Dongsheng Zhang wrote:
Dear David,
I forgot one more information. The computer administrator told me I did
not need to use mpirun. As I told you in the previous email, I have done
tests for parallel computing. It worked fine.
try it with mpirun anyway.
I suspect you are just running a single process which crashes as soon as
it needs to do REMD communication.
Dongsheng
On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote:
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
problem.
Best Wishes!
Dongsheng
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.
Mark
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--
David.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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