[gmx-users] compile mdrun for parallel run

[Marc Vogt]

Sorry, I obviously completely missed the second part of your post......

Not sure after that.  I think I had the same problem at some point
and it only worked if I got rid of the suffix option and didn't make
a second mdrun executable with suffix.  Instead I just made the main mdrun
be mpi capable.  And it worked.  Not sure why though.

Marc

> 
> I think you need a second -np 10 as an argument for mdrun_mpi
> 
> 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 -np 10
> 
> 
> Marc
> 
> 
> 
> > 
> > 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
> > 
> > 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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> 
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