COMSOL Commands on Linux
Use the comsol command to start COMSOL products with detailed start-up options.
The general syntax of the COMSOL command is
comsol [<target>] [<options>] [<target arguments>]
where square brackets indicate optional arguments. The comsol command can be combined with optional targets to achieve various results. The table below lists the command and targets:
Start MATLAB® and connect to a COMSOL Multiphysics server
Requires LiveLinkfor MATLAB® license
The comsol command is located in the bin folder in the COMSOL installation directory.
INI Files
There is a number of .ini files in the subdirectories glnx86 and glnxa64 in the bin directory. It is sometimes recommended that you edit these files. For example, you can add options to any of the above commands by modifying the corresponding ini file. To change the option opt to value val, add the line
-Dopt=val
to the file comsol.ini. Change the file comsolbatch.ini for comsol batch, and similarly for the other COMSOL targets.
Options
You can enter various options after the comsol command and target. Table 22-17 lists the options (See [<options>] in the command syntax) available for all comsol commands. Always issue these options between the command and the target (if any).
-alloc {native} | scalable
-blas {auto} | mkl | blas | blis | path
-c <path>
-clusterstorage all | single | shared
Cluster storage format. The single format does I/O only from the root node, while the shared format does I/O using distributed I/O operations. The shared format requires that all nodes have access to the same storage area and the same temporary storage area.
Path to a workspace directory for storing internal workspace information. The workspace directory is by default a subdirectory to the preference directory. However, the default location of the workspace directory is not affected by the -prefsdir option. The workspace directory is cleared when COMSOL is launched. When running in batch or cluster mode, add @process.id to get a unique identifier to the path (for example, -data /tmp/comsol_@process.id).
-docroot <path>
-memoptassem {off} | matrix | vector | on
-mpmode throughput | turnaround | owner
-np <no. of cores>
-numafirst <numa number>
-numasets <no. of sets>
-tmpdir <path>
-v, -version
For the -tmpdir option, the COMSOL Multiphysics software uses the specified directory to store temporary files. Use the -prefsdir option to specify the directory where COMSOL Multiphysics stores the preference file.
Documentation and Application Libraries Root Directories
In a default COMSOL Multiphysics installation, the documentation files are located in the directory doc under the installation root directory. You can use the -docroot option if you want to move the documentation directory to a different location. Similarly, use the -applicationsroot option if you want to move the Application Libraries root directory applications from its default location under the COMSOL Multiphysics installation root. Relocating the documentation and Application Libraries root directories can be useful for administering Application Library Update; see The Application Library Update Window.
Shared-Memory Options
Use the option -np to control the number of cores used. The default is to use all available cores (processing units).
Use the option -numasets to control the number of nonuniform memory access (NUMA) node sets that the COMSOL Multiphysics software should take into account. This is usually the number of processor sockets that the hardware is using. If you only set the -np option, the number of sockets is determined automatically so that sufficient number of sockets are used by default.
Depending on how loaded the machine is, you can control how COMSOL Multiphysics uses the available processors with the -mpmode option. The following options are available:
Use the option -alloc to specify memory allocator type. The default is to use the native memory allocator. The scalable memory allocator can increase performance significantly for computers with many cores but uses more memory.
You can also specify the number of cores and sockets and the use of the scalable allocators as preferences on the Multicore and Cluster Computing page in the Preferences dialog box. To specify those numbers manually, select the Number of cores and Number of sockets check boxes to enter a number in the associated text fields. By default, all cores are used and the number of sockets are set automatically. If you lower the number of cores, it is good practice to also lower the number of sockets. The preference option for the scalable allocator is called Optimized for multicore. If you want to choose another memory allocator than the default setting, select the Memory allocator check box and the choose Native or Optimized for multicore. To control the scalability assembling mode, which can be useful even when running on a single node, select the Memory scalability optimization for assembling check box. You can then select Off (the default, for no scalability mode), Matrix for activating scalability mode only for matrix assembling, Vector for activating scalability mode only for vector assembling, or All for activating scalability mode for all cases. You can also control these options with a command-line argument -memoptassem.
