Hi Carsten Thanks a lot for this tip. It worked!
George > 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 > 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