[gmx-users] parallelizing gromacs2018.4

[Mark Abraham]

Hi,

Looks like nodes=1:ppn=20 sets the number of openmpi threads per rank to be
20, on your cluster. Check the documentation for the cluster and/or talk to
your admins.

Mark

On Fri, Nov 23, 2018 at 3:45 PM praveen kumar <praveenche at gmail.com> wrote:

> Dear all
> I have successfully installed gromacs 2018.4 in local PC and HPC center
> (Without GPU)
> using these commands
> CMAKE_PREFIX_PATH=/home/sappidi/software/fftw-3.3.8
> /home/sappidi/software/cmake-3.13.0/bin/cmake ..
> -DCMAKE_INCLUDE_PATH=/home/sappidi/software/fftw-3.3.8/include
> -DCMAKE_LIBRARY_PATH=/home/sappidi/software/fftw-3.3.8/lib
>       -DGMX_GUP=OFF
> -DGMX_MPI=ON
> -DGMX_OPENMP=ON
> -DGMX_X11=ON -DCMAKE_INSTALL_PREFIX=/home/sappidi/software/gromacs-2018.4
> -DCMAKE_CXX_COMPILER=/home/sappidi/software/openmpi-2.0.1/bin/mpicxx
> -DCMAKE_C_COMPILER=/home/sappidi/software/openmpi-2.0.1/bin/mpicc
> make && make install
> the sample job runs perfectly without using mpirun.
> but when I want to run on multiple processors on single node or multi
> nodes, I am getting following error message
>
> "Fatal error:
> Your choice of number of MPI ranks and amount of resources results in using
> 20
> OpenMP threads per rank, which is most likely inefficient. The optimum is
> usually between 1 and 6 threads per rank. If you want to run with this
> setup,
> specify the -ntomp option. But we suggest to change the number of MPI
> ranks."
>
> I have tried to rectify the problem using several ways but could not
> succeed.
> The sample job script file for my HPC run is shown below.
>
> #!/bin/bash
> #PBS -N test
> #PBS -q mini
> #PBS -l nodes=1:ppn=20
> #PBS -j oe
> #$ -e err.$JOB_ID.$JOB_NAME
> #$ -o out.$JOB_ID.$JOB_NAME
> cd $PBS_O_WORKDIR
> export I_MPI_FABRICS=shm:dapl
> export I_MPI_MPD_TMPDIR=/scratch/sappidi/largefile/
>
>
> /home/sappidi/software/openmpi-2.0.1/bin/mpirun -np 20 -machinefile
> $PBS_NODEFILE /home/sappidi/software/gromacs-2018.4/bin/gmx_mpi  mdrun -v
> -s NVT1.tpr -deffnm test9
>
> I wondering what could be the reason,
>
> Thanking in advance
> Praveen
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