[gmx-users] compile mdrun for parallel run

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 16 08:54:07 CET 2004

On Wed, 2004-12-15 at 22:08 +0100, Shirley Siu wrote:
> Hi,
> I have been trying compiling mdrun for parallel runs in a machine with 64
> processors with the SUNWhpc library. After many failures and some
> modifications, I compiled it successfully
> >> i configure with this:
> configure --disable-fortran --enable-mpi --program-suffix=_mpi
> make mdrun
> make install-mdrun
> >> then i try running it:
> grompp -np 10 -v -f em.mdp -c b4em.gro -p complex.top -o em.tpr
> mprun -np 10 mdrun_mpi -v -s em.tpr -o em.trr -c b4pr.gro -g em.log -e em.edr
> error that i got in "mprun":
> Fatal error: run input file em.tpr was made for 10 nodes,
>              while mdrun_mpi expected it to be for 1 nodes.
> >> if i run with "-np 10" option for mdrun, another error appears:
> mprun -np 10 mdrun_mpi -v -s em.tpr -o em.trr -c b4pr.gro -g em.log -e em.edr -np 10
> Fatal error: GROMACS compiled without MPI support - can't do parallel runs
This message is probably correct. Maybe you compiled without mpi first
and then with mpi, such that object files are present without mpi
support. Try to do:

make distclean
configure --disable-fortran --enable-mpi --program-suffix=_mpi
make install

> I have checked over the mailing list and the methods mentioned, but it
> still doesn't work. Can anyone help? Tks.
> Utako
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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