Sometimes you might want to experiment to find the options that work best for your configuration.
BLAS Options
BLAS is a set of functions for basic linear algebra operations. A large portion of the computational engine in the COMSOL software relies on BLAS. The COMSOL software provides for the following BLAS-related options:
Table 22-19: COMSOL BLAS Options
Use a BLAS library specified using the option -blaspath or the environment variable COMSOL_BLAS_PATH.
MKL, BLAS, and BLIS are distributed with COMSOL Multiphysics. BLIS is similar to BLAS but can in some case provide improved performance.
If you want to use a different BLAS library than the ones provided by COMSOL, make sure that COMSOL Multiphysics can find the library. The simplest way for COMSOL Multiphysics to find a library is to put it in /lib/win64 or somewhere in the standard search path. Also provide the path to any sublibraries needed by the library. Set the search path to point to the directory where the library is installed. To do so, use the environment variable PATH. Your library must support both the standard FORTRAN LAPACK interface and the standard FORTRAN BLAS interface. If your LAPACK and BLAS interface consists of several libraries, use the path to the LAPACK library.
GCC Options
By default COMSOL Multiphysics uses the GCC libraries installed on the system. If COMSOL Multiphysics is unable to start, the software uses the GCC libraries shipped with COMSOL Multiphysics. The option -forcegcc is intended for use together with the LiveLink™ for MATLAB®; use it if you are unable to make function callbacks to MATLAB.
Application Options
The following options are used to specify inputs to an application with command-line options.Find more information about these options in the section The Application Argument Node in the Application Builder Reference Manual.
-appargsfile <filename>
-appargfilelist <filenames>
COMSOL Commands
In additions to the options in Table 22-17, the standalone COMSOL command supports the following options on Linux.
-open <file>
-run <file>
COMSOL Multiphysics Server Commands
Use a COMSOL Multiphysics server command to start a COMSOL process ready to process computational requests. A COMSOL Multiphysics server listens for TCP/IP connections from COMSOL Multiphysics clients. A COMSOL Desktop can become a COMSOL Multiphysics client by connecting to a COMSOL Multiphysics server. The LiveLink™ for MATLAB® also needs to connect to a COMSOL Multiphysics server.
The syntax for the COMSOL Multiphysics server command is
comsol [<options>] mphserver [<target arguments>]
The following target arguments are available for a COMSOL Multiphysics server command.
-login {info} | force | never | auto
Ask for login information. info means that only missing information is asked for. force resets the password. never requires that the login information is available. auto automatically creates a new username and password.
-multi {auto} | on | off
-passwd reset | nostore
-port <port>
-user <user>
Accessing the COMSOL Multiphysics Server Computer
To access the computer running the COMSOL Multiphysics server, simply log in on the server computer by using ssh or a similar command, then enter the comsol mphserver command.
Login Information
When you start a COMSOL Multiphysics server for the first time, you are asked for a username and password. Select a username and a password, which COMSOL then uses in communications between the COMSOL Multiphysics client and the server. You must also specify a matching username and password in the Connect to Server dialog box. The software writes this login information in the subdirectory .comsol/v56/login.properties in your home directory.
Client/Server Security Issues
COMSOL Multiphysics can operate in a client/server mode where COMSOL Multiphysics runs as a separate client and a server. The COMSOL software uses a TCP/IP connection to send data between the server and the client.
Always make sure that untrusted users cannot access the COMSOL login information. Protect the file .comsol/v56/login.properties in your home directory. This is important when using the COMSOL Multiphysics client/server configuration. Alternatively, start the COMSOL Multiphysics server with the -passwd nostore option, and clear the Remember username and password check box when connecting to the server. This ensures that your login information is not stored on file.
Once you start a COMSOL Multiphysics server, a person with access to your login information could potentially connect to your COMSOL Multiphysics server. When a COMSOL Multiphysics client connects or disconnects from a remote computer, the COMSOL Multiphysics server displays a message. The connection from the client to the server is made with the TCP protocol.
