Training: Difference between revisions

From Research Computing Center Wiki
Jump to navigation Jump to search
 
(648 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==
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).


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.
We will offer:


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


1. Four Sapelo cluster new user training sessions (mandatory for new user account creation)
2. Sapelo2 cluster new user training (3 sessions)


2. Three Linux-I introductory sessions and Three Linux-II introductory sessions (each combined with a Linux hands-on practice session)
3. Using Sapelo2 Cluster at the GACRC, Part II (1 session)


3. One Python language basics I session and One Python basics II session


4. One Perl language basics I session


5. Four topical sessions on:
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).


(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)
We will offer:


(2) One session of NCBI Blast application on Sapelo
1. Linux training for Linux-inexperienced cluster new users (3 sessions)


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!)
2. Sapelo2 cluster new user training (3 sessions)


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




====Training Location:====


Davison Life Sciences Complex (Life Science Building), Room C128


120 East Green Street, Athens, GA 30602


'''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


==Event Schedule==
* Understand how to transfer files to and from the cluster


===Sapelo New User Training===
* Understand how to get support from GACRC support team when you have any issues on cluster


{| 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
|November 14th, 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
|November 20th, 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
|December 5th, Thursday, 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
|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 Basics and Hands-on===
===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


{| 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 Linux Basics I and Hands-on || August 4th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to Linux Basics II and Hands-on || August 4th, Friday, 11:30 AM - 1:00 PM
|-
| Introduction to Linux Basics I and Hands-on || August 10th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || August 17th, Thursday, 11:00 AM - 12:30 PM
|-
|-
| Introduction to Linux Basics I and Hands-on || August 22nd, Tuesday, 11:00 AM - 12:30 PM  
|Use Linux on Cluster
|December 3rd, Tuesday, 1:00 PM - 3:00 PM
|-
|-
| Introduction to Linux Basics II and Hands-on || August 24th, Thursday, 11:00 AM - 12:30 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
|}
|}


===Python Basics===
===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


{| 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
|-
|-
| Python Language Basics I || August 18th, Friday, 10:00 AM - 11:30 AM
|Using Sapelo2 Cluster at the GACRC, Part II
|-
|November 15th, Friday, 2:00 PM - 4:00 PM
| Python Language Basics II || August 18th, Friday, 11:30 AM - 1:00 PM
|-
|-
|Using Sapelo2 Cluster at the GACRC, Part II
|December 13th, Friday, 2:00 PM - 4:00 PM
|}
|}


===Perl Basics===
===Python Basics===
'''Prerequisite:''' No prerequisites
 
'''Training Goals:'''
 
1. Understand Python scientific modules and distributions


{|  width="100%" border="1"  cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
2. Understand Python general lexical conventions; Python built-in data types, like string, list, tuple, dictionary, etc.
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || August 31st, Thursday, 11:00 AM - 12:30 PM
|-
|}


===Topical Sessions===
3. Understand Python programming structures and procedural programming using functions


{| 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
|-
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 3rd, Thursday, 11:00 AM - 12:30 PM
|-
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 11th, Friday, 11:30 AM - 1:00 PM
|Python Basics I||Not scheduled
|-
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 25th, Friday, 11:30 AM - 1:00 PM
|Python Basics II||Not scheduled
|-
|-
| 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
 
'''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. 


{| 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
|-
| Question-and-Answer || August 1st, Tuesday, 14:00 PM - 15:30 PM
|-
|-
| Question-and-Answer || August 3rd, Thursday, 14:00 PM - 15:30 PM
| R Basics I||Not scheduled
|-
|-
| Question-and-Answer || August 10th, Thursday, 14:00 PM - 15:30 PM
|R Basics II||Not scheduled
|-
|-
|}
|}


===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.


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 .
==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.


==How to Register==
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.


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.
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.


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.
== Topic Introduction==


Title: '''Sap2test cluster migration training'''


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


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.
The new software environment on Sap2test


Other important topics related to Sap2test working environment




==Topic Introduction==
Title: '''Using Sapelo2 Cluster at the GACRC'''


Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''
Focus: Sapelo2 HPC cluster and computational batch job submission workflow


Focus: What's the Sapelo cluster at GACRC
Cluster's storage environment


Sapelo cluster's computing resources
Computational queues on cluster


Sapelo cluster's software environment
Software environment


How to operate with Sapelo cluster and batch job submission workflows
How to submit computational batch jobs


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.
Other tips and guidelines for users
   
   


Title: '''Introduction to HPC Using zcluster at GACRC'''
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)?


