Mathematica
Overview
Mathematica is an integrated technical computing environment which combines numeric and symbolic compute engines, a graphics system, a programming language, a documentation system and connectivity to other programs. Mathematica may be used for handling complex symbolic calculations involving millions of terms, analyzing and visualizing data, numerical modeling and simulation, rapid application development, producing publication-quality output and presentations.
Version 11.2.0 and 11.3.0 are currently installed on the CSF.
Set up procedure
To set up the Mathematica environment you need to issue one of the following commands
module load apps/binapps/mathematica/13.2.1 module load apps/binapps/mathematica/12.2.0 module load apps/binapps/mathematica/11.3.0 module load apps/binapps/mathematica/11.2.0
Running the application interactively
To run Mathematica interactively you should first log into the CSF using the -X switch as follows
ssh -X -l username csf3.itservices.manchester.ac.uk
Next, load the Mathematica modulefile
module load apps/binapps/mathematica/13.2.1
Finally, run Mathematica via qrsh
qrsh -l short -V mathematica
- Further information about how to start X-Windows and GUI applications on the CSF.
- More details concerning qrsh
Serial batch job submission
It is not possible to run Mathematica .nb files in batch mode. Instead, you must create a text-only file containing your Mathematica program. For example, create a text file called input.m containing the following
Table[
NIntegrate[Sin[x^n], {x, 1, 10}, MaxRecursion -> 1000]
, {n, 1, 70}]
A suitable SGE submission script, mathematica_job.sge, for the above would be
#!/bin/bash --login #$ -cwd #$ -V module load apps/binapps/mathematica/13.2.1 math -noprompt < input.m > out.txt
Note that the executable that runs your script is math (i.e. the Mathematica Kernel) and not mathematica (The notebook interface)
To run the above job you should then use qsub
qsub mathematica_job.sge
Parallel batch job submission
A parallel version of input.m is
LaunchKernels[4];
ParallelTable[
NIntegrate[Sin[x^n], {x, 1, 10}, MaxRecursion -> 1000], {n, 1, 70}] // AbsoluteTiming
CloseKernels[];
A suitable submission script is
#!/bin/bash --login #$ -cwd #$ -pe smp.pe 4 module load apps/binapps/mathematica/13.2.1 export OMP_NUM_THREADS=$NSLOTS math < input.m > out.txt
Note that the only difference is the -pe switch. Job submission is similar to that of serial jobs: use qsub.
Using ‘Export’ in batch job to create an image file
A simple .m file example
Export["testred.png", Graphics@{Red, Disk[{0, 0}, 1]}];
Issue
If you receive the following error:
The 'Export' option relies on the linux DISPLAY variable which is not available to a batch job and results in errors similar to:
Qt issued a fatal error: QXcbConnection: Could not connect to display localhost:21.0
Aborted "${MathematicaFE}" -topDirectory "${TopDirectory}" "$@"
and an empty image file, try the following jobscript.
Solution
Use a utility called xvfb-run. An example batch script:
#!/bin/bash --login #$ -cwd module load apps/binapps/mathematica/13.2.1 xvfb-run math -noprompt < input.m > out.txt