This just tells that two GPU-s were detected but only the first one was automatically selected to be used - presumably because you manually specified the number of ranks (-np or -ntmpi) to be one.
However, your mail contains neither the command line you started mdrun with, nor (a link to) the log file mdrun produces. -- Szilárd On Wed, May 14, 2014 at 2:43 PM, Albert <mailmd2...@gmail.com> wrote: > Hi Mark: > > thanks a lot for the messages. In most cases, job failed with following > messages if I used intel MPI to evoke two GPU: > > [mpiexec@cudaA.compuBio] HYDU_getfullhostname > (./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio, > error: Name or service not known) > [mpiexec@cudaA.compuBio] HYDU_sock_create_and_listen_portstr > (./utils/sock/sock.c:999): unable to get local hostname > [mpiexec@cudaA.compuBio] HYD_pmci_launch_procs > (./pm/pmiserv/pmiserv_pmci.c:313): unable to create PMI port > [mpiexec@cudaA.compuBio] main (./ui/mpich/mpiexec.c:877): process manager > returned error launching processes > > > for one GPU job, here is the informations: > > 2 GPUs detected on host cudaA.compuBio: > #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 > > 1 GPU auto-selected for this run. > Mapping of GPU to the 1 PP rank in this node: #0 > > > NOTE: potentially sub-optimal launch configuration, mdrun_mpi started with > less > PP MPI process per node than GPUs available. > Each PP MPI process can use only one GPU, 1 GPU per node will be used. > > thank you verymuch. > > > 2014-05-14 9:11 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>: > >> Hi, >> >> Nobody can tell unless you upload .log files and mdrun command lines >> somewhere >> >> Mark >> >> >> On Wed, May 14, 2014 at 7:03 AM, Albert <mailmd2...@gmail.com> wrote: >> >> > Hello: >> > >> > I've compiled Gromacs in a GPU machine with two GTX780Ti with following >> > command: >> > >> > env CC=icc F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/soft/intel/ >> > mkl/include/fftw:/soft/intel/impi/4.1.3.049/intel64:/soft/ >> > intel/mkl/lib/intel64 <http://4.1.3.049/intel64:/ >> > soft/intel/mkl/lib/intel64> cmake .. -DBUILD_SHARED_LIB=OFF >> > -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/soft/gromacs-5.0rc1 >> > -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda >> > >> > >> > I've got 40ns/day for a 65,000 atoms membrane system under CHARMM36 FF >> > when one GPU is used, but it is only 27ns/day if I used two GPUs. In >> > another machine with two GTX690, I used ICC+openmpi instead of ICC+intel >> > MPI. The same system, I obtained 40ns/day for one GPU, and 60ns/day for >> two >> > GPU. >> > >> > I am just wondering, why it is even slower with two GTX780Ti for my >> > system, which doesn't happen to GTX690? >> > >> > thx a lot >> > >> > Albert >> > -- >> > 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. >> > >> -- >> 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. >> > -- > 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. -- 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.