High Performance Computing

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

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
....

Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

1. packages might be out of sync between what is listed and what is actually available
2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.

Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv

Managing Environment with SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

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