Biowulf High Performance Computing at the NIH
Mathematica on Biowulf

Mathematica is a fully integrated environment for technical and scientific computing. Mathematica combines numerical and symbolic computation, visualization, and programming in a single, flexible interactive system. The Mathematica system is very broad, and provides a systematic interface to all sorts of computations, from traditional numeric and symbolic computation, to visualization, to data format conversion, and the creation of user interfaces.

Running the Mathematica GUI Interactively

To run the Mathematica graphics interface, an X-Windows connection is required (preferably using Nomachine). Open an X-Windows connection to biowulf.nih.gov, and check that it is working by typing 'xclock' at the prompt.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ module load mathematica
[user@cn3144 ~]$ mathematica &

You should see the Mathematica Welcome Screen as below:

Mathematica Welcome Screen

The main Mathematica Notebook window will appear when you open a file by clicking Open or a file listed on the Welcome screen.

To run a demo, in the main Mathematica window, click Open. Enter the file name /usr/local/apps/Mathematica/11.3/Documentation/English/System/HowTos/Create3DGraphics.nb. You should see a window appear with a mathematica notebook example:

Mathematica demo image

Run Mathematica interactively without the GUI

It is also possible to run Mathematica interactively on the command-line, without the GUI. This would be useful if you do not wish to use Xwindows, and is obviously most useful for calculations rather than interactive graphics. Sample session (user input in bold):

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ math
Mathematica 11.3.0 Kernel for Linux x86 (64-bit)
Copyright 1988-2018 Wolfram Research, Inc.

In[1]:=  data=ReadList["rmsdplot.list",{Number,Number,Number}];

In[2]:= [..enter other Mathematica commands..]

In[22]:= Exit[]
[user@cn3144 ~]$
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$
Run Mathematica using a math command file

You can insert Mathematica commands into a math command file, and run that file interactively at the prompt. This is convenient if you perform the same Mathematica tasks frequently. Let us use the following Math command file test.math.

------------------------ test.math -------------------------------
A = Sum[i, {i,1,100}]
B = Mean[{25, 36, 22, 16, 8, 42}]
Answer = A + B
Print["Answer=", Answer]
Exit[]
-------------------- test.math -----------------------------------

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ math
Mathematica 11.3.0 Kernel for Linux x86 (64-bit)
Copyright 1988-2018 Wolfram Research, Inc.

In[1]:= <<test.math

       30449
Answer=-----
         6

[user@cn3144 ~]$

Alternatively, you can type directly at the command prompt:

[user@cn3144~] math -noprompt -run "<<test.math"
Answer=30449/6
[user@cn3144 ~]
Running Mathematica Jobs on Biowulf

Mathematica provides a seamless, integrated and automated environment for parallel computing. To submit a Mathematica job to the batch system, you must create a .m file containing the mathematica commands. The .m script will be passed to the math command in an sbatch file.

The above example can be sent to batch with the following script:

------------------------ test.sh-------------------------------
#!/bin/bash

module load mathematica

math -run < test.math
--------------------end test.sh -------------------------------

Submit with sbatch test.sh

Documentation

Wolfram Mathematica Documentation Center
Mathematica FAQs