The server and client are mutually authenticated using a challenge handshake authentication protocol, which means that login information cannot be easily obtained by someone eavesdropping on the network communication. The TCP connection between the client and the server is otherwise not encrypted. If you require encryption of the TCP connection, you can use third-party software based on protocols such as SSH or IPSEC.
To enhance security, you can limit the address range that can access the COMSOL Multiphysics server, both in your firewall and by changing the COMSOL Multiphysics server configuration. To limit the allowed address range in the server, edit the file <COMSOL Installation Directory>/bin/conf/server.xml and find the lines:
<!-- To restrict access to the COMSOL server you can uncomment the block below.
and follow the instructions.
The default port for the COMSOL Multiphysics server is 2036. You can change this by using the option -port <port> when launching COMSOL and COMSOL Multiphysics server.
Documentation Security Issues
To serve the COMSOL Desktop with documentation, COMSOL Multiphysics opens a separate documentation server on the client computer when you open the documentation. The documentation server program, comsoldocserver.exe, is always installed, even when you choose online documentation. It is nontrivial to start the documentation server, so it is typically only started from comsol.exe or comsoldoc.exe.
To enhance security, you can limit the address range that can access the documentation server, both in your firewall and by changing the documentation server configuration. To limit the allowed address range in the server, edit the file <COMSOL Installation Directory>/doc/help/conf/server.xml and find the lines:
<!-- To restrict access to the documentation server you can uncomment the block below.
and follow the instructions. The default port for the documentation server when started from comsol.exe is 8090 or the nearest higher free port. You can change this by using the option -docport <docport> when launching COMSOL. The port used by the documentation server when started from comsoldoc.exe is 8390 or the nearest higher free port.
The communication via the COMSOL documentation server is not protected by a password or encrypted but can only access the locally installed COMSOL Multiphysics documentation. If you do not want the documentation server to access any locally installed data, use the online documentation.
Port Summary
The following table lists the default ports used by the COMSOL Multiphysics servers:
Table 22-23: Port Usage
COMSOL Multiphysics Client Commands
Use a COMSOL Multiphysics client command to start a COMSOL Desktop with the Connect to Server dialog box open.
The syntax for the COMSOL Multiphysics client command is
comsol [<options>] mphclient [<target arguments>]
The following target arguments are available for a COMSOL Multiphysics client command:
-open <file>
-port <port>
-server <server name>
COMSOL Batch Commands
Use the COMSOL batch command to run COMSOL jobs without a GUI. You can run both Model MPH files and model files for Java with the COMSOL batch command. Model files for Java need to be compiled before running.
The syntax for the COMSOL batch command is
comsol [<options>] batch [<target arguments>]
Its detailed target arguments are:
-alivetime <seconds>
-batchlog <filename>
-checklicense <filename>
-dev <filename>
-inputfile <filename>
-job <job tag>
-methodcall <tag>       -inputfile <filename>
-mode {batch} | desktop
-outputfile <filename>
-paramfile <filename>
-pindex <parameter indices>
-plist <parameter value>
-pname <parameter name>
-study <study tag>
Stopping and Canceling a Batch Job
You can stop a batch job using the following command:
comsol batch -stop <level> -inputfile <filename>
where <level> is the level to stop the process on. Set the level to a high value in order to stop as soon as possible. By default, it is set to 100. The -inputfile option indicates the filename of the model that another process is running. The inputfile arguments should be consistent with the one specified to launch another process. That is, either the same inputfile arguments should be provided or the -inputfile should be the same as the -outputfile specified to launch another process.
You can cancel a batch job using the following command:
comsol batch -cancel -inputfile <filename>
The -inputfile option indicates the filename of the model that another process is running. The inputfile arguments should be consistent with the one specified to launch another process. That is, either the same inputfile arguments should be provided or the -inputfile should be the same as the -outputfile specified to launch another process.
