[gmx-users] Re: no speedup with mpirun on dual processor

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 10 16:22:39 CET 2004

On Fri, 2004-12-10 at 10:07 -0500, Marc Vogt wrote:
> Hi David
> I don't think my email to gmx-users went through that I sent last night since I
> haven't seen it.  I am trying to run a job in parallel on a dual processor
> machine.  Everything seems to go fine and both processors have mdrun at
> 99% utilization, but I see no speed up over running the job in serial.
> It is almost the same exact rate.  
> I used grompp with the -np 2 option to make the tpr file
> and then did
> mpirun -np 2 mdrun (options) -np 2
> It's like the second processor is just waiting and spinning, but not really
> ever getting any of the job.   I've seen this behavior before trying to run 
> code that was not tagged with mpi at all, but I compiled with --enable-mpi
> and no prefix option. 
do you have hyperthreading turned on? if so, turn it off.

> Any ideas on what could be wrong.  Also, please forward to the list
> of you would please.
> Thanks,
> Marc
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

More information about the gromacs.org_gmx-users mailing list