David van der Spoel
spoel at xray.bmc.uu.se
Thu Apr 13 09:52:42 CEST 2006
Dongsheng Zhang wrote:
> dear Mark,
> Thank you very much for your prompt reply. I try to use parallel
> computing. It works fine.
> for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle
> to get replica0.tpr
> then, mdrun_mpi -np 2 -s replica0.tpr
please give EXACT command line and do use mpirun
> The error message mentioned in the previous email looks very strange to
> me. MPI works fine, and individual tpr runs fine. The error message
> comes out before replica exchange. replica0 stops at step 500, replica1
> stops at step 400, even the output informatio can't be complted. The
> last lines in replica1.log is
> Step Time Lambda
> 400 0.80000 0.00000
> Rel. Constraint Deviation: Max between atoms RMS
> I hope these further information can help you to figure out what's the
> Best Wishes!
> On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
>>> Dear gmx users:
>>> I am trying to run REMD with two replicas (for testing). I used
>>> grompp -f -c -p -o replica0 to get replica0.tpr
>>> grompp -f -c -p -o replica1 to get replica1.tpr
>>> then used
>>> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
>>> -v -N 2
>>> to run it.
>> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
>> looks fine to me.
>>> I got an error message "Segmentation fault" from my script output, but
>>> no error message in both log files. When I tried to run individual tpr
>>> file, it worked fine.
>>> Could someone can comment why I got "Segmentation fault"? Thank you for
>>> your help!
>> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
>> ..." to make it work - the segfault might be a gromacs-MPI interaction
>> problem. If you can run an MPI process from the command line you may get
>> more helpful feedback.
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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://folding.bmc.uu.se
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