Comsol
Contents
Category
PhysicsDescription
COMSOL Multiphysics is a finite element analysis, solver and simulation software / FEA software package for various physics and engineering applications, especially coupled phenomena, or multiphysics. In addition to conventional physics-based user interfaces, COMSOL Multiphysics also allows entering coupled systems of partial differential equations (PDEs). The PDEs can be entered directly or using the so-called weak form.Available versions (Euler, old software stack)
| Legacy versions | Supported versions | New versions |
|---|---|---|
| 4.4, 5.0, 5.1 | 5.2, 5.2.0.200, 5.2a, 5.3 | 5.3a, 5.4, 5.5 |
Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.
Environment modules (Euler, old software stack)
| Version | Module load command | Additional modules loaded automatically |
|---|---|---|
| 4.4 | module load legacy comsol/4.4 | |
| 5.0 | module load legacy comsol/5.0 | |
| 5.1 | module load legacy comsol/4.4 | |
| 5.2 | module load comsol/5.2 | |
| 5.2.0.200 | module load comsol/5.2.0.200 | |
| 5.2a | module load comsol/5.2a | |
| 5.3 | module load comsol/5.3 | |
| 5.3a | module load new comsol/5.3a | |
| 5.4 | module load new comsol/5.4 | |
| 5.5 | module load new comsol/5.5 |
Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.
Interactive session
You can start the graphical user interface (GUI) of COMSOL in a batch interactive job with X11 forwarding. This can be useful to change your COMSOL preferences or to prepare a model or check the result of a COMSOL job. Please follow the description from the wiki page about batch interactive jobs with X11 forwarding to start an interactive job.Afterwards, you can load one of the COMSOL modules
module load comsol/5.2
and finally start the GUI with the comsol command.
comsol -np 1If the COMSOL GUI runs slow through X11, then please have a look at the troubleshooting section of this wiki page. Don't start the COMSOL GUI on a login node, as login nodes only have few resources and are shared by many users.
How to submit a job
You need to submit your COMSOL jobs through the batch system. For a single processor calculation a typical command could look likesbatch [Slurm options] --wrap="comsol batch -inputfile infile.mph -outputfile outfile.mph"
Here you need to replace [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.
For using the COMSOLBATCH licenses, you would need to add the -usebatchlic option:
sbatch [Slurm options] --wrap="comsol batch -usebatchlic -inputfile infile.mph -outputfile outfile.mph"
For parallel jobs using shared memory, you can specify the number of cores to be used with the -np option of COMSOL:
sbatch --ntasks=1 --cpus-per-task=4 [Slurm options] --wrap="comsol batch -np 4 -inputfile infile.mph -outputfile outfile.mph"
Please make sure that the --ntaks= option of sbatch and the -np option of COSMOL always have the same value. Please be careful to not use the -clustersimple option for shared memory jobs as this would make COMSOL start MPI processes instead of using threads.
If you plan to run parallel COMSOL jobs, then we strongly recommend to first do a small scaling study to find out the sweet spot for the parallel efficiency of your model. Since COMSOL can be strongly memory bound, the sweet spot might be to use 4 cores (see scaling study below).
Parallel jobs using distributed memory
If you would like to run COMSOL in distributed memory mode, then you need to add the -mpibootstrap slurm option to your COMSOL command:
sbatch --ntasks=4 [Slurm options] --wrap="comsol batch -mpibootstrap slurm -inputfile infile.mph -outputfile outfile.mph"
Please be careful to not mix the -mpibootstrap slurm option with the -np option as this will start too many threads. The -mpibootstrap slurm option will tell COMSOL to get the required MPI information like hostnames etc. directly from the batch system.
If you plan to run parallel COMSOL jobs, then we strongly recommend to first do a small scaling study to find out the sweet spot for the parallel efficiency of your model. Since COMSOL can be strongly memory bound, the sweet spot might be to use 4 cores (see scaling study below).Example
LSF examples are obsolete. They will soon be replaced with Slurm examples.As an example for a Comsol job, we use the Plasmonic Wire Grating Analyzer which can be downloaded from the Comsol web site. It computes the coefficients of refraction, specular reflection, and first-order diffraction as functions of the angle of incidence for a plasmonic wire grating on a dielectric substrate.
