Mathematica Batch Jobs

The simplest way is to create a file with your mathematica commands, e.g. 'math-input.m', and just input that in the batch file.

# the following option makes sure the job will run in the current directory
#$ -cwd
# this option makes sure the job has the same environment variables as the submission shell
#$ -V

MATHDIR=/opt/sw/Mathematica/90/bin
$MATHDIR/math < math-input.m

If we name the above file as math-job.sh and place it in the same directory as math-input.m we can submit it from the same directory with

user@l01 $ qsub math-job.sh

The output will be left in file math-job.sh.o$JOB_ID and any errors in math-job.e$JOB_ID.

You could also incorporate mathematica commands in the job file itself, rather then have them in a separate file:

#$ -cwd
#$ -V

MATHDIR=/opt/sw/Mathematica/90/bin

$MATHDIR/math <<END_MATH_COMMANDS
1+1
3*3
END_MATH_COMMANDS

The above notations means that everything between “«END_MATH_COMMANDS” and “END_MATH_COMMANDS” will be used as math program's input. You can again submit this job with qsub.

Jobscript:

#$ -N parallel
#$ -q all.q
#$ -pe mpich 32


# $TMPDIR/machines shows which host machines are reserved for the current job;
# copy this file to a temporary file which will be read in by Mathematica;
# in the following the small Mathematics m-file will start a kernel on each machine;
# since the kernel on the master is already running, it is sufficient
# to start the kernels beginning with the second host in the machines file.

cp -v $TMPDIR/machines machines_tmp

/opt/sw/Mathematica/90/bin/math -run "<<math.m"

Mathematica script named math.m:

(* configuration for starting remote kernels *)

Needs["SubKernels`RemoteKernels`"]
$RemoteCommand= "ssh `1` -n -l `3` \"/opt/sw/Mathematica/90/bin/math -mathlink -linkmode Connect `4` -linkname `2` -subkernel -noinit >& /dev/null &\""


(* initialize the kernels on all machines defined in the host file *)

hosts=Import["machines_tmp","List"] 

(* since the kernel on the master is already running, initialization starts with host 2 *)
imin=2;
imax=Length[hosts];
idelta=1;

Do[
	Print["starting Kernel: ",i," on ",hosts[[i]]];
	LaunchKernels[RemoteMachine[hosts[[i]]]];,
	{i,imin,imax,idelta}
]


(* actual calculation *)
primelist = ParallelTable[Prime[k], {k, 1, 20000000}];
Print[primelist]

In order to be able to use Mathematica, you have to load the program with the module load xyz command

[username@l32]$ module avail  # select a Mathematica version
[username@l32]$ module load Mathematica/10.0.2 # load desired version
[username@l32]$ module list   # check loaded modules
Currently Loaded Modulefiles:
  1) Mathematica/10.0.2  

(See also the introduction to the module command.)

Now, Mathematica can be called by

[username@l32]$ math 

Mathematica script example math-vsc3.m:

GetEnvironment["MATH_BIN"]
math = Environment["MATH_BIN"]
kernelsperhost = 16
hosts=Import["nodelist","List"];



Needs["SubKernels`RemoteKernels`"]
$RemoteCommand = "ssh -x -f -l `3` `1` " <> math <> " -mathlink -linkmode Connect `4` -linkname '`2`' -subkernel -noinit" 


(* first host with one kernel less *)
LaunchKernels[RemoteMachine[hosts[[1]], kernelsperhost-1]];

imin=2;
imax=Length[hosts];
idelta=1;

Do[ 
        LaunchKernels[RemoteMachine[hosts[[i]], kernelsperhost]];
        , {i, imin, imax, idelta}] 

primelist = ParallelTable[Prime[k], {k, 1, 20000000}];
Print[primelist]

sbatch job script jobPar.sh:

#!/bin/bash
#
#SBATCH -J par
#SBATCH -N 2
#SBATCH -L mathematica@vsc


module purge
module load Mathematica/10.0.2 # load desired version


export MATH_BIN=`which math`
#export MATH_PROC=16
scontrol show hostnames $SLURM_NODELIST > nodelist
#execute prolog for getting access to license everywhere
srun hostname


math -run < math-vsc3.m

[username@l32]$ sbatch jobPar.sh      # submit your job
[username@l32]$ squeue -u username    # check state of your job