Training

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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 May 2020, the GACRC hosts eleven remote training sessions (Sapelo2 cluster new user training, Sapelo2 cluster advanced topics, Linux basics and Python basics).

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Topical session: Sapelo2 advanced topics (1 session)


Please Note:

The training will be offered remotely via Zoom meeting. Detailed information on how to join the Zoom meeting will be sent to your UGA email 1 day before the meeting.


Event Schedule

Sapelo2 Cluster New User Training

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

Training Goal:

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

Title Date/Time
Using Sapelo2 Cluster at the GACRC April 28, Tuesday, 10 AM - 12:30 PM
Using Sapelo2 Cluster at the GACRC May 6, Wednesday, 10 AM - 12:30 PM
Using Sapelo2 Cluster at the GACRC May 15, Friday, 10 AM - 12:30 PM
Using Sapelo2 Cluster at the GACRC May 18, Monday, 10 AM - 12:30 PM
Using Sapelo2 Cluster at the GACRC May 29, Friday, 10 AM - 12:30 PM

Linux Training for Linux-inexperienced Cluster New Users

Prerequisite: No prerequisites

Training Goal:

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 April 27, Monday, 10 AM - 12 PM
Use Linux on Cluster May 4, Monday, 10 AM - 12 PM
Use Linux on Cluster May 13, Wednesday, 10 AM - 12 PM
Use Linux on Cluster May 22, Friday, 10 AM - 12 PM
Use Linux on Cluster May 27, Wednesday, 10 AM - 12 PM

Python Basics I/II

Prerequisite: No prerequisites

Training Goal:

1. Python language overview, scientific modules and distributions

2. Understand basic built-in data types, like string, list, tuple, dictionary, etc.

3. Python programming structures: control flow and loop; Python function: procedural programming with examples, lambda expression, factory function and generator

Title Date/Time
Python Basics I May 8, Friday, 10 AM - 12 PM
Python Basics II May 11, Monday, 10 AM - 12 PM


Sapelo2 Advanced Topics

Prerequisite: Sapelo2 cluster user having passed Sapelo2 cluster new user training

Training Goal:

1. Understand Sapelo2 computational queues; how to request computing resources, e.g., how to request and use local scratch on a compute node

2. Topics on running MPI jobs

3. Topics on running GPU jobs

4. How to obtain details of a job, like actual memory and time being used by the job

Title Date/Time
Sapelo2 cluster advanced topics May 20, Wednesday, 10 AM - 12 PM

How to Register

Please Note, the training workshops Using Sapelo2 Cluster at the GACRC and Use Linux on Cluster are ONLY offered to new users who need computing user accounts on the GACRC Sapelo2 cluster, or any current users who have never attended the GACRC Sapelo2 cluster new user training before. Please ask your group PI/UGA faculty member to send us a request for you, using the GACRC User Account Request form at https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839

If you want to attend Python Basics 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 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.


Topic Introduction

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: 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: 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


Title: R Language Introduction

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

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

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

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.


Title: Basic Graphs in R

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Description: This course will assume little to no background knowledge in R

Understand fundamentals of graph plotting in R; Know how to how to load data in R; Learn how to draw a variety of univariate and bivariate graphs, such as histograms, bar charts, and scatter plots

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.


Download

Sapelo2 Cluster Training

media: GACRC Sapelo2 cluster new user training workshop v7.pdf

Teaching Cluster Training

media: GACRC Teaching cluster new user training workshop ver3.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 Workshop v5.pdf
media: Python Language Basics II Workshop v2.pdf

Perl Basics

media: Perl Language Basics I Workshop v1.pdf

Topical Sessions

media: Using GACRC Sapelo2 Cluster-Advanced Topics v2.pdf
media: Using conda on the GACRC Sapelo2 Cluster.pdf
media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf
media: Python on GACRC Computing Resources v1.pdf
media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf
media: Blast Workshop GACRC 02012017.pdf
media: Next-Generation Sequencing Applications at GACRC 10282016.pdf
media: Software installation on zcluster.pdf

Out-Reach/On-Class Talk

Dept./Center/Institute Type Workshop PDF
College of Veterinary Medicine - Spring2020 Out-Reach (jlslab) media: Using GACRC Sapelo2 Cluster-Advanced Topics(1).pdf
Byod Data Center - Fall2019 On-Class (FYOS1001) media: High Performance Computing (HPC) on Cluster.pdf
Department of Linguistics - Fall2019 On-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 On-Class (PHYS4601/6601) media:GACRC Teaching cluster new user training workshop-phys4601.pdf media:Gacrc handout2019 phys4601.pdf
The Center for Simulational Physics On-Class (PHYS8601) media:GACRC Teaching cluster new user training workshop-phys8601.pdf media:Gacrc handout2020 phys8601.pdf
The Center for Simulational Physics On-Class (PHYS8602) media:GACRC Teaching cluster new user training workshop-phys8602.pdf media:Gacrc handout2019 phys8602.pdf
Food Science - Fall2018 On-Class (FYOS1001) media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf
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 On-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 On-class (PHYS4601/6601) media: phys4601.pdf
Computational Physics - Spring2017 On-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 On-Class (MIBO8150) media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf
Statistics On-Class (STAT8060) media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf
Biochemistry and Molecular Biology On-Class (BCMB8211) media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf
Plant Biology On-Class (PBIO/BINF8350) media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf
Plant Biology - Bioinformatics Applications Fall2016 On-Class (PBIO4550) media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf
Bioinformatics - Essential Computing Skills for Biologists Fall2016 On-Class (BINF4005) media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf
Computers in Experimental Genetics Fall2016 On-Class (GENE4220) media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf
Statistics - Advanced Applications and Computing in R Fall2016 On-Class (STAT8330) media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf

NOTE: The slides may become outdated and you should always check GACRC Wiki for up to date information.

Past Sessions

Past Sessions in 2020

Past Sessions in 2019

Past Sessions in 2018

Past Sessions in 2017

Past Sessions in 2016

Past Sessions in 2015