This version is outdated by a newer approved version.This version (2021/12/09 20:20) is a draft.
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Mathematica Batch Jobs
SLURM
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
Example: Parallel Mathematica Task
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
remote kernel connection
The setup follows Local mathematica with remote kernel with the
Shell command to launch kernel:
for VSC3+
/Users/<LOCAL-USERNAME>/Library/tunnel.sh <VSC-USERNAME>@localhost:9998 /opt/sw/x86_64/generic/Mathematica/11.3/bin/math `linkname`
for VSC4
/Users/<LOCAL-USERNAME>/Library/tunnel.sh <VSC-USERNAME>@localhost:9998 /opt/sw/vsc4/VSC/x86_64/generic/Mathematica/12.3.1/bin/math `linkname`
Note that on VSC4, the salloc command [as described on the cc-mathematik.univie.ac.at web link] does not specify the Mathematica license but typically needs a granted reservation.