Example
To use the COMSOL batch mode to solve a model, run the following command:
comsol batch -inputfile in.mph -outputfile out.mph -study std1
This command starts COMSOL Multiphysics in batch mode, solves the model in the Model MPH-file with the given filename using the active solver settings in the model, and stores the solution in the out.mph.
The -study option directs COMSOL Multiphysics to run a certain study. The study is identified by its tag. In the COMSOL Desktop, select Show Name and Tag under Model Builder Node Label to see the tags of the jobs under Study within curly braces in the Model Builder. In the model object, determine the tags of the jobs by the command model.study().tags(). You can determine the name of each study by model.study(<tag>).name() using one of the job tags.
The -job option works similarly to the -study option. It directs COMSOL Multiphysics to start a certain job. The job is identified by its tag. In the model object, determine the tags of the jobs by the command model.batch().tags(). You can determine the name of each job by model.batch(<tag>).name() using one of the job tags..
If the model uses an inner parametric solver (in a nested parametric sweep), the Job Configurations node is ignored by the batch job. In such cases, you need to switch to an outer parametric solver.
The -usebatchlic option makes COMSOL use batch licenses for the job. This option is equivalent to the Use batch license check box available in the Cluster Computing and Cluster Sweep study nodes. Using batch licenses for a cluster computing or cluster sweep job means that you can continue working in the COMSOL Desktop while the job is running using only a single FNL license.
For the -recover option, the working directory (where all .log, and .status files are generated) will contain the recovery file, which contains information about the recovery folder in the case that the COMSOL software stops working. If the -recover option is specified, the model from the recovery directory will be opened. If opening that model succeeds, a continue operation will be performed; otherwise, the input filename model will be simulated.
The COMSOL Compile Command
The comsol compile command compiles a model file for Java for use by the COMSOL batch command or for loading class files into the GUI. With the COMSOL Compiler, you can also use it to compile COMSOL applications into standalone executable applications. The Linux syntax for the COMSOL compile command is
comsol [<options>] compile [<target arguments>] <file>.java
The Java file is mandatory. The following optional target arguments are available:
-classpathadd <classpath>
-jdkroot <path>
To compile an application in an MPH-file into a standalone executable application using COMSOL Compiler, use
comsol compile <full path to MPH-file> [<compile arguments>]
The following arguments are available:
-icon <path>
-runtime default | ask | <path>
Specify where to store the runtime when running the application. The default option is the platform’s default location. The ask option asks the user for the location of the runtime when running the application. The <path> option provides a location where the runtime should be unpacked and stored. Only specify a path when compiling for a single platform.
-splash <path>
Options not given are taken from the application’s Compiler node, except for -outputdir and -platforms.
COMSOL Cluster Commands
Use the comsol command with the option -nn <no. of nodes>. -nn specifies the total number of compute nodes created. A COMSOL instance resides in each compute node and communicates with other compute nodes using MPI. A compute node is a process running on the operating system, and multiple compute nodes can be assigned to run on a single host.
The syntax for the COMSOL cluster command is
comsol -nn <no. of nodes> [<options>] [<target>] [<target arguments>]
The following cluster commands are available:
comsol -nn <nn> batch
comsol -nn <nn> mphserver
The preferred way of starting COMSOL cluster jobs is from the Study node in the COMSOL Desktop. If you need to start COMSOL cluster jobs from the command line, the preferred way is to use the comsol -nn <nn> batch command because the comsol -nn <nn> mphserver and comsol -nn <nn> commands require TCP/IP access from your client computer to the cluster node where COMSOL runs.
The following options are available for clusters on Linux:
-mpi {auto} | intel | mpich2 | whpc2008 | user | path
-mpibootstrap {ssh} | rsh | fork | slurm | ll | lsf | sge | jmi
Select network fabrics where fabric1 is one of <shm | dapl | tcp | tmi | ofa>, and fabric2 is one of <dapl | tcp | tmi | ofa>.
