[gmx-users] mdrun using mpirun
kay.gottschalk at weizmann.ac.il
Wed Nov 3 08:50:48 CET 2004
mpirun -np 2 mdrun -np 2 works for me...
On Nov 3, 2004, at 9:45 AM, jianzou wrote:
>> 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 taken?
> 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 each.
> 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 -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.
> Jian Zou
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
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