[gmx-users] MPI GPU job failed

[Szilárd Páll]

PPS: given the double output (e.g. "Reading file 61.tpr, ...") it's
even more likely that you're using a non-PI build.

BTW, looks like you had the same issue about two years ago:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092046.html

--
Szilárd


On Thu, Aug 11, 2016 at 4:06 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
> PS: Or your GROMACS installation uses _mpi suffixes, but it is
> actually not building with MPI enabled.
> --
> Szilárd
>
>
> On Thu, Aug 11, 2016 at 4:05 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>> On Wed, Aug 10, 2016 at 4:03 PM, Albert <mailmd2011 at gmail.com> wrote:
>>> Hello:
>>>
>>> I am trying to submit gromacs jobs with command line:
>>>
>>> mpirun -np 2 gmx_mpi mdrun -s 61.tpr -v -g 61.log -c 61.gro -x 61.xtc -ntomp
>>> 10 -gpu_id 01
>>>
>>> However, it failed with messages:
>>>
>>>
>>>
>>>    Number of GPUs detected: 2
>>>     #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
>>>
>>> Reading file 61.tpr, VERSION 5.1.3 (single precision)
>>> Reading file 61.tpr, VERSION 5.1.3 (single precision)
>>> Using 1 MPI process
>>> Using 10 OpenMP threads
>>>
>>> 2 GPUs user-selected for this run.
>>> Mapping of GPU IDs to the 1 PP rank in this node: 0,1
>>> -------------------------------------------------------
>>> Program gmx mdrun, VERSION 5.1.3
>>> Source code file:
>>> /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/gmxlib/gmx_detect_hardware.cpp,
>>> line: 458
>>>
>>> Fatal error:
>>> Incorrect launch configuration: mismatching number of PP MPI processes and
>>> GPUs per node.
>>> gmx_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
>>> -------------------------------------------------------
>>>
>>>
>>>
>>> I have used the option "mpirun -np 2" and I don't know why it calimed
>>> "gmx_mpi was started with 1 PP MPI"
>>
>> Most likely because your MPI is not configured correctly.
>>
>>> Thanks a lot
>>>
>>>
>>> --
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