-mpihosts <hostnames>
-mpiio {on} | off | gpfs | lustre | panfs
Set the MPI I/O mode. Setting this property to off means that COMSOL doesn’t search for a distributed file system. Setting this property to gpfs, lustre, or panfs makes COMSOL assume it is running on the selected file system.
-mpipath <file>
-mpiroot <path>
-nn <no. of nodes>
-nnhost <no. of nodes>
Number of compute nodes on each host. For the path option, the environment variable COMSOL_SCALAPACK_PATH must be set.
-scalapack {auto} | mkl | user | path
Scalapack library to use. For the path option, the environment variable COMSOL_SCALAPACK_PATH must be set.
Running on Linux
COMSOL Multiphysics uses Hydra to initialize the MPI environment. To launch COMSOL Multiphysics with MPI, use the command line
comsol -nn <number of compute nodes> -f <filename>
The file <filename> should contain the hostnames of the physical nodes (or, alternatively, host) that you intend to use. You can find out the hostname of each physical node from the hostname command. Each physical node should be listed on a separate line in the file. You can also list the IP address of each physical node. The file can contain more hosts than you intend to use.
You can set the remote node access mechanism that is used for connecting using the switch -mpibootstrap. The valid options are ssh, rsh, fork, slurm, ll, lsf, sge, and jmi. This is important if the cluster only supports a different remote node access mechanism than ssh because ssh is the default protocol used.
Use the switch -mpibootstrapexec to set the path to the remote node access mechanism such as /usr/bin/ssh.
The option -mpidebug sets the output level from MPI. The default is level 4.
You can control the network fabrics used for communication with the option -mpifabrics fabric1:fabric2 where fabric1 is one of shm, dapl, tcp, tmi, or ofa, and fabric2 is one of dapl, tcp, tmi, or ofa. Use this option if you are having trouble with the default fabrics used.
Use -mpienablex to enable Xlib forwarding. Xlib forwarding is off by default.
Previously there was a shorthand for performing the COMSOL MPI environment initialization and starting COMSOL Multiphysics. The -clustersimple option is still supported but performs the same Hydra MPI initialization as other COMSOL command with cluster options specified. For example,
comsol -clustersimple batch -inputfile input.mph -outputfile output.mph
is equivalent to the following command when the specified number of compute nodes is 4:
comsol -nn 4 batch -inputfile input.mph -outputfile output.mph
So when no COMSOL cluster options are included in the command, the use of -clustersimple instructs the Intel MPI library to automatically detect the number of nodes that were scheduled to the program. However, explicitly setting the number of processes with the -nn option is common practice, as COMSOL Multiphysics can combine MPI with multithreading to obtain more efficient performance. If the -nn option is specified, then the -clustersimple option has no additional effect.
Starting Distributed COMSOL — Linux Examples
Make sure that COMSOL Multiphysics is able to start on all nodes where you intend to run it.
The following three examples show the command for starting distributed computing with COMSOL Desktop, COMSOL Multiphysics Server, and COMSOL batch mode, respectively. Each starts 4 computational nodes, one on each of the 4 hosts listed in the file hostfile:
comsol -nn 4 -f hostfile
comsol -nn 4 -f hostfile mphserver
comsol -nn 4 -f hosts batch -inputfile in.mph -outputfile out.mph
It is possible to specify the number of CPU cores for each COMSOL process. The following command uses the option -np 2 to assign 2 CPU cores to each compute node:
comsol -nn 4 -np 2 -f hostfile
It is also possible to have more compute nodes than hosts. The following command initializes 8 compute nodes, assigning 2 compute nodes to each host:
comsol -nn 8 -nnhost 2 -f hostfile
For additional command-line options, see COMSOL Cluster Options in Table 22-29.
