Running your OpenFOAM application on Farber

Using the openmpi-ib.qs job script template found in /opt/shared/templates/gridengine/openmpi provides the best performance for a parallel MPI run for OpenFOAM applications. Once you have copied the template for your job script (e.g. qsub_sowfa.qs), then edit the following for your OpenFOAM application:

  1. Modify NPROC to select the number of slots (cores).
  2. Modify the memory specification -l m_mem_free according to the instructions if you want to have more than 1GB of memory per slot (core).
  3. Modify the email notification -m and -M according to the instructions if you want email to be sent at the end of the job, if the job is aborted, rescheduled, or suspended.
  4. Setup your environment with your newly built OpenFOAM application by replacing the vpkg_require openmpi/1.4.4-gcc with your VALET package name (e.g. sowfa/2.0-OF2.1-gcc)
  5. Setup the MPI executable and options (arguments) for your OpenFOAM application (e.g. ABLSolver -parallel > log.ABLSolver.3.${JOB_ID} 2>err.ABLSolver.3)

Now submit your job script using

qsub qsub_sowfa.qs
There is a 1.5.x Grid Engine integration error when only using OpenFOAM 2.1.1 compiled with openmpi-1.5.3 which causes the following warning when initiating an MPI run
 mca: base: component_find: unable to open /opt/shared/openfoam/2.1.
1-gcc/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi-1.5.3/lib/openmpi/mca_plm_rs
hd: /opt/shared/openfoam/2.1.1-gcc/ThirdParty-2.1.1/platforms/linux64Gcc/openmpi
-1.5.3/lib/openmpi/mca_plm_rshd.so: cannot open shared object file: Permission d
enied (ignored)

This is a warning and not an error. Please ignore.