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


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.
Title: '''Use Linux on Cluster'''


Focus: Linux OS fundamentals


Title: '''Introduction to Linux Basics I and II'''
Linux common commands, filesystem, and shell


Focus of I: Linux OS and brief history
Linux shell scripting basics


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


Linux common commands, etc.
Linux Hands-on practice


Focus of II: Linux shell


Common practices on Linux shell scripting
Title: '''Python Basics I, II'''


Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.
Focus of I: Python language overview, scientific modules and distributions


Python general lexical conventions


Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''
Basic built-in data types, like string, list, tuple, dictionary, etc.


Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.
Focus of II: Programming structures: control flow and loop


Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.
Function: procedural programming with examples, lambda expression, factory function and generator




Title: '''Python Language Basics I, II, and III'''
Title: '''R Basics I, II'''


Focus of I: Overview of Python language, scientific modules and distributions
Focus of I: R language overview,general lexical conventions, data types, functions, and packages.


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


Basic built-in data types
Focus of II: Programming structures: control flow, loops and functions


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 338:
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 278: Line 352:


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 380:




Title: '''R Language Introduction'''
Title: '''Perl Language Basics I, II'''
 
Focus of I: Overview of Perl language,


Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)
Perl general scripting style


Focus: Common general topics about R language
Perl fundamental data types


Description:This short course will introduce users to the program R and how to use it for data analysis.
Focus of II: Program structure: control flow and loop


Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.
Perl subroutine


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 I/O


==Download==
==Download==


====Sapelo2 Cluster Training====
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.8.pdf]]
|-
|}


====Sapelo and zcluster New User Training====
====Sap2test Migration 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: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.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).
 
==== 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_Fall2024.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====
==== Python 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_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|[[Media:Python_Basics_v6.1.pdf]]
|-
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|}
 
====R Basics====
 
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|-
|}
|}


====Python Basics====
====Perl Basics====


{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|[[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|-
|}
|}
Line 376: Line 465:
====Topical Sessions====
====Topical 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"
|-
|
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
| [[Media:AI_Resources_on_the_GACRC_Sapelo2_Cluster.pdf]]
|-
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
| [[Media:Using_Sapelo2_Cluster_at_the_GACRC_Part_II_Rocky8.pdf]]
|-
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
| [[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|-
| [[media: Software installation on zcluster.pdf]]
|[[Media:Blast_Workshop_GACRC_02012017.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/On-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" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Type
! scope="col" | Workshop PDF
! scope="col" |Workshop PDF
|-
|-
| Center for Simulational Physics || Lunch Seminar Talk 20170831 || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|Engineering FYOS - Fall 2024||In-Class||[[Media:GACRC_overview_20240920-FYOS.pdf]]
|-
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|CSP seminar - Fall 2024||Out-Reach||[[Media:GACRC_overview_20240820-CSP.pdf]]
|-
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
| BCMB8330 - Spring2024||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330_Spring2024.pdf]]
|-
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|PHYS4601/6601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys4601.pdf]]
|-
|-
| The Center for Simulational Physics || Out-Reach || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|PHYS8601 - Spring2024||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601-Spring2024.pdf]] ; [[Media:Gacrc_handout2024_phys8601.pdf]]
|-
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|CSP seminar - Fall 2023||Out-Reach||[[Media:GACRC_overview_20230822-CSP.pdf]]
|-
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|BCMB8330 - Spring2023||In-Class||[[Media:GACRC-Teaching-cluster-new-user-training-workshop_bcmb8330.pdf]]
|-
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|PHYS4601/6601 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2023_phys4601.pdf]]
|-
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|PHYS8602 - Spring2023||In-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] ; [[Media:Gacrc_handout2023_phys8602.pdf]]
|-
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|ILS GradFIRST course - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220901-ILS.pdf]]
|-
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|FYOS1001 - Fall 2022||Out-Reach||[[Media:High_Performance_Computing_(HPC)_on_GACRC_Sapelo2_Cluster.pdf]]
|-
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|CSP seminar - Fall 2022||Out-Reach||[[Media:GACRC_overview_20220830-CSP.pdf]]
|-
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|CSP seminar - Fall 2022||Out-Reach||[[Media:Compile_and_Run_HPC_code_on_Sapelo2.pdf]]
|-
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.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.
'''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]]

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

Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=Training&oldid=22169"