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COMSOL

COMSOL in Umbrella On Demdand COMSOL is licensed software and only usable if the user is a member of the correct group.

Getting a license

Please check KI 6824 for the procedure on how to get a license for using COMSOL.

Using Application interactive
(Graphical User Interface)

Use your browser to connect to Umbrella On Demand

Using COMSOL in SLURM batch jobs
(Command Line Interface)

COMSOL SLURM sbatch jobscript example using Shared Memory

#!/bin/bash
#SBATCH --partition=tue.default.q     # Partition/Queue
#SBATCH --job-name=test_comsol        # Job name
#SBATCH --nodes=1                     # Run 1 Node(s)
#SBATCH --ntasks=1                    # Run 1 Task
#SBATCH --cpus-per-task=16            # Run on 16 CPU per Task
#SBATCH --mem-per-cpu=2gb             # 2 GB of Memory per CPU
#SBATCH --time=01:00:00               # Time limit hrs:min:sec
#SBATCH --output=test.%j.log          # Standard output and error log

cd $HOME/Jobs/Comsol

module load COMSOL/6.2.0.339

MODEL=comsol_smalltest

comsol batch -inputfile $MODEL.mph -outputfile $MODEL\_out.mph -np ${SLURM_CPUS_PER_TASK}

Using local COMSOL to run COMCOL SLURM batch jobs (Client/Server)

Comsol Settings

This short tutorial is about this second possibility. It is focused on configuring your simulation using a TU/e cluster. For more information, visit the COMSOL blog where the procedure is explained in detail.

Once you are done with building your model and specifying the physics of your study on COMSOL, you can configure your simulation on a cluster. Check the settings used in the figure or follow the instructions bellow.

On the Model Builder menu, click on Study # with the left button of your mouse and selecting Cluster Computing from the menu. This will add Cluster Computing as an item under Study #. By clicking on this item, the settings for cluster computing are open on the right of the Model Builder menu.

On the Computer cluster settings submenu, choose from the dropdown menu user controlled in Settings and SLURM in Scheduler type. Leave the next two fields, i.e. the fields Scheduler type and User, empty. In the field Queue name, fill the queue you want to use, e.g. tue.default.q. Choose the queue according to your department and the information in Technical Specifications of the clusters.

In the same submenu, check the boxes of Specify external COMSOL batch directory path and Specify external COMSOL installation directory path and respectively type the paths /home/tue/ (or home/phys/ if you belong to the Applied Physics department) and /cm/shared/apps/comsol/5.5/multiphysics/.

Assuming that you are using PuTTY and that you have generated a SSH key to log in, you can fill the remainder fields as follows. On the Remote and Cloud Access submenu, choose from the dropdown menu user controlled in Settings and `check the box of Run remote. In the dropdown menu select SSH in Remote invoke command and Putty in Remote invoke command. In the SSH directory field, browse to the directory where PuTTY is installed and, in the SSH key file, browse to the directory where you save you private key, select the key, and click Open. You do not need to fill the fields Forward ports and Port host. As SSH user, fill your cluster username.

For the File transfer command field, choose from the dropdown menu SCP. Fill the SCP fields similarly to the SSH fields, i.e., choose PuTTY and fill the directory for the program and public key. Once again use you cluster username in SCP user. In the Remote hosts table, add the cluster address hpc.tue.nl (or compass.phys.tue.nl if you belong to the Applied Physics department).

You are nearly done, before pressing the run button to have your simulations calculated on the cluster, read the next sections to learn how to select the number of cores in your calculation and to log out your computer while a simulation is running on the cluster.

Selecting the number of cores

By default, COMSOL uses the total amount of available cores in a computing node. This means that, depending on the queue that you are going to use, the job can use up to 64 cores, which may (probably) be too many for your calculation.

You can choose the number of cores by expanding the options under Study # on the Model Builder menu. Do the same with Job configurations and select Batch 1 to open the Settings menu. If this menu is not visible, select the eye icon on the Model Builder menu to show more options. This will open a popup menu from which you can check the Solver and Job Configurations option. On the Batch 1 settings, check the option Number of cores and type the desired number of cores.

Finally, click on run to submit your job on the cluster. Follow the status of your simulation in the table in the External process tab.

Detaching/attaching/stopping jobs

If you want to log out or close the local interface, you should detach your job first by clicking on the button in the right bottom corner of the local interface (near the progress bar).

If you want to keep your job running on the cluster while you are logged out of your computer or the COMSOL interface is closed, just close it and click yes when asked if you want to save the changes to the file. When you open your file again to resume your work, open the External process tab on the right side under Graphics. Click on the first icon to attach the job. The table below should update the current status of your simulation.

If, instead, you want to stop your simulation, click on the second icon in the External process tab. If you think that there is a problem with your simulation or if the program did not respond as expected, you can also log in on the cluster and cancel your jobs with scancel. Learn more about the scheduler commands in Using Slurm page of this wiki.