[gmx-users] GROMACS PBS GPU JOB submission

[Tuanan Lourenço]

Hi everyone

I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue
system is PBS. I am having some issues with the GPU selection, what I want
is to use 1 GPU per job but GROMACS is always using all the four GPUs.

My submission script is the following:

#PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1

mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod.tpr
-deffnm TEST -ntomp 1


However, looking to the gromacs log file I see "On host gn01 4 GPUs
auto-selected for this run".

I know if I use the flag -gpu_id I can tell for GROMACS what GPU I want to
use and in this case, everything is ok, GROMACS does what I say.
But this can be a problem if I submit more than one job to the node,
because the jobs will use the same GPU card.

My question is; there is any way to say for GROMACS or PBS to use the GPU
that is available at that moment? I have 4 GPU in the server, thus, I want
to submit 4 jobs each one using one GPU.


Thank you very much.



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Dr. Tuanan C. Lourenço