[gmx-users] gromacs on multiple gpus

Neha Gandhi n.gandhiau at gmail.com
Tue May 10 05:51:15 CEST 2016

Dear List,

I have compiled GROMACS 5.0.7 using following options

CMAKE_PREFIX_PATH=/home/gandhin/fftw cmake .. -DGMX_BUILD_OWN_FFTW=OFF
-DGMX_BUILD_MDRUN_ONLY=on -DCMAKE_INSTALL_PREFIX=/home/gandhin/gromacs-5.0.7

The machine has two K40 gpus and 12 cpus per node. When I submit jobs using
mpirun gmx_mpi mdrun -v.. the program mdrun detects two gpus with ids #0
and #1 but it still runs the job with only one gpu i.e. gpu id #0. What is
the correct way of submitting job (using PBS) so that both gpus and 12
cores on the same node are utilised by mdrun for the simulation?

My apologies to post this question to GROMACS mailing list, this post is
more related to the system admin who aren't able to help.

Thank you for kind attention


Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Research Gate

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