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New Installation
module load comsol/61
(uses matlab/2022b)
OR
module load comsol/56
(uses matlab/2021a)
OR:
module load comsol/55
(It was installed with matlab/2019b)
OLD Installation (old cluster)
========================
module load comsol/4.3
OR
module load comsol/4.3-withMatlab2011a
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Ref: https://www.comsol.com/blogs/how-to-run-simulations-in-batch-mode-from-the-command-line/
ReRef: https://doc.comsol.com/5.5/doc/com.comsol.help.comsol/comsol_ref_running.29.30.html
Ref models: https://www.comsol.com/models
An example is this: comsol batch -inputfile Model1.mph -outputfile Model1_solved.mph
comsol batch -inputfile /sw/comsol/55/multiphysics/demo/builder/thermoelectric_leg.mph -outputfile thermoelectric_leg_solved.mph
Sample pbs script to run a comsol job in batch mode
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#!/bin/bash #PBS -N ComsolJobTest #PBS -m abe #PBS -M YourEmail@griffith.edu.au #PBS -l select=1:ncpus=1:mem=12gb32gb,walltime=0010:50:00 #PBS -q workq module load comsol/5561 echo "Starting job: " cd $PBS_O_WORKDIR comsolbatch##comsol batch -inputfile Model1.mph -outputfile Model1_solved.mph comsol batch -inputfile /sw/comsol/55/multiphysics/demo/builder/thermoelectric_leg.mph -outputfile thermoelectric_leg_solved.mph |
Installation
Use instructions in this manual to install comsol on /sw/comsol/4.3.
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module load comsol/4.3-withMatlab2011a comsol |
Serial batch run
cd ~/data
cp /sw/comsol/4.3/models/COMSOL_Multiphysics/Quantum_Mechanics/conical_quantum_dot.mph .
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module load comsol/4.3 comsol batch -inputfile model_in~/data/conical_quantum_dot.mph -outputfile modelconical_quantum_dot_out.mph |
##model_in.mph is the name of your model. Change it to your model name. If output model name is not specified, results will be written to the model specified in input switch
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#PBS -m abe #PBS -M emailID@griffith.edu.au #PBS -N TestRun_Comsol #PBS -l select=1:ncpus=1:mem=7g,walltime=24:00:00 cd $PBS_O_WORKDIR module load comsol/4.361 comsol batch -inputfile model_in~/data/conical_quantum_dot.mph -outputfile modelconical_quantum_dot_out.mph |
Batch run- parallel
The parallel sections of Comsol are based on the parallel shared memory model. The solvers, assembly and meshing in Comol Multiphysics and the linear algebra functions in Comsol script benefit from parallelism
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##!/bin/bash #PBS -m abe #PBS -M emailID@griffithYourEmail@griffith.edu.au #PBS -N TestRun_ComsolParallelComsol #PBS -l select=1:ncpus=4:mpiprocs=4:mem=7g,walltime=24:00:00 ## The number of nodeschunks is given by the select =<NUM > above NODESCHUNKS=1 ###$PBS_NODEFILE is a node-list file created with select and mpiprocs options by PBS ###### The number of threads available is ncpus * NODESCHUNKS (=NPROCS) NPROCS=4 cd $PBS_O_WORKDIR module load comsol/4.361 export COMSOL_NUM_THREADS=$NPROCS comsol batch -np $NPROCS -inputfile model_in~/data/conical_quantum_dot.mph -outputfile modelconical_quantum_dot_out.mph |
Comsol in Matlab
As we use the command "comsol server" , it needs to record your username. So before you could run any batch jobs, you will have to do this once. From gowonda console, type
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#!/bin/bash #PBS -m abe #PBS -M YourEmail@griffith.edu.au #PBS -q mpi #PBS -N TestRun_Comsol #PBS -l select=1:ncpus=12:mpiprocs=2:mem=7g,walltime=4:00:00 ## The number of nodes is given by the select =<NUM > above NODESCHUNKS=1 ###### The number of threads available is ncpus * NODESCHUNKS (=NPROCS) NPROCS=12 module load comsol/4.3-withMatlab2011a61 cd $PBS_O_WORKDIR comsol server < /dev/null > comsolserver1.log & matlab -nodesktop -nosplash -r "addpath /sw/comsol/4.3comsol61/multiphysics/mli/, mphstart, pseudoperiodicity_llmatlab, exit" |
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#!/bin/bash #PBS -m abe #PBS -M YourEmail@griffith.edu.au #PBS -q mpiworkq #PBS -N TestRun_ComsolTestRunComsol #PBS -l select=1:ncpus=8:mem=7g,walltime=4:00:00 ## The number of nodes is given by the select =<NUM > above NODES=1 ###### The number of threads available is ncpus * NODES (=NPROCS) NPROCS=8 module load comsol/4.3-withMatlab2011a61 cd $PBS_O_WORKDIR comsol server -np $NPROCS < /dev/null > comsolserver1.log & matlab -nodesktop -nosplash -r "addpath /sw/comsol/4.3/mli/, mphstart, myfile, exit" |
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