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--- hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:charmm:c41b2_mpi [2019/01/08 16:29] – kraus
+++ hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:charmm:c41b2_mpi [2020/02/14 18:11] (aktuell) – kraus
@@ Zeile 1: / Zeile 1: @@
+====== CHARMM c41b2 MPI (built with Intel compiler) ======
+Launch this script shown below by typing: \\
+<file>qsub jobscript_charmm-c41b2_mpi.sh</file>
+<html>
+<span style="font-family:monospace;font-size:115%;white-space:pre;color:red;"> Remark: Evtl. jobs could crash with illegal CPU instructions on some old computing nodes (will be fixed in the future). </span>
+</html>
+\\
+<code bash jobscript_charmm-c41b2_mpi.sh>
+#!/bin/bash --login
+##### example for a serial job with CHARMM c41b2
+#$ -cwd
+##### please define your own job resources
+# time in hh:mm:ss
+#$ -l h_rt=00:30:00
+#$ -l mem_free=500M
+#$ -pe ompi* 4
+### Nehalem???
+#$ -l cputype="!(opteron2*|xeon54*|xeon53*)"
+#$ -N jobname
+#$ -e jobname_err.out
+#$ -o jobname_stdout.out
+#$ -j n
+#$ -m n
+##########
+module unload ompi-gcc-1.5.5
+module load intel/2017.2 ompi-intel-2.1.1
+export PATH=/net/work/kraus/mroginski/charmm/c41b2/exec/em64t_M:$PATH
+# only stdout captured/redirected
+# mpirun charmm -i input.inp -o output.out
+# both stdout and stderr redirected
+mpirun -n $NTASKS charmm -i input.inp > output.out
+</code>
+\\
+<WRAP rightalign>
+date of revision: 02-14-2020 © kraus
+</WRAP>