Magma is accessed by first loading the module

module load chpc/math/magma/2.26

and then simply executing the command

magma

However, Magma is licensed software and only licensed to run on the large memory nodes (usually called the “fat” nodes).

You will thus need to request a fat node using qsub for an interactive session or by submitting a job script.

To request a login shell on a fat node use

qsub -I -P PROJECTID -q bigmem -W group_list=bigmemq  -l select=1:ncpus=4:mpiprocs=4:nodetype=haswell_fat

where you must replace PROJECTID by your project name.

If you receive the error message:

qsub: Bad GID for job execution

then you do not currently have access to the bigmem queue and must ask your PI to request that access through our Helpdesk.

Otherwise you should see a message similar to

qsub: waiting for job 4068905.sched01 to start

Note: the job ID number (“4068905” in the above example) will be different for you.

Depending on how busy the bigmem queue is you could wait several minutes (or hours) for the session to start — which is why it is preferable to use a job script.

When the interactive session starts you will see that your command line prompt changes from login1 to fat01 (or other fat0N). Now you can load the module as above:

module load chpc/math/magma/2.26

and start Magma with the command

magma

After you have finished running Magma and exited back to the command shell (the fat01 prompt) simply use the Ctrl-D key combination to end the interactive session.

fat04:~$ module load chpc/math/magma/2.26
fat04:~$ magma
Magma V2.26-10    Fri Mar 18 2022 09:59:31 on fat04    [Seed = 3853761563]
Type ? for help.  Type <Ctrl>-D to quit.
> 
 
Total time: 0.399 seconds, Total memory usage: 32.09MB

Please see the CHPC Quick Start Guide and PBSPro Scheduler Guide for information on job scripts and the scheduler used on the CHPC cluster.

This video demonstrates job scripts for the bigmem queue and fat nodes:

• Advanced Jobscripts Demo