[leonhard@euler02 comsol]$ ls
plasmonic_wire_grating.mph
[leonhard@euler02 comsol]$ module load comsol/5.2
[leonhard@euler02 comsol]$ bsub -n 4 -W 0:30 -R "rusage[mem=2048, scratch=2000]" "comsol batch -np 4 -autosave off -tmpdir \$TMPDIR -inputfile plasmonic_wire_grating.mph -outputfile output.mph"
Generic job.
Job <26018628> is submitted to queue <normal.4h>.
[leonhard@euler02 comsol]$ bjobs
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
26018628 leonhard PEND normal.4h euler02 *utput.mph Aug 29 09:47
[leonhard@euler02 comsol]$ bjobs
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
26018628 leonhard RUN normal.4h euler02 4*e1441 *utput.mph Aug 29 09:47
[leonhard@euler02 comsol]$ bjobs
No unfinished job found
[leonhard@euler02 comsol]$ ls
lsf.o26018628 output.mph output.mph.bin output.mph.status plasmonic_wire_grating.mph
[leonhard@euler02 comsol]$ grep -A8 "Current Progress: 100 %" lsf.o26018628
---------- Current Progress: 100 % - Solving linear system
Memory: 1062/1069 5666/5666
Stationary Solver 1 in Study 1/Solver 1 (sol1): Solution time: 0 s
Physical memory: 1.06 GB
Virtual memory: 5.67 GB
Run time: 42 s.
Saving model: /cluster/home/leonhard/comsol/output.mph
Save time: 0 s.
Total time: 55 s.
Comsol can create a large number of files in your home directory, therefore we recommend to have a look at the Comsol tutorial about redirecting files created by Comsol from your home directory to the local scratch.Benchmark study
For evaluating the parallel efficiency of COMSOL, we performed a scaling study with a model having 150K mesh elements. The result of the study shows (at least for this model that requires a large amount of memory to run), that COMSOL simulations can be heavily memory bound and for certain cases going above 4 cores can be counterproductive.For this study, we performed the simulation on 1, 2, 4, 6, 8, 12 and 24 cores. All runs were performed twice. The table below shows the run times and the speedup.
| Cores | runtime 1 [s] | speedup 1 | runtime 2 [s] | speedup 2 |
|---|---|---|---|---|
| 1 | 26779 | - | 26811 | - |
| 2 | 15237 | 1.76 | 15193 | 1.76 |
| 4 | 6743 | 3.97 | 6719 | 3.99 |
| 6 | 11815 | 2.27 | 11752 | 2.27 |
| 8 | 13435 | 1.99 | 13421 | 2.00 |
| 12 | 19369 | 1.38 | 19365 | 1.38 |
| 24 | 18761 | 1.43 | 18667 | 1.44 |
License information
Commercial (centrally provided by IT shop)https://www.comsol.de/products/licensing
Troubleshooting
In case of a problem with COMSOL on one of our clusters, please first contact the cluster support. We have very good relations to the COMSOL support and if we cannot solve a problem, we will open a ticket at the COMSOL support and add the user to this ticket, such that he also gets the answers from COMSOL support.Problems with the COMSOL GUI
We noticed, that in some cases, the COMSOL 5.2 GUI updates very slowly when staring it on Euler or sometimes it even crashes. If you experience this kind of problem, then you can try to start the COMSOL GUI with the following option:
comsol -np 1 -3drend swIf the problem still persists, the reason could be that you are on a login node, which is overloaded. We recommend in this case to log out and log in to the cluster again.
Notes
Please, do NOT use the comsol parameters -mpmode -nnhost and -mpi ...Theoretically you can combine the -np and -nn parameters, but unless you
REALLY know what you are doing, we suggest that you avoid it.Links
Using Comsol BATCH licensesComsol files and direcories in the users home directory
Comsol MATLAB LiveLink
Comsol workshop 10.12.2015
https://www.comsol.com/
https://en.wikipedia.org/wiki/COMSOL_Multiphysics
https://www.youtube.com/user/COMSOLmultiphysics
