This page explains how to submit your COMSOL calculations to IBEX clusters using the COMSOL GUI running on your workstation whether you are working on Linux, Mac, or Windows.

1) You first need to load COMSOL from the terminal by doing the following:

module load comsol

2) Invoke the application

comsol

It is mandatory to do the following in order to delete any previous configurations from previous studies that could affect your current calculations. Make sure to perform these steps before you submit your calculation:

3) Open your model preparing it to run on a cluster

4) Go to Study 1 > Cluster Computing > Right click choose Settings

5) Edit the following fields:

• Scheduler Type: SLURM
• Scheduler: specify the cluster's name e.g. ibex
  • Allowed values are ibex.
• User: specify your username
• Number of nodes: specify the number of nodes you want e.g. 4
• Queue: specify the queue name e.g. batch
  • Check queues available on each cluster.
• Specify the Directory: specify your testing directory
  • This is local on your PC/workstation.
• Specify external COMSOL batch directory path: specify the directory you want your results(output) in
  • This path should always be in your scratch for performance, e.g. /ibex/scratch/<username>/comsol/results.
  • This path must exist on remote cluster, i.e. create it.
• Specify external COMSOL installation directory path: installation directory of COMSOL on the cluster e.g. /opt/share/comsol/5.2
  • This path is always /opt/share/comsol/<version>.
• Check the Use batch license box
  • This is checked to be able to submit jobs to the cluster and also work locally on your machine using the same license.

6) Go to Remote and Cloud Access

• Run Remote: check this box
• Remote invoke command : SSH
• SSH command : SSH
• SSH directory : blank (ssh is on the system)
• Forward ports : Fill in 1718 or 1719 or 1718,1719
• Port Host : WTHFXNSR03.KAUST.EDU.SA
• SSH user : specify your user name
• File transfer command : SCP
• SCP command : SCP
• SCP directory : blank (scp is on the system)
• SCP user: specify your username
• Remote hosts : clustername
  • Allowed values are glogin.ibex.kaust.edu.sa or ilogin.ibex.kaust.edu.sa. It depends if you're using GPU or Intel nodes; Intel nodes are preferred ones.
• Remote OS : Linux

7) More Cluster Configurations :

You can find more cluster configurations by right clicking on “Study” node then select “Show Default Solver”. Furthermore, click on “Batch 1” that you can find under “Job Configurations”.

• You can specify the Number of processes on hosts
• You can specify the Number of cores
  • We suggest you tick this box and specify the cores. This number is defined by number of nodes * cores per node on specific cluster, e.g. 4 20-core nodes means 80 total cores.
• You can specify the Memory per node
• You can specify the Runtime
• You must specify wall time by using -t <SLURM time format>
• You must specify cluster type by using, e.g -C intel depending on which cluster you're using

• The license file licenseinfo.ini found in COMSOL installation root on your Mac has to be changed to

#ff0000>#License properties.
#Mon Feb 22 17:21:55 AST 2016
Company=
Name=arenaam
Vendorstring=C,5ffd178034d1

• The external batch directory used for output of jobs has to already exist.
• SSH key file in Remote and Cloud access section has to be changed to id_rsa not the public one.

8) Run your computations by pressing Compute on the Study

1) How do I setup passwordless SSH with PuTTY on Windows?

2) Open COMSOL and then open your model

3) From the Cluster computing section under Study 1 in the Model Builder window, edit the following:

• Scheduler Type: SLURM
• Scheduler: leave it blank
• User: specify your username
• Number of nodes: specify the number of nodes you want e.g. 4
• Queue: specify the queue name e.g. batch
  • Check queues available on each cluster.
• Specify the Directory: specify your testing directory
  • This is local on your PC/workstation.
• * Specify external COMSOL batch directory path: specify the directory you want your results(output) in
  • This path should always be in your scratch for performance, e.g. /ibex/scratch/<username>/comsol/results.
  • This path must exist on remote cluster, i.e. create it.
• Specify external COMSOL installation directory path: installation directory of COMSOL on the cluster e.g. /opt/share/comsol/5.2
  • This path is always /opt/share/comsol/<version>.
• Check the Use batch license box
  • This is checked to be able to submit jobs to the cluster and also work locally on your machine using the same license.

• Run Remote: check this box
• Remote invoke command : SSH
• SSH command : Putty
• SSH directory : path were Putty is installed
• SSH key file : Filename of private key, including path
• Forward ports : Fill in 1718 or 1719 or 1718,1719
• Port Host : WTHFXNSR03.KAUST.EDU.SA
• SSH user : specify your user name
• File transfer command : SCP
• SCP command : Putty
• SCP directory : path were plink and pscp are installed
• SCP key file : Filename of private key, including path
• SCP user: specify your username
• Remote hosts : clustername
  • Allowed values are glogin.ibex.kaust.edu.sa or ilogin.ibex.kaust.edu.sa. It depends if you're using GPU or Intel nodes; Intel nodes are preferred ones.
• Remote OS : Linux

4) Compute