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--- howto:magma [2022/03/10 15:10]
wikiadmin created
+++ howto:magma [2024/06/21 15:59] (current)
wikiadmin
@@ Line 9: / Line 9: @@
   magma
-However, Magma is licensed software and only licensed to run on the large memory nodes (usually called the "fat nodes).
+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 of by submitting a job script.
+You will thus need to request a fat node using ''qsub'' for an interactive session //or// by submitting a job script.
-====Interactive Session====
+=====Interactive Session=====
 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.
@@ Line 27: / Line 27: @@
 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 ''fat0''N).  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 ''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=====
+Please see the [[quick:start|CHPC Quick Start Guide]] and [[guide:pbspro|PBSPro Scheduler Guide]] for information on job scripts and the scheduler used on the CHPC cluster.
+===Video===
+This video demonstrates job scripts for the ''bigmem'' queue and fat nodes:
+  * [[https://www.youtube.com/watch?v=ZZc1Iic6bDc| Advanced Jobscripts Demo]]
+====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.

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