Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.
COMSOL Multiphysics provides a range of simulation, finite element analysis and solver functionality.
COMSOL Multiphysics is installed on Iceberg but is not presently supported by IT Services. There is no site license for COMSOL so to run it on Iceberg you will need either your own license or access to licenses managed by others. For example, a research group may operate a license server that can issue COMSOL licenses to (approved) users. If you need access to a license on a temporary basis then you could try contacting Prof. Will Zimmerman, who has purchased several licenses for his research group and may be willing to hire out licenses to other researchers. See Interactive usage for information on how to specify a COMSOL license when starting COMSOL on Iceberg.
The following COMSOL Multiphysics 5.2 modules are installed:
Batteries and Fuel Cells
Chemical Reaction Engineering
LiveLink for Excel
LiveLink for MATLAB
Nonlinear Structural Materials
After connecting to iceberg (see Establishing a SSH connection), start an interactive graphical session with the
Alternatively, if you require more memory, for example 16 GB, use the command
qrshx -l rmem=16G
Next, run the following to make COMSOL Multiphysics available in your current session:
module load apps/binapps/comsol/5.2
Specify the location of your license information:
Finally, start COMSOL Multiphysics:
The COMSOL Multiphysics user interface should then appear. Here
mylicensefile.dat is a file containing either:
details of your license (which components you can use) or
details of the license server that you want COMSOL to request licenses from.
If you are using a license server then your license file needs to contain no more than the following:
SERVER mylicenseserver.sheffield.ac.uk ANY 65321 USE_SERVER
mylicenseserver.sheffield.ac.uk is the hostname of your license server and
654321 is the port to connect to on that machine to request a COMSOL license.
The person responsible for managing the license server may ask for your Iceberg username to allow you to request licenses (whilst preventing others from doing so).
To submit a batch job that will run on just one CPU core create a file called e.g.
#!/bin/bash #$ -l h_rt=02:00:00 #$ -l rmem=16G #$ -m bea #$ -M firstname.lastname@example.org #$ -j y #$ -o myjob.log module load apps/binapps/comsol/5.2 export _JAVA_OPTIONS="-Xmx2g" export LM_LICENSE_FILE=/path/to/mylicence.dat INPFILE=myinput.mph OUTFILE=myoutput.mph BATCHLOG=myjob_comsol_own_log.log comsol batch -tmpdir $TMPDIR -inputfile $INPFILE -outputfile $OUTFILE -batchlog $BATCHLOG
You will need to change:
The email address used for email notifications;
The path to your COMSOL license file;
The name of the COMSOL input file (with a
You may want to change:
The amount of time that the job is allowed to run for;
The amount of real (
rmem) memory that the job can use;
The maximum amount of virtual memory used by Java (
-Xmx2G means that it can use 2GB of virtual memory);
The name of the output file generated by COMSOL (has a
The name of the
BATCHLOG log file generated by COMSOL;
The name of the log file generated by the cluster’s scheduling software (which is
Next, submit this using:
and await an email to notify you that the job has completed.
This section is primarily of interest