[gmx-users] GROMACS with MPICH on Linux Cluster

[Arijit Tarafdar]

Hi,

I am trying to run GROMACS in parallel on a linux cluster with MPICH. The
configuration I use is as follows:

./configure --prefix=/home/atarafda/HPC/gromacs-3.2.1 \
--enable-mpi --disable-x86-asm --program-suffix=_mpi --with-x \
--without-xml CXX=g++ CC=gcc F77=g77 MPICC=mpicc \
LIBS="-lmpich -lfmpich -lpmpich" \
CPPFLAGS="-I/home/atarafda/HPC/mpich-1.2.6/include
-I/home/atarafda/HPC/fftw-2.1.5/include" \
LDFLAGS="-L/home/atarafda/HPC/mpich-1.2.6/lib
-L/home/atarafda/HPC/fftw-2.1.5/lib"

The compilation goes fine. But when I try to run a job on 10 nodes using
the command

mpirun -np 10 mdrun_mpi -np 10 ...

I get the following error:

Fatal error: run input file /home/atarafda/Solutions/amishra/dpp.tpr was
made for 10 nodes,
             while mdrun_mpi expected it to be for 1 nodes.
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_29480:  p4_error: : -1
    p4_error: latest msg from perror: No such file or directory

The cluster runs other MPI jobs. I use mpich-1.2.6, fftw-2.1.5 and
gromacs-3.2.1

Any suggestion will be highly appreciated.

Thanks,

Arijit


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