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mvapich2

About

MVAPICH2 is an implementation of the MPI 2.2 Message Passing Interface standard. It is produced by the Network-Based Computing Labortory, Dept of Computer Science and Engineering, The Ohio State University. It is optimized for use over InfiniBand interconnects and related protocols.

Versions and Availability

Softenv Keys for mvapich2 on supermike2
Machine Version Softenv Key
supermike2 1.9 +mvapich2-1.9-Intel-13.0.0-CUDA-5.0
supermike2 1.9 +mvapich2-1.9-Intel-13.0.0
supermike2 1.9 +mvapich2-1.9-pgi-12.8
▶ Softenv FAQ?

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.

Usage

  1. Set up your .soft file to select the library version, and the compilers you want to use for building and executing your code. Keep in mind that keys take effect in the order they appear. The following shows how to select and MVAPICH2 library and use it with the GNU gcc compiler. Do not simply copy them, as they are subject to change. Use the softenv command to verify them before use.
  2. +mvapich2-1.4-gcc-4.3.2 
    +gcc-4.3.2
    @default
    
  3. The compiler, mpicc, will use gcc and link with mvapich2 with no further ado.
  4. Run with: mpirun_rsh -hostfile $PBS_NODEFILE -np $NPROCS /path/to/executable
  5. An example PBS script can be viewed below.
  6. ▶ Open Example?
    #!/bin/sh
    #
    # No shell commands until PBS setup is completed!
    #
    # Before you submit your job, make sure the following are customized
    # for your particular needs:
    #
    # Provide your allocation code.
    #PBS -A ALLOCATION_CODE
    #
    # "workq" is the default job queue.
    #PBS -q workq
    #
    # Set to your email address.
    #PBS -M EMAIL_ADDRESS
    #
    # Queen Bee uses "ppn=8", all others use "ppn=4"
    #PBS -l nodes=1:ppn=4
    #
    # Set amount of time job may run in hh:mm:ss
    #PBS -l walltime=00:10:00
    #
    # Have PBS pass all shell variables to the job environment
    #PBS -V
    #
    # Send stdout and stderr to named files.
    #PBS -o MPI_test.out
    #PBS -e MPI_test.err
    #
    # Give the job a name to make tracking it easier
    #PBS -N MPI_test 
    #
    # Shell commands may begin here.
    
    # Your executable should either be in your path, or defined explicitly.
    # Here we'll assume a custom program named "hello" that exists in the
    # work directory:
    
    export EXEC=hello
    export WORK_DIR=/work/uname/path
    export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
    cd $WORK_DIR 
    
    # Note that order in which the options appear is important, and the
    # names may have changed since MVAPICH:
    
    mpirun_rsh -np $NPROCS -hostfile $PBS_NODEFILE $WORK_DIR/$EXEC 
    

Resources

Last modified: November 11 2014 16:58:42.