Hi, On Mar 11, 2013, at 10:50 AM, George Patargias <g...@bioacademy.gr> wrote:
> 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. Have you compiled mdrun_mpi with OpenMP threads support? Then, if you do mpirun -np 1 mdrun_mpi … it should start one MPI process with 12 OpenMP threads, which should give you what you want. You can also manually specify the number of OpenMP threads by adding -ntomp 12 Carsten > > > 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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists