Training: Difference between revisions
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|Using Sapelo2 Cluster at the GACRC|| | |Using Sapelo2 Cluster at the GACRC||August 5th, Friday, 1:00 PM - 2:30 PM | ||
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|Using Sapelo2 Cluster at the GACRC|| | |Using Sapelo2 Cluster at the GACRC||August 11th, Thursday, 1:00 PM - 2:30 PM | ||
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|Using Sapelo2 Cluster at the GACRC|| | |Using Sapelo2 Cluster at the GACRC||August 17th, Wednesday, 1:00 PM - 2:30 PM | ||
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|Use Linux on Cluster|| | |Use Linux on Cluster||August 3rd, Wednesday, 1:00 PM - 3:00 PM | ||
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|Use Linux on Cluster|| | |Use Linux on Cluster||August 9th, Tuesday, 1:00 PM - 3:00 PM | ||
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|Use Linux on Cluster|| | |Use Linux on Cluster||August 15th, Monday, 1:00 PM - 3:00 PM | ||
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|Sapelo2 Cluster Advanced Topics|| | |Sapelo2 Cluster Advanced Topics||Not scheduled in August | ||
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|Python Basics I||Not scheduled in | |Python Basics I||Not scheduled in August | ||
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|Python Basics II||Not scheduled in | |Python Basics II||Not scheduled in August | ||
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|Conda Basics||Not scheduled in | |Conda Basics||Not scheduled in August | ||
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Revision as of 09:53, 19 July 2022
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 2022, the GACRC is hosting eight training sessions (Sapelo2 cluster new user training, Linux basics, and Python basics).
We offer:
1. Linux training for Linux-inexperienced cluster new users (3 sessions)
2. Sapelo2 cluster new user training (3 sessions)
3. Python basics (2 sessions)
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. The instructional videos are required to be viewed prior to the training workshop, and they can be found here
Prerequisites:
- Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
Video Playlist Training Goals:
- Understand the layout of Sapelo2
- Understand the Sapelo2 file systems
- Understand the Sapelo2 partitions
- Understand the Sapelo2 software environment
Workshop Training Goals:
- 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 | August 5th, Friday, 1:00 PM - 2:30 PM |
| Using Sapelo2 Cluster at the GACRC | August 11th, Thursday, 1:00 PM - 2:30 PM |
| Using Sapelo2 Cluster at the GACRC | August 17th, Wednesday, 1:00 PM - 2:30 PM |
Linux Training for Linux-inexperienced Cluster New Users
Prerequisite: No prerequisites
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 | August 3rd, Wednesday, 1:00 PM - 3:00 PM |
| Use Linux on Cluster | August 9th, Tuesday, 1:00 PM - 3:00 PM |
| Use Linux on Cluster | August 15th, Monday, 1:00 PM - 3:00 PM |
Sapelo2 Cluster Advanced Topics
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. Understand HPC Conceptual Framework
2. Investigate Sapelo2 HPC resources by using sinfo, sinfo-nodes, scontrol show, sacctmgr show, etc.
3. Understand how to request computing resources on memory, CPU cores, and GPU device for your jobs
4. Understand how to use local scratch storage to improve job IO performance
5. Learn about new MPI libraries and how to compile/run MPI jobs on Sapelo2
| Title | Date/Time |
|---|---|
| Sapelo2 Cluster Advanced Topics | Not scheduled in August |
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 in August |
| Python Basics II | Not scheduled in August |
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 in August |
| R Basics II | Not scheduled in August |
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 in August |
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: Sapelo2 Cluster Advanced Topics
Focus: More advanced topics on how to use Sapelo2 cluster
Understand HPC Conceptual Framework
Investigate Sapelo2 HPC resources by using sinfo, sinfo-nodes, scontrol show, sacctmgr show, etc.
Understand how to request computing resources on memory, CPU cores, and GPU device for your jobs
Understand ow to use local scratch storage to improve job IO performance
Learn about New MPI libraries 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_v10.7.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_v5.2.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
Out-Reach/On-Class Talk
NOTE: The slides may become outdated and you should always check GACRC Wiki for up to date information.