Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP threads, are started. Maybe there is something wrong with your MPI setup (did you by mistake compile with thread-MPI instead of MPI?)
Carsten On 09 Sep 2014, at 09:06, Albert <mailmd2...@gmail.com> wrote: > Here are more informations from log file: > > mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g > npt2.log -gpu_id 01 -ntomp 0 > > > Number of hardware threads detected (20) does not match the number > reported by OpenMP (10). > Consider setting the launch configuration manually! > > Number of hardware threads detected (20) does not match the number > reported by OpenMP (10). > Consider setting the launch configuration manually! > Reading file npt2.tpr, VERSION 5.0.1 (single precision) > Reading file npt2.tpr, VERSION 5.0.1 (single precision) > Using 1 MPI process > Using 10 OpenMP threads > > 2 GPUs detected on host cudaB: > #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible > #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible > > 2 GPUs user-selected for this run. > Mapping of GPUs to the 1 PP rank in this node: #0, #1 > > > ------------------------------------------------------- > Program mdrun_mpi, VERSION 5.0.1 > Source code file: > /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, > line: > 359 > > Fatal error: > Incorrect launch configuration: mismatching number of PP MPI processes > and GPUs per node. > mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 > GPUs. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > Halting program mdrun_mpi > > gcq#314: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists > in Your Family?" (Gogol Bordello) > > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode -1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > Using 1 MPI process > Using 10 OpenMP threads > > 2 GPUs detected on host cudaB: > #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible > #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible > > 2 GPUs user-selected for this run. > Mapping of GPUs to the 1 PP rank in this node: #0, #1 > > > ------------------------------------------------------- > Program mdrun_mpi, VERSION 5.0.1 > Source code file: > /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, > line: > 359 > > Fatal error: > Incorrect launch configuration: mismatching number of PP MPI processes > and GPUs per node. > mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 > GPUs. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > Halting program mdrun_mpi > > gcq#56: "Lunatics On Pogo Sticks" (Red Hot Chili Peppers) > > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode -1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > > > > > > > > > > On 09/08/2014 11:59 PM, Yunlong Liu wrote: >> Same idea with Szilard. >> >> How many nodes are you using? >> On one nodes, how many MPI ranks do you have? The error is complaining about >> you assigned two GPUs to only one MPI process on one node. If you spread >> your two MPI ranks on two nodes, that means you only have one at each. Then >> you can't assign two GPU for only one MPI rank. >> >> How many GPU do you have on one node? If there are two, you can either >> launch two PPMPI processes on one node and assign two GPU for them. If you >> only want to launch one MPI rank on each node, you can assign only one GPU >> for each node ( by -gpu_id 0 ) >> >> Yunlong > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
