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 August 2019, the GACRC hosts twelve regular training sessions (Sapelo2 cluster new user training, Linux basics, and Python) and one hands-on session on using Conda environment for software installation on Sapelo2 cluster.

We offer:

1. Sapelo2 cluster new user training (5 sessions)

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

3. Python basics (2 session)

4. Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly (1 session)

Brief introduction: Conda is an open source package management system and environment management system that you can use to quickly install, run and update Python packages and their dependencies. Since Conda easily creates, saves, loads and switches between environments in your home directory on the Sapelo2 cluster, it will become very easy for you to create and maintain your own software environment for your research needs on the Sapelo2 cluster.

Training Location:

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

120 East Green Street, Athens, GA 30602


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 August 2nd, Friday, 10 AM - 12 PM
Using Sapelo2 Cluster at the GACRC August 9th, Friday, 1 PM - 3 PM
Using Sapelo2 Cluster at the GACRC August 16th, Friday, 10 AM - 12 PM
Using Sapelo2 Cluster at the GACRC August 21st, Wednesday, 1 PM - 3 PM
Using Sapelo2 Cluster at the GACRC August 28th, Wednesday, 1 PM - 3 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 August 9th, Friday, 10 AM - 12 PM
Use Linux on Cluster August 14th, Wednesday, 1 PM - 3 PM
Use Linux on Cluster August 23rd, Friday, 1 PM - 3 PM
Use Linux on Cluster August 30th, Friday, 10 AM - 12 PM

Python Basics I/II

Prerequisite: No prerequisites

Training Goal:

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

Title Date/Time
Python basics I August 16th, Friday, 1 PM - 3 PM
Python basics II August 30th, Friday, 1 PM - 3 PM

Topical Sessions

Prerequisite: Regular Sapelo2 users who have user account on the Sapelo2 cluster

Training Goal:

1. Understand what is Conda and its virtual environment

2. Know how to use conda to create and configure your own python virtual environments in your home directory

3. Know how to activate your environments to run python apps from your home directory

Title Date/Time
Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly August 23rd, Friday, 10 AM - 12 PM


How to Register

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.

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.

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.


Download

Sapelo2 Cluster Training

media: GACRC Sapelo2 cluster new user training workshop v6.pdf

Teaching Cluster Training

media: GACRC Teaching cluster new user training workshop ver2.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 Workshop20160328 v4.pdf
media: Python Language Basics II Workshop20160425 v1.pdf

Perl Basics

media: Perl Language Basics I Workshop v1.pdf

Topical Sessions

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
The Center for Simulational Physics - Fall 2019 Out-Reach (CSP Seminar Talk 20190820) media: Introduction to GACRC Computing Facility - Sapelo2 Cluster.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 (PHYS8602) media:GACRC Teaching cluster new user training workshop-phys8602.pdf media:Gacrc handout2019 phys8602.pdf
Food Science - Fall 2018 On-Class (FYOS1001) media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf
The Center for Simulational Physics - Summer 2018 Out-Reach (CSP Seminar Talk 20180821) media: Introduction to GACRC Sapelo2 cluster.pdf
Miller plant science - Summer 2018 Out-Reach (jlmlab) media: Introduction to GACRC Sapelo2 cluster.pdf
Biochemistry and Molecular Biology - Spring 2018 On-Class (BCMB8330) media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf
The Center for Simulational Physics - Summer 2017 Out-Reach (CSP Seminar Talk 20170831) media: Introduction on HPC Resources at the GACRC.pdf
Computational Physics - Spring 2017 On-class (PHYS4601/6601) media: phys4601.pdf
Computational Physics - Spring 2017 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 (CSP 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 Fall 2016 On-Class (PBIO4550) media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf
Bioinformatics - Essential Computing Skills for Biologists Fall 2016 On-Class (BINF4005) media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf
Computers in Experimental Genetics Fall 2016 On-Class (GENE4220) media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf
Statistics - Advanced Applications and Computing in R Fall 2016 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 2019

Past Sessions in 2018

Past Sessions in 2017

Past Sessions in 2016

Past Sessions in 2015