Training
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 September 2019, the GACRC hosts eleven regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics, and using Conda environment for software installation). We will also offer a topical session on plotting graphs using R.
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 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.
5. Basic Graphs in R Brief introduction: Briefly recap how to load data in R. Know how to draw a variety of univariate and bivariate graphs, such as histograms, bar charts, and scatterplots.
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 28th, Wednesday, 1 PM - 3 PM |
| Using Sapelo2 Cluster at the GACRC | September 6th, Friday, 1 PM - 3 PM |
| Using Sapelo2 Cluster at the GACRC | September 11th, Wednesday, 1 PM - 3 PM |
| Using Sapelo2 Cluster at the GACRC | September 20th, Friday, 10 AM - 12 PM |
| Using Sapelo2 Cluster at the GACRC | September 25th, 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 30th, Friday, 10 AM - 12 PM |
| Use Linux on Cluster | September 4th, Wednesday, 1 PM - 3 PM |
| Use Linux on Cluster | September 13th, Friday, 10 AM - 12 PM |
| Use Linux on Cluster | September 18th, Wednesday, 1 PM - 3 PM |
| Use Linux on Cluster | September 27th, Friday, 1 PM - 3 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 | September 13th, Friday, 1 PM - 3 PM |
| Python basics II | September 20th, Friday, 1 PM - 3 PM |
Topical Sessions
Prerequisite: This course will assume little to no background knowledge in R
Training Goal:
1. Understand fundamentals of graph plotting in R
2. Know how to how to load data in R
3. Know how to draw a variety of univariate and bivariate graphs, such as histograms, bar charts, and scatterplots
| Title | Date/Time |
|---|---|
| Basic Graphs in R | September 6th, Friday, 10 AM - 12 PM |
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 | September 27th, 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 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 Workshop20160328 v4.pdf |
| media: Python Language Basics II Workshop20160425 v1.pdf |
Perl Basics
| media: Perl Language Basics I Workshop v1.pdf |
Topical Sessions
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.