Setting up Mathematica to work well on a cluster was painful for me. I don't know how to get it working on PBS, but you may find the following general information useful.
Do look at the ClusterIntegration package. If it doesn't work as it is, you will have to customize things.
Your Mathematica program should be in an
.m file which should be run from the job file as
math -script myprogram.m
This script is responsible for launching the correct number of subkernels on all the compute nodes that were allocated to you. The job file is launched in an environment where information about these nodes is available in some form (different for each job schedulnig system). You will need to retrieve this information from the environment (see the PBS documentation) and use it to construct subkernel specifications. These will include the commands to launch the subkernels. On many systems this is done through
ssh. Again, see the PBS documentation.
To construct a subkernel specification, load
then write each specification as
SubKernels`RemoteKernels`RemoteMachine[host, command, cores]
host must be the hostname,
command must be the launch command in a form suitable for execution within the job script, and
cores is the number of CPU cores on that host that you can use (i.e. how many subkernels will be launched there).
The launch command will have templates in it. They are of the form
`1`, which will be automatically filled out. Probably the only one you need to be concerned about is
1, as this will expand to the host name. You'll need to pass this to
The subkernel must be launched with a command similar to
math -mathlink -linkmode Connect `4` -linkname '`2`' -subkernel -noinit >& /dev/null
math is the Mathematica kernel executable.
ssh to launch that may look something like
ssh `1` mathcommand &
where mathcommand is the subkernel launch command from above and
`1` will have the host name auto-inserted. This part will be specific to your cluster, so ask your admin.
When you have your subkernel specifications, put them in a list and assign that to
$ConfiguredKernels. Then use
LaunchKernels without any arguments to launch the subkernels.
An example you can refer to is the solution I used on our cluster (SGE, not PBS) a long time ago: https://bitbucket.org/szhorvat/crc/src The details (e.g. how to retrieve the available nodes, how to launch a process on another node, etc.) will be different for your cluster.