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How To Run Magma on the Cluster

Magma is accessed by first loading the module

module load chpc/math/magma/2.26

and then simply executing the command


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.

Interactive Session

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


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.

Example 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

Job Script

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:

Example Job Script

This example job script requests 8 cores on a fat node, and a maximum wall time (run time) of 1 hour and 30 minutes.

#PBS -N magma-example
#PBS -l select=1:ncpus=8:mpiprocs=8:nodetype=haswell_fat
#PBS -l walltime=1:30:00
#PBS -q bigmem
#PBS -W group_list=bigmemq
cd $CWD
module load  chpc/math/magma/2.26
nproc=`cat $PBS_NODEFILE | wc -l`


  • Replace PROJID with your project name.
  • Always use a working sub-directory in your Lustre directory.
  • Replace workingdirectory with the path of your working directory on Lustre.
  • Replace MAGMAPROGTORUN with the appropriate options and arguments to the magma application.

Save the file, for example as magma1.pbs and then submit to the scheduler with

qsub magma1.pbs

You can check the status of the queue with

qstat -u $USER

which should display something like:

Job id            Name             User              Time Use S Queue
----------------  ---------------- ----------------  -------- - -----  
4088494.sched01   magma-example    username                 0 Q bigmem

The Q under S (for State) indicates that this job is queued and waiting to run. A running job would look like:

Job id            Name             User              Time Use S Queue
----------------  ---------------- ----------------  -------- - -----
4088497.sched01   magma-example    username          00:38:21 R bigmem

with R indicating running state.

username will be replaced by your cluster account user name.
/app/dokuwiki/data/pages/howto/magma.txt · Last modified: 2022/03/25 13:36 by wikiadmin