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Tutorials

HPC@LSU invites you to attend our weekly training scheduled every Wednesdays, except university holidays. All training sessions are from 9:00AM to 11:00AM at 307 Frey Computing Services Center. The sessions will be available on WebEx for remote participants and will be recorded for later review.

The training sessions are subject to cancellation due to lack of registrations, so please register if you plan on attending. Registration closes in the afternoon on the day prior to the training.

Click on the tutorial topic to obtain more information and registration details. WebEx remote connect links to attend the training will be provided via email to all registered participants.

Note: The Slide and Support Materials links are placeholders until content is added after the tutorial.

Spring 2016 Training Schedule

1. February 17,2016: Basic Shell Scripting

TopicBasic Shell Scripting
DateFebruary 17,2016
Time9:00 AM - 11:00 AM
Place307 Frey
DescriptionFor anyone who works in a Linux/Unix environment, a working knowledge of shell scripting is essential and will boost their efficiency and productivity tremendously. For this tutorial, we will focus on bash as it is one of the most popular shells. This tutorial will include topics such as creating simple bash scripts, flow control, command line arguments, regex, grep, awk and sed. This is a practical tutorial, so we will provide examples and/or hands-on exercises for most of the covered materials.

Prerequisites
  • LONI or LSU HPC account
  • Familiarity with Linux/Unix
  • Editors such as vi or emacs
  • SSH client such as Putty for Windows

Slides
Downloads_1 Downloads_2
RegistrationClick Here

2. February 24,2016: Introduction to OpenFOAM

TopicIntroduction to OpenFOAM
DateFebruary 24,2016
Time9:00 AM - 11:00 AM
Place307 Frey
DescriptionOpenFOAM is a free, open source Computational Fluid Dynamics (CFD) software package developed by OpenCFD Ltd at ESI Group and distributed by the OpenFOAM Foundation. This training will provide a breif introduction to OpenFOAM and how to use OpenFOAM under HPC environment. No prior knowledge of OpenFOAM, C++ or Linux is required but some basic knowledge of Linux and programming is beneficial.
Prerequisites:
  • Access to a computer with OpenFOAM (2.x.x preferred) installed.
  • LONI cluster QuenBee and LSU HPC cluster Super Mike II will have OpenFOAM installed
  • Training accounts will be provided to in person attendees only

Slides
Recordings
Downloads
RegistrationClick Here

3. March 2,2016: Introduction to R

TopicIntroduction to R
DateMarch 2,2016
Time9:00 AM - 11:00 AM
Place307 Frey
DescriptionR is a powerful language for data analysis. In this tutorial, you will learn the basics of R, including language fundamentals, basic programming and data visualization. A few examples of using R to process real-life data will be presented as well.
Prerequisites
  • Basic understanding of any programming language.

Slides
RegistrationClick Here

4. March 9,2016: Introduction to Python

TopicIntroduction to Python
DateMarch 9,2016
Time9:00 AM - 11:00 AM
Place307 Frey
DescriptionThis training will provide a brief introduction to the python programming language, introduce you to some useful python modules for system management and scientific computing.

Prerequisites

Slides

RegistrationClick Here

5. March 16,2016: Introduction to IPython

TopicIntroduction to IPython
DateMarch 16,2016
Time9:00 AM - 11:00 AM
Place307 Frey
Description
RegistrationClick Here

6. March 30,2016: Distributed Job Execution

TopicDistributed Job Execution
DateMarch 30,2016
Time9:00 AM - 11:00 AM
Place307 Frey
DescriptionWhile the steadily increasing core counts of modern day processors continue to favor large-scale distributed and multi-threaded applications, the demand for serial processing has surged as non-traditional fields, such as computational biology, increasingly adapt computational methods. This presents a problem on clusters tuned for massively parallel processing. One solution is to tune the job scheduler to carve out resources primarily for serial jobs which complicates system management. The other, taken here, is to adapt existing shell features to facilitate running many essentially embarrassingly parallel tasks under one job script. Running tasks in the background works well for small numbers of tasks, but recent requirements for managing 10's of thousands of such tasks required a better approach – motivating the creation of WQ. It consists of a Python script that implements a run-time aware distribution-worker model, a PBS script with an absolute minimum number of moving parts, and a script or command to execute a single task. This presentation reviews existing shell job control features, then discusses the implementation of WQ. Examples will include purely serial, multi-threaded, and small MPI tasks.

Prerequisites
  • Beginner to intermediate level knowledge of shell scripting and PBS job submission is assumed, but not required.

Slides

Supporting materials

RegistrationClick Here

7. April 6,2016: Introduction to OpenMP

TopicIntroduction to OpenMP
DateApril 6,2016
Time9:00 AM - 11:00 AM
Place307 Frey
DescriptionThis tutorials provides an introduction to OpenMP Programming. It is structured to introduce the components of OpenMP in a concise, progressive fashion, so users can begin to apply OpenMP to their codes in a minimum amount of time.
Prerequisites
  • LONI or LSU HPC accounts
  • Understand programming in C, Fortran or C++
  • Examples will be in C or Fortran, Laptop with an SSH client such as Putty.

Slides Downloads
RegistrationClick Here

8. April 13,2016: Xeon Phi Programming

TopicXeon Phi Programming
DateApril 13,2016
Time9:00 AM - 11:00 AM
Place307 Frey
DescriptionIntel Xeon Phi is a coprocessor based on Many Integrated Core Architecture or MIC. Computer codes can be accelerated substantially with Xeon Phi. More importantly, the programming architecture is based on traditional OpenMP and MPI. It is convenient to migrate your current CPU-based OpenMP or MPI codes to Xeon Phi. The recently launched supercomputer SuperMIC at LSU provides hundreds of compute nodes with Xeon Phis. If you want to accelerate your codes on SuperMIC, this is really the training you can not miss. You will learn how to write, compile and run Xeon-phi codes in this two-session training. In the first session, computing features of Xeon phi and its usage in HPC will be introduced. Then we will focus on state-of-the-art Xeon-phi programming, including native mode and offloading. In the second session, we will introduce symmetric processing with both CPU and Xeon phi. Optimizing and debugging codes will be also covered. Finally we will show some examples for running Xeon-phi enabled applications.
Prerequisites
  • OpenMP and MPI parallel computation
  • C or Fortran programming (Either one is fine.)
  • All of the above are assumed but not required.

RegistrationClick Here

9. April 20,2016: HPC in Biology

TopicHPC in Biology
DateApril 20,2016
Time9:00 AM - 11:00 AM
Place307 Frey
Description
RegistrationClick Here

Virtual Images

For benefit of Training particpants who do not have ready access to a Linux machine, we have created a virtual image of CentOS 6.3. You can use this image in lieu of a LONI or LSU HPC account for some, but not all of our training courses. More details about this image and installation instructions are provided here

Past Tutorials

We offer many tutorial sessions for our HPC users both on campus and through the access grid to LSU partners. Topics covered vary from:

  • Introduction to Linux
  • More Linux
  • LaTeX
  • CVS
  • Subversion
  • MPI
  • OpenMP
  • HPC Environment.

To read descriptions or access PDF's of the slides from past tutorials Past Tutorials.