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Revision as of 10:25, 21 March 2019
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 April 2019, the GACRC is going to host twelve regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics, Perl basics) and one topical session on Conda 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. Perl basics (1 session)
4. Conda basics (1 session)
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 | March 25th, Monday, 1:00 PM - 3:00 PM |
| Using Sapelo2 Cluster at the GACRC | April 4th, Thursday, 1:45 PM - 3:30 PM |
| Using Sapelo2 Cluster at the GACRC | April 8th, Monday, 1:00 PM - 3:00 PM |
| Using Sapelo2 Cluster at the GACRC | April 16th, Tuesday, 1:45 PM - 3:30 PM |
| Using Sapelo2 Cluster at the GACRC | April 25th, Thursday, 1:45 PM - 3:30 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 | March 26th, Tuesday, 1:45 PM - 3:30 PM |
| Use Linux on Cluster | April 2nd, Tuesday, 1:45 PM - 3:30 PM |
| Use Linux on Cluster | April 11th, Thursday, 1:45 PM - 3:30 PM |
| Use Linux on Cluster | April 15th, Monday, 1:00 PM - 3:00 PM |
| Use Linux on Cluster | April 23rd, Tuesday, 1:45 PM - 3:30 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 Language Basics I | April 9th, Tuesday, 1:45 PM - 3:30 PM |
| Python Language Basics II | April 18th, Thursday, 1:45 PM - 3:30 PM |
Perl Basics I
Prerequisite: No prerequisites
Training Goal:
1. Understand Perl general scripting style
2. Know how to run how to make a simple perl script and run it on command line
3. Understand Perl language fundamentals, e.g., scalar data and variable, list data and array, scalar and list context
| Title | Date/Time |
|---|---|
| Perl Language Basics I | April 22nd, Monday, 1:00 PM - 3:00 PM |
Topical Sessions
Prerequisite: Regular Sapelo2 users who have user account on the Sapelo2 cluster
Training Goal:
1. Conda environment on Sapelo2
2. How to use conda for configuring your own Python environment on the cluster
| Title | Date/Time |
|---|---|
| Conda Basics on Sapelo2 | April 29th, Monday, 1:00 PM - 3:00 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 cluster and batch job workflow
Cluster's storage environment
Computing queues on cluster
Software environment
Batch job workflow, how to submit a computational batch job
Other tips and guidelines for Sapelo2 users
Title: Use Linux on Cluster
Focus: Linux OS fundamentals
Linux common command, filesystem, and shell
Linux shell scripting
Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.
Linux Hands-on practice
Title: Python Language Basics I, II
Focus of I: Overview of Python language, scientific modules and distributions
General Lexical conventions
Basic built-in data types
Focus of II: Program structure: control flow and loop
Function: procedural and functional programming with examples
Title: Python on GACRC Sapelo2 Cluster
Focus: Installation of Python packages/modules on Sapelo2 cluster
How to know Python versions installed on Sapelo2
How to know Python environment details on Sapelo2
How to know if a Python package is installed or not on Sapelo2
How to install a Python package in user's 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 v5.1.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 02202019.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 | 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.