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Local Workshops

The UA High Performance Computing (HPC) offers introductory workshops for students and faculty. The workshops aim to introduce users to the computational resources offered by UA HPC and provide users with the basic knowledge and skills they might need to use UA HPC systems. 

We currently offer HPC workshops in 50-minute and 90-minute formats. The 50-minute workshop introduces users to the resources of UA HPC and the 90-minute workshop includes a practical exercise of working with the HPC system. Additional topics relevant to the specific group of users (e.g. X-forwarding, Python virtual environments, working with Matlab etc.) can be covered by request. 

We strongly advise for all the attendees to obtain an HPC account prior to the workshop. It is also desirable for the Windows users to download and install Putty (ssh client and terminal emulator) and WinSCP (program for secure data transfer). Both application are available for the free download from the UA software license website:
https://softwarelicense.arizona.edu/ssh-clients-windows-and-mac

The 50-minute UA HPC Introduction workshop covers the following topics:
-       Brief description of the UA HPC computing and storage resources
-       Requesting an HPC account
-       Accessing the HPC system
-       Data transfer between local and UA HPC storage
-       Using software on the HPC system with environment modules
-       Batch jobs and scheduler (PBS)
-       Writing a PBS script
-       UA HPC documentation and support


Additional topics covered in 90-minute workshop:
-       Basic commands for working within Linux environment
-       Running a batch job on the HPC system
-       Checking a status of the batch job
-       Reading standard output and standard error files
-       Modifying parameters in the PBS script for a multicore batch job


Extensive Training Courses

We have linked to relevant training courses from other institutions.  
Rather than recreate them we recommend that you access them directly.
Here is a partial list from each site:
Cornell Virtual Workshops

  • Introduction to Linux
  • Introduction to C Programming
  • Introduction to Fortran Programming
  • Introduction to Python
  • Introduction to R
  • MATLAB Programming
  • Introduction to GPU and CUDA
  • Parallel Computing Courses including MPI and OpenMP
  • Code Improvement
  • Data Management including Globus, HDF5 and VisIt

CyberInfrastructure Tutor from NCSA

  • Debugging Code
  • MPI
  • Introduction to Performance Tools
  • Introduction to Visualization
  • Parallel Computing

Software Carpentry

  • The Unix Shell
  • Version Control with Git
  • Using Databases and SQL
  • Programming with Python
  • Programming with R
  • Programming with MATLAB
  • Automation and Make




Linux Self Guided 

We run RHEL/CentOS 6 Linux on our high-performance systems.

If you have never used Linux before or have had very limited use, read this useful guide:

http://www.ee.surrey.ac.uk/Teaching/Unix/


If you have learned Linux in the past but want a quick reference to the syntax of commands, then read this:

Bash Cheat Sheet






Intel® Modern Code Training

Intel brought a workshop to campus in 2014 and the material is covered here.  If you want to do any work on the Intel® Xeon Phi™ Coprocessors we have 40 of them installed in ElGato.  You can obtain "standard" queue access and can request access to the nodes with them installed. 

Created by Colfax International and Intel, and based on the book, Parallel Programming and Optimization with Intel® Xeon Phi™ Coprocessors, this short video series provides an overview of practical parallel programming and optimization with a focus on using the Intel® Many Integrated Core Architecture (Intel® MIC Architecture).

Length: 5 hours

Parallel Programming and Optimization with Intel Xeon Phi Coprocessors

https://software.intel.com/en-us/modern-code/training/short-video-series?utm_source=HPCwire&utm_medium=newsletter_2&utm_content=HPC_Developers&utm_campaign=DRD_16_80


Intel® Software Tools

Intel offers the Cluster Studio XE.  On Ocelote we have installed modules (module avail intel ) as:

  • intel-cluster-checker/2.2.2

  • intel-cluster-runtime/ia32/3.8

  • intel-cluster-runtime/intel64/3.8

  • intel-cluster-runtime/mic/3.8

We have installed the Intel high performance libraries (module avail intel ):

  • Intel® Threading Building Blocks
  • Intel® Integrated Performance Primitives
  • Intel® Math Kernel Library
  • Intel® Data Analytics Acceleration Library

The University is licensed and has access to this toolset separate from HPC.   Portions of it are FREE for use in teaching/instruction and to students.   

https://software.intel.com/en-us/qualify-for-free-software

https://software.intel.com/en-us/server-developer

 





Introduction to OpenMP


This PDF file is a presentation from a series called Xsede*  HPC Workshop.

* XSEDE, the Extreme Science and Engineering Discovery Environment, is the most advanced, powerful, and robust collection of integrated digital resources and services in the world. It is a single virtual system that scientists and researchers can use to interactively share computing resources, data, and expertise. XSEDE integrates the resources and services, makes them easier to use, and helps more people use them.





Singularity


Singularity containers let users run applications in a Linux environment of their choosing.  This is different from Docker which is not appropriate for HPC due to security concerns.  Singularity is like a container for Docker images, but is not just for Docker.  

The most important thing to know is that you create the singularity container called an image on a workstation where you have root privileges, and then transfer the image to HPC where you can execute the image. If root authority is an issue then the answer might be a virtual environment on your laptop, like Vagrant for MacOS

For an overview and more detailed information refer to:
http://singularity.lbl.gov

Here are some of the use cases we support using Singularity:

  • You already use Docker and want to run your jobs on HPC
  • You want to preserve your environment so that a system change will not affect your work
  • You need newer or different libraries than are offered on HPC systems
  • Someone else developed the workflow using a different version of linux
  • You prefer to use something other than Red Hat / CentOS, like Ubuntu 

There are some tutorials located at this link

Tutorials


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