[gmx-users] Mismatching number of PP MPI processes and GPUs per node

[George Patargias]

Hi Carsten

Thanks a lot for this tip. It worked!

George

> Hi,
>
> On Mar 11, 2013, at 10:50 AM, George Patargias <gpat at 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
>>
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>
> --
> 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
>
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Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568