In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|PHYS4601/6601 - Spring2024|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|PHYS8602 - Spring2023|| In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|Terry College IT - Spring2022||Out-Reach ||[[Media:GACRC_overview_20220506-Terry.pdf]]
|-
|PHYS8601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021 ||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab)||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||In-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
|Department of Linguistics - Fall2019||In-class (LING6570)|| [[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||In-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
|-
! scope="col" | Dept./Center/Institute
| The Center for Simulational Physics||In-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
! scope="col" | Type
! scope="col" | Workshop PDF
|-
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|The Center for Simulational Physics||In-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: 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]]
|-
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|Miller plant science - Summer2018||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|-
| The Center for Simulational Physics || Out-Reach || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|Biochemistry and Molecular Biology - Spring2018||In-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831)||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|Computational Physics - Spring2017 ||In-class (PHYS4601/6601)||[[Media:Phys4601.pdf]]
|-
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|Computational Physics - Spring2017||In-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group||Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|The Center for Simulational Physics||Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|Microbiology||In-Class (MIBO8150)||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|Statistics||In-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|Biochemistry and Molecular Biology||In-Class (BCMB8211)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.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.
'''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]]
[[Past Sessions in 2020]]
[[Past Sessions in 2019]]
[[Past Sessions in 2018]]


[[Past Sessions in 2017]]
[[Past Sessions in 2017]]
Line 439: Line 675:


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

Latest revision as of 15:02, 14 May 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 June 2025, the GACRC is hosting 9 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

5. Job Parallelization with GNU Parallel and SLURM Arrays (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 May 15th, Thursday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC May 21st, Wednesday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC June 4th, Wednesday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC June 12th, Thursday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC June 20th, Friday, 2:00 PM - 4:00 PM


Linux Training for Linux-inexperienced Cluster New Users

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

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

Prerequisite:

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

Training Goals:

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

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

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

Scheduled Sessions:

Title Date/Time
Use Linux on Cluster May 19th, Monday, 1:00 PM - 3:00 PM
Use Linux on Cluster June 2nd, Monday, 1:00 PM - 3:00 PM
Use Linux on Cluster June 10th, Tuesday, 1:00 PM - 3:00 PM
Use Linux on Cluster June 18th, Wednesday, 1:00 PM - 3:00 PM


Using Sapelo2 Cluster at the GACRC, Part II

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

Prerequisites:

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

Training Goals:

1. Learn about high-performance computing framework

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

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

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

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

Scheduled Sessions:

Title Date/Time
Using Sapelo2 Cluster at the GACRC, Part II May 16th, Friday, 2:00 PM - 4:00 PM
Using Sapelo2 Cluster at the GACRC, Part II June 27th, 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 May 26th, Monday, 2:00 PM - 3:00 PM
Installing Software Packages in Virtual Environments on Sapelo2 June 17th, Tuesday, 2:00 PM - 3:00 PM


Job Parallelization with GNU Parallel and Slurm Arrays

Learn how to run multiple commands in parallel using GNU Parallel and Slurm Arrays. These tools greatly reduce the runtime of certain types of jobs by running multiple instances of the same command in parallel. The workshop focuses on problems that involve executing the same command on multiple different inputs. This workshop is intended for users comfortable writing job submission scripts and using a command line. Concurrent and parallel programming techniques are not covered in this workshop.

Prerequisite:

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

Training Goals:

1. Understand which jobs benefit from GNU Parallel and Slurm Arrays

2. Use GNU Parallel and Slurm Arrays to parallelize jobs

3. Understand the differences and similarities between GNU Parallel and Slurm Arrays

Scheduled Sessions:

Title Date/Time
Job Parallelization with GNU Parallel and Slurm Arrays May 29th, Thursday, 1:00 PM - 2:30 PM
Job Parallelization with GNU Parallel and Slurm Arrays June 26th, Thursday, 1:00 PM - 2:30 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, the Installing Software Packages in Virtual Environments on Sapelo2, and/or the Job Parallelization with GNU Parallel and Slurm Arrays training workshops, please send us a request using the GACRC Training Request Form. In your request, please tell us which session(s) you would like to attend.


Download

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

Sapelo2 Cluster Training

Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf

Teaching Cluster Training

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

Linux Training for New Cluster Users

Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf

Installing Software Packages in Virtual Environments on Sapelo2

Media:GACRC_virtual_environments_training_v1.1.pdf

Job Parallelization with GNU Parallel and Slurm Arrays

Media:GNU_Parallel_and_SLURM_Arrays_v1.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=22391"