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--- doku:machine_file [2014/08/06 10:17] – ir
+++ doku:machine_file [2014/08/12 09:57] – removed ir
@@ Line 1: / Line 1: @@
-====== Starting fewer MPI processes per node than slots available ======
-===== Modifying the machine file =====
-==== Manually modifying the machine file ====
-In cases when not all CPUs of one node are required, the machines file can be modified to guarantee the right behaviour of mpirun. The $TMPDIR/machines file on VSC-1 consists of a number of machine/node names. Each name stands for one CPU on the given machine/node. For an exclusive job on 2 nodes the machine file looks like:
-<code>
-r10n01
-r10n01
-r10n01
-r10n01
-r10n01
-r10n01
-r10n01
-r10n01
-r12n10
-r12n10
-r12n10
-r12n10
-r12n10
-r12n10
-r12n10
-r12n10
-</code>
-For running a job on less than eight cores the $TMPDIR/machines file has to be replaced within the job script:
-<code>
-#$ -N test
-#$ -pe mpich 16
-NSLOTS_PER_NODE_AVAILABLE=8
-NSLOTS_PER_NODE_USED=4
-NSLOTS_REDUCED=`echo "$NSLOTS / $NSLOTS_PER_NODE_AVAILABLE * $NSLOTS_PER_NODE_USED" | bc  `
-echo "starting run with $NSLOTS_REDUCED processes; $NSLOTS_PER_NODE_USED per node"
-for i in `seq 1 $NSLOTS_PER_NODE_USED`
-do
-	uniq $TMPDIR/machines >> $TMPDIR/tmp
-done
-sort $TMPDIR/tmp  > $TMPDIR/myhosts
-cat $TMPDIR/myhosts
-mpirun -machinefile $TMPDIR/myhosts -np $NSLOTS_REDUCED sleep 2
-</code>
-The reduced form would look like:
-<code>
-r10n01
-r10n01
-r10n01
-r10n01
-r12n10
-r12n10
-r12n10
-r12n10
-</code>