Differences

This shows you the differences between two versions of the page.

--- howto:magma [2022/03/11 16:13]
wikiadmin
+++ howto:magma [2024/06/21 15:59] (current)
wikiadmin
@@ Line 17: / Line 17: @@
 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
+  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 43: / Line 43: @@
   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=====
@@ Line 58: / Line 69: @@
 ====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.

wiki.chpc.ac.za

User Tools

Site Tools

Differences

Page Tools