[gmx-users] why two GTX780ti is slower?

[Albert]

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 at cudaA.compuBio] HYDU_getfullhostname
(./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio,
error: Name or service not known)
[mpiexec at cudaA.compuBio] HYDU_sock_create_and_listen_portstr
(./utils/sock/sock.c:999): unable to get local hostname
[mpiexec at cudaA.compuBio] HYD_pmci_launch_procs
(./pm/pmiserv/pmiserv_pmci.c:313): unable to create PMI port
[mpiexec at 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.abraham at 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 <mailmd2011 at 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
> > --
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