[gmx-users] Mismatching number of PP MPI processes and GPUs per node

[George Patargias]

Hello

Sorry for posting this again.

I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration
(CUDA 5.0 lib) using the following SGE batch script.

#!/bin/sh
#$ -V
#$ -S /bin/sh
#$ -N test-gpus
#$ -l h="xgrid-node02"
#$ -pe mpi_fill_up 12
#$ -cwd

source /opt/NetUsers/pgkeka/gromacs-4.6_gpu_mpi/bin/GMXRC
export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-5.0/lib:$DYLD_LIBRARY_PATH

mpirun -np 12 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu

After detection of the installed GPU card

1 GPU detected on host xgrid-node02.xgrid:
  #0: NVIDIA Quadro 4000, compute cap.: 2.0, ECC:  no, stat: compatible

GROMACS issues the following error

Incorrect launch configuration: mismatching number of PP MPI processes and
GPUs per node. mdrun_mpi was started with 12 PP MPI processes per node,
but only 1 GPU were detected.

It can't be that we need to run GROMACS only on a single core so that it
matches the single GPU card.

Do you have any idea what has to be done?

Many thanks.

Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568