MPI Options
There are several implementations of MPI. COMSOL Multiphysics is shipped with the Intel MPI library but also supports most MPI implementations based on MPICH2. It is recommended that you use the default Intel MPI library. For running COMSOL Multiphysics on a computer that has MPICH2 installed, the COMSOL software also has a compatibility mode that you can activate by adding the option -mpi mpich2. When using this option, both the variables PATH and LD_LIBRARY_PATH must include your MPI implementation. It is also possible to use other MPI libraries based on MPICH2 using the option -mpipath <path to shared library> and -mpiroot <path to root of mpi library installation>. Table 22-17 lists the MPI related options, -mpi, -mpipath, -scalapack, and -scalapackpath. Additionally, the COMSOL MPI arguments are configurable inside the COMSOL start script. To configure COMSOL to work with a job scheduler through the Cluster Computing study, you can set the options
-Dcs.precmd=<Command line>
-Dcs.postcmd=<Command line>
in the comsol.ini file. This adds commands prior to the comsol command and after the comsol command. You can add {nn} or {perhost} to any of these pre- or postcommands. This configures the Cluster Computing study to use the number of nodes and number of nodes on each host from the corresponding settings for the Cluster Computing study. For more information, see Cluster Computing.
Troubleshooting Distributed COMSOL and MPI
The following syntax can be used to troubleshoot the MPI environment without running a COMSOL Multiphysics model:
comsol [<options>] hydra [<Hydra command>] [<target arguments>]
Use the -h switch for more information about each command, typing, for example, comsol -h hydra cleanup.
COMSOL Multiphysics ships with the Intel MPI library but should be compatible with most MPICH2 compatible MPI libraries. To download the latest version of Intel MPI library runtime visit http://software.intel.com/en-us/intel-mpi-library. To run COMSOL Multiphysics with another version of Intel MPI or other MPI library, set -mpiroot to the root path of the MPI library. In case the downloaded library is not compatible with the version COMSOL Multiphysics uses (this should usually not be the case), also set -mpipath to the dynamically loaded library that should be used. The default of the Intel MPI library is to use ssh as communication protocol. If you require another communication protocol, use the option -mpibootstrap <protocol>. If you are using a scheduler, the Intel MPI library can often detect the environments it is running in automatically, in which case you may not need to provide additional cluster options in the COMSOL command.
If you are using a PBS-based scheduler, add -mpirmk pbs to the command line in order for Intel MPI to interpret the environment correctly. The Intel MPI library automatically tries to detect the best option for communication and uses InfiniBand if it detects it. To verify that COMSOL is using InfiniBand, check the output from the startup of COMSOL:, it should not mention TCP transfer mode.
In some cases it helps if you combine the option with the environment variable PSM_SHAREDCONTEXTS_MAX set to 1. You can control the fabrics used for communication with the option -mpifabrics fabric1:fabric2, where fabric1 is equal to fabric2 or fabric1 is shm.
If COMSOL Multiphysics aborts during start, make sure that all nodes can access the license manager and that COMSOL Multiphysics can be started on each node when not running distributed. Sometimes there is additional information in the log files located in $HOME/.comsol/v56/configuration/comsol/*.log. If this does not help, start the MPI test program to make sure that the MPI library is working as it should using the following command:
comsol -nn <number of nodes> -f <hostfile> hydra mpitest
For more verbose information about the startup process when using Hydra, use -mpiarg -verbose, or set -mpidebug to a value greater than the default 4.
COMSOL MATLAB Command
Use the COMSOL matlab command to access the COMSOL API through MATLAB®. Enter:
comsol mphserver matlab [<options>]
which launches a COMSOL Multiphysics server in a console window, starts MATLAB, and connects MATLAB to the COMSOL Multiphysics server.
The following options are available for the comsol mphserver matlab command:
-host <hostname>
-mlroot <path>
-port <hostname>
The comsol trust Command
Use the comsol trust command to trust methods used in add-ins. The following commands are supported:
comsol trust list, to list the content of the trust store.
comsol trust add -addinmethods <path_to_addin> [<method_name1> ...], to trust the listed methods for an add-in. If no methods are give, all methods in the add-in are trusted. A TrustID is created for the trusted methods
comsol trust revoke <TrustID>, to revoke the trust in the methods for the named TrustID.