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--- doku:molecular_dynamics [2020/04/23 19:21]
ir
+++ doku:molecular_dynamics [2021/10/22 09:02] (current)
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@@ Line 148: / Line 148: @@
 ----
-====== COMSOL ======
-----
-===== COMSOL 5.2a =====
-==== Module ====
-<code>
-load module COMSOL/5.2a
-</code>
-----
-===== COMSOL 5.2a =====
-==== Job script threaded version (no MPI) ====
-You can use only one node in this case. Create a job file called ''%%job_smp.sh%%'':
-''%%/opt/ohpc/pub/examples/slurm/mul/comsol%%''
-<code>
-#!/bin/bash
-#
-#SBATCH -J comsol
-#SBATCH -N 1
-#SBATCH -o job.%j.out
-#SBATCH -p E5-2690v4
-#SBATCH -q E5-2690v4-batch
-#SBATCH --ntasks-per-node=28
-#SBATCH --threads-per-core=1
-#SBATCH --time=04:00:00
-#SBATCH --mem=16G
-# Details of your input and output files
-INPUTFILE=micromixer_cluster.mph
-OUTPUTFILE=micromixer.out
-# Load our comsol module
-module purge
-module load COMSOL/5.2a
-# create tmpdir
-TMPDIR="/tmp1/comsol"
-mkdir -p $TMPDIR
-## Now, run COMSOL in batch mode with the input and output detailed above.
-comsol batch -np $SLURM_NTASKS -inputfile $INPUTFILE -outputfile $OUTPUTFILE -tmpdir $TMPDIR
-</code>
-----
-===== COMSOL 5.2a =====
-==== Job script with MPI ====
-You can use more than one node in this case. Create a job file called ''%%job_mpi.sh%%'':
-''%%/opt/ohpc/pub/examples/slurm/mul/comsol%%''
-<code>
-#!/bin/bash
-#
-#SBATCH -J comsol
-#SBATCH -N 2
-#SBATCH -o job.%j.out
-#SBATCH -p E5-2690v4
-#SBATCH -q E5-2690v4-batch
-#SBATCH --ntasks-per-node=28
-#SBATCH --threads-per-core=1
-#SBATCH --time=04:00:00
-#SBATCH --mem=16G
-# Details of your input and output files
-INPUTFILE=micromixer_cluster.mph
-OUTPUTFILE=micromixer.out
-# Load our comsol module
-module purge
-module load COMSOL/5.2a
-module load intel-mpi/2018
-# create tmpdir
-TMPDIR="/tmp1/comsol"
-mkdir -p $TMPDIR
-## Now, run COMSOL in batch mode with the input and output detailed above.
-comsol -clustersimple batch \
--inputfile $INPUTFILE \
--outputfile $OUTPUTFILE \
--tmpdir $TMPDIR \
--mpiroot $MPIROOT -mpi intel -mpifabrics shm:dapl
-</code>
-----
-===== COMSOL 5.2a =====
-==== Submit job ====
-<code>
-sbatch job_xyz.sh
-</code>
-----
-===== COMSOL 5.2a =====
-==== Restarting jobs ====
-To continue your calculation from the last saved state on use the options:
-<code>
--recover -continue
-</code>