View source for Running Mathematica on compute nodes

Here are some instructions on how to run Mathematica on the cluster. 

=== Step 1. ===

Load the mathematica module:

<pre>
>>module load astro
>>module load mathematica
</pre>

=== Step 2. ===

Prepare our test script. You can make mathematica scripts in different ways, but .wls files are good option. Here is an example script, you can make it into a file called <code>test.wls</code>:

<pre>
#!/usr/bin/env wolframscript
outdir = "Data/";
fn1 = outdir<>"test.dat";
values = Table[{x, x^2},{x,0,1,0.1}];
Export[fn1, values, "Table"];
</pre>

=== Step 3. ===

Now prepare your bash script to submit the job. Here's a template:

<pre>
#!/bin/bash
#SBATCH --job-name=math_test     # shows up in the output of squeue
#SBATCH --time=00:59:00          # specify the requested wall-time
#SBATCH --partition=astro3_devel # specify the partition to run on
#SBATCH --ntasks=1               # number of tasks
#SBATCH --cpus-per-task=1        # number of OpenMP threads per MPI rank
#SBATCH --threads-per-core=1     # number of threads active per CPU core (=1: Hyperthreading off)
# Make sure that Mathematica is loaded

module load astro
module load math

# Set up port forwarding so that Mathematica finds the license

ssh astro01.hpc.ku.dk -L16286:mathlm.nbi.dk:16286 -L16287:mathlm.nbi.dk:16287 -Nf

# Execute the code

wolframscript stupid_test.wls

# Make sure that the ssh tunnel is killed

pkill -fu $USER astro01
</pre>

Now you are ready to submit your job and have fun. Before submitting, make sure you create the directory <code>>>mkdir Data</code>. If it runs successfully, you will see a <code>Data/test.dat</code> file.