[gmx-users] gromacs in parallel version

Diego Enry Gomes diego.enry at gmail.com
Mon Mar 9 09:15:29 CET 2009

Looks like you are using MPICH2 as "mpi" software.
Try including "mpirun" before mdrun_mpi.

mpirun -n 4 mdun_mpi -v -s topol.tpr

If that doesn't work you shoud run start the MPI DAEMON ( MPD ) before  

mpirun -n 2 mdun_mpi -v -s topol.tpr

after you job finishes you might want to stop the mpi daemon by running:


Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA.  +1 (509) 372.6363
diegoenry.gomes at pnl.gov

On Mar 6, 2009, at 5:13 AM, ANINDITA GAYEN wrote:

> Dear all,
>             Sorry for the former post without any subject.
>             I want to install gromacs in parallel version. I already  
> have the normal version of gromacs and i want an MPI version of  
> mdrun. The commands i have used are as followed.........
> make distclean
> ./configure --enable-float --enable-mpi --prefix=/home/x --program- 
> suffix=_mpi
> make mdrun -j 4
> make install-mdrun
> [ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and  
> in .bashrc include .......
>    export CPPFLAGS=-I/home/x/fftw-3.2.1/include
>    export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
> grmmacs installation run successfully.
> But when i run
> mdrun_mpi ..................i got the message  "Can't read  
> MPIRUN_MPD" and the mdrun_mpi program does not run.
> Any suggestion regarding this problem will be highly acceptable.
> thanks in advance,
> Ms. Anindita Gayen
> C/O Dr. Chaitali Mukhopadhyay
> Senior Research Fellow
> Department of Chemistry
> University of Calcutta
> 92, A. P. C. Road
> Kolkata-700 009
> India
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