[gmx-users] mdrun using mpirun
zouj01 at mails.tsinghua.edu.cn
Wed Nov 3 08:45:45 CET 2004
> Hi Jianzou,
> it was a bit unclear for me, but did you use
> grompp -np 2 ...
> mpirun -np 2 mdrun_mpi -np 2 ...
> works for me at least.
> Best regards,
Thanks a lot, but I tried this but failed again:(
I've checked some posts here, and wonder that why someone use "mpirun -np 2
mdrun_mpi ...", but you use "mpirun -np 2 mdrun_mpi -np 2". Which should be
I wrote bhost for lam as
and run as lamboot -v bhost, grompp -np 2 -v, mpirun -np 2 mdrun_mpi -v
but got singal 11 error.
I also tried to include the full path for mpirun and mdrun, but it does not
work in my case.
I check GROMACS User Manual v3.2 - Appendix A. Technical Details - Appendix
A.5 Running GROMACS in parallel, which gives 2 examples
1. A typical command line looks like
% mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30
this runs on each of the machines goofus,doofus,fred with 10 processes on
2. If you have a single machine with multiple processors you don't have to
use the mpirun command, but you can do with an extra option to mdrun:
% mdrun -np 8 -s topol -v -N 8
In this example MPI reads the first option from the command line. Since
mdrun also wants to know the number of processes you have to type it twice.
I tried "mdrun -np 2 -s topol.tpr -v -N 2" like the second example above,
got the segmentation error.
Could anyone please help me out of this?
Thanks in advance.
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