Mathematica
Mathematica is technical computing software from Wolfram.[1][2]
Installed Versions
Picotte
'Mathematica 12.3, 13.0, and 13.2 are installed on Picotte. Use the appropriate modulefile:
mathematica/12.3
mathematica/13.0
mathematica/13.2
Activation
Each user must activate Mathematica for themselves, even though everyone uses the same installation. This will be a one-time process, but will have to be repeated for each new version of Mathematica.
- Create a Wolfram ID using your
@drexel.eduemail address at https://user.wolfram.com beforehand which gives access to Wolfram Alpha cloud resources. It also gives you an Activation Key which you will use in the following steps.- After registration, go to: https://user.wolfram.com/portal/myProducts.html
- Near the bottom of that page is a section “My Products and Services” which should show “Mathematica for Sites” and a download link “Get downloads” in the same line. Click on the “Get downloads” link and you will be on an information page for “Mathematica for Sites”: you just need the Activation Key (a string of text) from that page. You DO NOT need to download anything.
- Run the "
math" command after loading the module.
[juser@picotte001 ~]$ module load mathematica
[juser@picotte001 ~]$ math
Mathematica 13.2.0 Kernel for Linux x86 (64-bit)
Copyright 1988-2022 Wolfram Research, Inc.
Mathematica 13.2.0 Kernel cannot find a valid password.
For automatic Web Activation enter your activation key
(enter return to skip Web Activation): [enter/paste your activation key here]
Automatic Web Activation received a password.
Creating password file entry in:
/home/juser/.Mathematica/Licensing/mathpass
In[1]:=
Documentation and Training
Documentation is provided within the application, and also online at http://reference.wolfram.com
There are also online training courses provided by Wolfram: http://www.wolfram.com/training/courses/ Of particular interest, is "HPC: Introduction to HPC and Grid Computing."
Using Mathematica on Picotte
You can use Mathematica interactively, or non-interactively.
Interactive Use
You can use Mathematica interactively on either login node. However, for "heavier" use, please request an interactive job which will run on one of the compute nodes.
To run on the login node, the instructions above for activating Mathematica will set your environment up for also running Mathematica.
To request an graphical interactive session on a compute node, the process is similar to the one for MATLAB#Interactive_Sessions. The command for the graphical version of Mathematica is (note the capitalization):
Mathematica
To run Mathematica without a GUI, the command is:
math
Non-interactive Use (Job Scripts)
You can use a Wolfram language script,[3] or a Mathematica .m file. We deal with .m files here.
The suggestions here are from Michigan State University's Inst. for Cyber-Enabled Research
You can start with an existing Mathematica notebook. The non-interactive script would just be the input lines. To prepare a script:
- Clear all output cells. Use the "Cell -> Delete All Output" menu item.
- Select all remaining cells, which should only be input cells. Use the "Edit -> Select All" menu item, or a keyboard shortcut.
- Copy the selected cells as "input text": use the "Edit -> Copy As -> Input Text" menu item.
- Paste the copied text into a new text document using your editor of choice. You can do this on your own computer and upload the newly created .m script to Proteus.
Writing Text Output to Files
You can use the ">>" (two greater than signs) operator to create the
file and empty it when created (i.e. overwrite any existing data):
N[Pi, 1000] >>"pi_digits.txt"
And you can keep appending to the file by using the ">>>" (three
greater than signs) operator:
N[Pi, 25] >>>"pi_digits.txt"
N[Pi, 50] >>>"pi_digits.txt"
N[Pi, 75] >>>"pi_digits.txt"
Consult Mathematica documentation for more complex output handling using
i/o streams and Write[].[4]
Writing Graphical Output to Files
You can export plots to files with the Export[] function:
Export[ "sine_result.svg", Plot[ Sin[ x ], { x, 0, 2*Pi } ] ]
For publication-ready plots, use a vector-based format such as SVG, PS (PostScript), or PDF.
Parallel Execution
Mathematica kernels can run multithreaded on multi-core machines. The default behavior is to use all available cores. That number depends on the specific machine assigned to the job.
Use the "sinfo_detail -p def" command in the shell to see a list of
all nodes in the def partition in Picotte; the "CPUS" column shows the
number of cores. Remove the "-p def" to see all nodes in all
partitions.
[juser@picotte001 ~]$ module load slurm_util
[juser@picotte001 ~]$ sinfo_detail -p def
NODELIST NODES PART STATE CPUS S:C:T GRES MEMORY FREE_MEM TMP_DISK CPU_LOAD REASON
node001 1 def* draining@ 48 4:12:1 (null) 192000 83516 864000 13.73 maint
node002 1 def* mixed 48 4:12:1 (null) 192000 186742 864000 3.04 none
node003 1 def* allocated 48 4:12:1 (null) 192000 100872 864000 48.08 none
node004 1 def* draining@ 48 4:12:1 (null) 192000 75582 864000 16.19 Drained by CMDaemon
node005 1 def* mixed 48 4:12:1 (null) 192000 186622 864000 3.01 none
node006 1 def* allocated 48 4:12:1 (null) 192000 4399 864000 48.04 none
node007 1 def* allocated 48 4:12:1 (null) 192000 1226 864000 48.05 none
...
node070 1 def* allocated 48 4:12:1 (null) 192000 170831 864000 48.06 none
node071 1 def* allocated 48 4:12:1 (null) 192000 172282 864000 48.02 none
node072 1 def* allocated 48 4:12:1 (null) 192000 106453 864000 48.06 none
node073 1 def* allocated 48 4:12:1 (null) 192000 31668 864000 48.27 none
node074 1 def* allocated 48 4:12:1 (null) 192000 51996 864000 21.00 none
Cluster Integration
TBA
Example Job Script
See: Slurm - Job Script Example 09 Mathematica
References
[1] Wolfram Mathematica website
[2] CoE - Mathematica and Wolfram Alpha Pro at Drexel
[3] Wolfram Language & System Documentation: Wolfram Language Scripts Tutorial