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comsol

About

COMSOL Multiphysics software, an interactive environment for modeling and simulating scientific and engineering problems.

Versions and Availability

▶ Display Softenv Keys for comsol on all clusters

Machine Version Softenv Key
None Available N/A N/A

▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

h4

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

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.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Softenv

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 ...
Managing SoftEnv

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:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

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.

▶ Display Module Names for comsol on all clusters.

Machine Version Module
supermike2 5.2a comsol/5.2a
supermike2 5.3 comsol/5.3
supermike2 5.3a comsol/5.3a

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

h4

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

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.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

Module is currently available only on SuperMIC.

Usage

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)

Resources

Last modified: June 11 2019 14:52:19.