High Performance Computing

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

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 SoftEnv. 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.

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

The command softenv will provide a list of available packages. The listing will look something like:

$ 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
... some stuff deleted ...

Managing 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

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.

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

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 SoftEnv. 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.

Module is currently available only on SuperMIC.

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