Gromacs on Mills
Templates for Grid Engine queue submission scripts are available for batch GROMACS jobs in /opt/shared/templates/gridengine/gromacs. Copy and edit the template based on your job by following the usage described in gromacs.qs.
/opt/shared/templates/gridengine/gromacs on a specific cluster for changes in existing templates, or the addition of new templates, designed to provide the best performance for a particular version of GROMACS on that cluster.
Batch job
On Mills, the template (/opt/shared/templates/gridengine/gromacs.qs specifies a number of resource options to provide the best performance. The number of slots specified for NPROC should be a multiple of 24 in conjunction with specifying exclusive access to allow your job to run on the node(s) required based on the number of slots requested without any other jobs running on those node(s) too. Also specifying vpkg_require gromacs/4.5.5-intel64 (single-precision intel) or vpkg_require gromacs/4.5.5-open64 (double-precision open64) has provided the best results. By default the template uses double-precision (md_rund), however uncommenting USE_SINGLE_PRECISION=YES will specify the single-precision version (md_run) instead. Again for best performance, binding cores and only using half of the slots per node are defined as the default due to the shared FP (Floating-Point) unit on Mills.