[gmx-users] Error while running gmx_mpi mdrun - Gromacs-5.1.1

[Ashalatha Sreshty]

Dear Gromacs Users,

I need help in resolving the error that occurred while executing the
gmx_mpi mdrun. I have compiled gromacs-5.1.1 using the following lines:

 with mpi and mdrun only

CMAKE_PREFIX_PATH=/home/ashas/Programs/Gromacs-5.1.1/fftw-3.3.4:/usr/mpi/gcc/mvapich2-1.7/bin
CMAKE_INCLUDE_PATH=/home/ashas/Programs/Gromacs-5.1.1/fftw-3.3.4/include
CMAKE_LIBRARY_PATH=/home/ashas/Programs/Gromacs-5.1.1/fftw-3.3.4/lib

cmake .. -DGMX_DEFAULT_SUFFIX=OFF -DGMX_DOUBLE=ON -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/home/ashas/Programs/Gromacs-5.1.1/gromacs-5.1.1
-DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_PREFIX_PATH=/home/ashas/Programs/Gromacs-5.1.1/fftw-3.3.4
-DREGRESSIONTEST_PATH=/home/ashas/Programs/Gromacs-5.1.1/regressiontests-5.1.1
-DGMX_BINARY_SUFFIX=_mpi
-DFFTW3F_LIBRARIES=/home/ashas/Programs/Gromacs-5.1.1/fftw-3.3.4/lib/libfftw3f.a
-DFFTW3F_INCLUDE_DIR=/home/ashas/Programs/Gromacs-5.1.1/fftw-3.3.4/include
-DGMX_THREADS=OFF -DBUILD_SHARED_LIBS=OFF -DGMX_X11=OFF
-DMPI_INCLUDE_PATH=/usr/mpi/gcc/mvapich2-1.7/include
-DMPI_COMPILER=/usr/mpi/gcc/mvapich2-1.7/bin/mpicc -DGMX_BUILD_MDRUN_ONLY=ON

make install

the installation has finished successfully with gmx_mpi executable in the
bin directory, however, when I execute the command as below:

mpirun -np 64 gmx_mpi mdrun -deffnm MtH_MD-1 -c MtH_MD-1.pdb

I get the following error:

Reading file MtH_MD-1.tpr, VERSION 5.1.1 (double precision)
Using 1 MPI process
Using 64 OpenMP threads


-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.1
Source code file:
/home/ashas/Programs/Gromacs-5.1.1/gromacs-5.1.1/src/programs/mdrun/resource-division.cpp,
line: 571

Fatal error:
Your choice of 1 MPI rank and the use of 64 total threads leads to the use
of 64 OpenMP threads, whereas we expect the optimum to be with more MPI
ranks with 1 to 6 OpenMP threads. If you want to run with this many OpenMP
threads, specify the -ntomp option. But we suggest to increase the number
of MPI ranks.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

I feel there is some issue with the compilation, if it is true, I need your
help to point it out and help me resolve it.

I hope I am clear with the issue, but if you require any other information
please let me know.

Thanks in advance!!

Dr. M. Asha Latha Sreshty,
Post Doctoral Fellow,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore