[gmx-users] about parallel work

sheerychen sheerychen at gmail.com
Tue Apr 21 17:04:47 CEST 2009

> Hello, every body. I have a question about parallel running of mdrun_mpi. I
> doubt that sometimes the parallel running of mdrun_mpi can not utilize the
> domain decomposition.
> This is the case when I use the batch work in the computer cluster which
> install the MPICH2. In the case, I use commond like ''mpirun -np 8 mdrun_mpi
> -deffnm *** -v'' . (The command ''mpirun -np 3 /usr/bin/mdrun_mpi -deffnm
> *** -v'' doesn't work) .The working didn't show any information about domain
> decomposition. And the computing rate is rather slow, which is only a little
> bit higher than single CPU.
> However, in my person computer which install the MPICH (not MPICH 2), I use
> the commond like this ''mpirun -np 3 /usr/bin/mdrun_mpi -deffnm *** -v''. It
> would show the domain decomposition and the speed is quicked than 8 CPUS.
> What is the problem???
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