COMSOL Multiphysics software, an interactive environment for modeling and simulating scientific and engineering problems.
Versions and Availability
Softenv Keys for comsol on supermike2
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The information here is applicable to LSU HPC and LONI systems.
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.
System Default Path
When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.
SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.
Viewing Available Packages
The command softenv will provide a list of available packages. The listing will look something like:
$ softenv These are the macros available: * @default These are the keywords explicitly available: +amber-8 Applications: 'Amber', version: 8 Amber is a +apache-ant-1.6.5 Ant, Java based XML make system version: 1.6. +charm-5.9 Applications: 'Charm++', version: 5.9 Charm++ +default this is the default environment...nukes /etc/ +essl-4.2 Libraries: 'ESSL', version: 4.2 ESSL is a sta +gaussian-03 Applications: 'Gaussian', version: 03 Gaussia ... some stuff deleted ...
The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:
To update the environment after modifying this file, one simply uses the resoft command:
The command soft can be used to manipulate the environment from the command line. It takes the form:
$ soft add/delete +keyword
Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.
Use the "comsol -help" command to print out the usage information:
[lyan1@mike5 ~]$ comsol -help Usage: comsol [options] [target] [target arguments] COMSOL commands: comsol Run COMSOL Multiphysics Desktop comsol batch Run a COMSOL job comsol compile Compile a COMSOL Model java file comsol mphclient Run COMSOL Multiphysics Desktop client comsol mphserver Run COMSOL Multiphysics Server comsol mphserver matlab Run MATLAB with COMSOL Multiphysics Server comsol hydra Run Hydra commands comsol mpd Run MPD commands COMSOL options: ...
Example: run COMSOL with one single host
Run a COMSOL job from the command line:
comsol batch -inputfile blasius_boundary_layer.mph -outputfile blasius_solved.mph -batchlog blasius.log
Here is an sample PBS job script:
#!/bin/bash #PBS -A your_allocation_name #PBS -l walltime=2:00:00 #PBS -l nodes=1:ppn=16 #PBS -q checkpt cd $PBS_O_WORKDIR comsol batch -inputfile blasius_boundary_layer.mph -outputfile blasius_solved.mph -batchlog blasius.log
Example: run COMSOL with multiple hosts
When running COMSOL with multiple hosts, the following flags need to be specified:
- -nn <the number of nodes> | Total number of compute nodes
- -nnhost <number of nodes per host> | Number of nodes per host
- -np <number of cores per node> | Number of cores per node
- -f </path/to/hostfile> | Path and file containing the list of hostnames
For instance, to run on 4 hosts (16 cores each) with 8 COMSOL nodes, you would need:
-nn 8 -nnhost 2 -np 8
In the above example, "-nn 8" means 8 COMSOL nodes. Since we have 4 hosts, the value for "-nnhost" is 8/4 = 2 (nodes per host). The value for "-np" can be obtained by dividing the number of cores each host by the value of "-nnhost": 16/2 = 8.
The hostfile can be created by running this command:
uniq $PBS_NODEFILE > myhosts
Putting everything together in a PBS job script:
#PBS -A your_allocation_name #PBS -l walltime=2:00:00 #PBS -l nodes=4:ppn=20 #PBS -q checkpt cd $PBS_O_WORKDIR uniq $PBS_NODEFILE > myhosts comsol batch -nn 8 -nnhost 2 -np 8 -f myhosts -inputfile blasius_boundary_layer.mph -outputfile blasius_solved.mph -batchlog blasius.log
If COMSOL started successfully on multiple hosts, you should see something like this:
(shelob017:0,1) (shelob018:2,3) (shelob019:4,5) (shelob020:6,7)
Last modified: June 11 2019 14:52:19.