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howto:magma

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howto:magma [2022/03/11 12:28]
wikiadmin 		howto:magma [2024/06/21 15:59] (current)
wikiadmin
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 To request a login shell on a fat node use To request a login shell on a fat node use
  
-  qsub -I -P PROJECTID -q bigmem -l ncpus=4 -W group_list=bigmemq+  qsub -I -P PROJECTID -q bigmem -W group_list=bigmemq  -l select=1:ncpus=4:mpiprocs=4
      
 where you must replace ''PROJECTID'' by //your// project name. where you must replace ''PROJECTID'' by //your// project name.
Line 43: Line 43:
   magma   magma
  
-After you have finished running Magma and exited back to the command shell (the ''fat01'' prompt) simply type ''exit'' to end the interactive session.+After you have finished running Magma and exited back to the command shell (the ''fat0'' prompt) simply use the Ctrl-D key combination to end the interactive session.
  
 +====Example interactive session:====
 +
 +<code bash>
 +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
 +</code>
  
 =====Job Script===== =====Job Script=====
Line 58: Line 69:
 ====Example Job Script==== ====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.
 +
 +<code bash>
 +#!/bin/bash
 +#PBS -N magma-example
 +#PBS -l select=1:ncpus=8:mpiprocs=8
 +#PBS -l walltime=1:30:00
 +#PBS -P PROJECTID
 +#PBS -q bigmem
 +#PBS -W group_list=bigmemq
 +
 +
 +CWD=/mnt/lustre/users/$USER/workingdirectory
 +cd $CWD
 +
 +module load  chpc/math/magma/2.26
 +
 +nproc=`cat $PBS_NODEFILE | wc -l`
 +
 +magma MAGMAPROGTORUN
 +</code>
 +
 +**Note:**
 +
 +  * 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/attic/howto/magma.1646994484.txt.gz · Last modified: 2022/03/11 12:28 by wikiadmin

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