High Performance Computing

The information here is applicable to LSU HPC and LONI systems.

h4

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
2. ~/.bashrc (interactive login only)
3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.

h3

Types of request

Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:

• The user's home directory
• Software packages installed here will be accessible only to the user.
• It is suitable for software packages that will be used by a single user.
• Python, Perl and R modules should be installed here.
• /project
• Software packages installed in /project can be accessed by a group of users.
• It is suitable for software packages that
  • Need to be shared by users from the same research group, or
  • are bigger than the quota on the home file syste.
• This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
• /usr/local/packages
• Software packages installed under /usr/local/packages can be accessed by all users.
• It is suitable for software packages that will be used by users from multiple research groups.
• This type of request must be sent by the PI of a research group.

h3

How to request

Please send an email to sys-help@loni.org with the following information:

• Your user name
• The name of cluster where you want to use the requested software
• The name, version and download link of the software
• Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
• Why the software is needed
• Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.

Please note that, once the software is installed, testing and validation are users' responsibility.

Transcribed but not verified

It is particularly easy to download Cactus using the GetCactus script.

Option 1:

1. Add +cactus to ~/.soft
2. Issue the resoft command
3. Run: GetCactus

                   -------------------------
                   Installer for Cactus Code
                   -------------------------
 
 This installer guides you through checking out the core (flesh)
 and modules (thorns) of the Cactus Code from the Cactus CVS server.
 
 For a description of the checkout procedure, and how to use this
 script, type  
 
               ./GetCactus -help
 
 The latest release of the Cactus Code (flesh and thorns) can also
 be obtained as a tar file from our web site at
 
             http://www.cactuscode.org
 
 For more information please contact cactusmaint@cactuscode.org
 
 --------------------------------------------------------------------
 
 Directory for Cactus installation [Cactus] : 
 
 Anonymous Flesh checkout? (y)es, n)o, h)elp) [yes] : 
 
 Checkout Flesh from
   [1] Last stable release
   [2] Standard development version (bug fixes/unstable)
 Choose version: (1-2, h)elp, q)uit) [1] : 1
 
 
 Verbose checkout (y)es, n)o, h)elp) [no] : yes
  
 --------------------------------------------------------------------
 
 Checking out Cactus Flesh
  (CVS repository: :pserver:cvs_anon@cvs.cactuscode.org:/cactus)
 cvs checkout: Updating Cactus
 U Cactus/CONTRIBUTORS
 U Cactus/COPYRIGHT
 #.... more output follows

At this point, a fresh copy of Cactus will be in the Cactus directory of your present working directory.

Option 2:

Use a browser to download the code from:

http://www.cactuscode.org/old/Download/CVS.html

Usage

After downloading Cactus, copy the configuration file to your Cactus directory:

$ cp /usr/local/packages/Cactus/share/cactus-eric-mvapich-optimise.options \
  ~/Cactus

Create a "thorn list" as described in the Cactus manual, or copy the thorn list for the Cactus WaveToy example:

$ cp /usr/local/packages/Cactus/share/cactus-wavetoy.thornlist ~/Cactus

Build a Cactus configuration, including the additional components you added:

 cd ~/Cactus
 make wavetoy-config options=cactus-eric-mvapich-optimise.options \
      THORNLIST=cactus-wavetoy.thornlist
 make wavetoy -j2

Submit Cactus jobs through PBS. A sample script looks like this:

 #! /bin/bash
 #PBS -A loni_numrel1
 #PBS -q checkpt
 #PBS -r n
 #PBS -l walltime=2:00:00
 #PBS -l nodes=16:ppn=4
 #PBS -V
 #PBS -N wavetoy
 #PBS -m abe
 #PBS -o Cactus/wavetoy.out
 #PBS -e Cactus/wavetoy.err
 
 set -e                          # Abort on errors
 cd Cactus
 
 MPICHDIR=/usr/local/packages/mvapich-0.98-intel9.1
 time ${MPICHDIR}/bin/mpirun -np 64 -machinefile ${PBS_NODEFILE}  \
      /bin/env OMP_NUM_THREADS=1 exe/cactus_wavetoy               \
      -L 3 ${HOME}/Cactus/arrangements/CactusWave/WaveToyC/par/wavetoyc_rad.par

Modify this script for your purposes, replacing e.g. the name of your allocation. A template for a more powerful job submission script for Cactus is also available at:

$ cp /usr/local/packages/Cactus/share/cactus-eric-mvapich.submit ~/Cactus