[gmx-users] about parallel run

Yang Ye leafyoung at yahoo.com
Tue Jan 15 03:11:07 CET 2008

i reckon that you have not built in mpi support to mdrun in GROMACS so 
each instance of mdrun produces one trajectory rather than running in 
parallel and produce only one trajectory.

Mark Abraham wrote:
> Yunierkis Perez Castillo wrote:
>> Hi all, I'm new to gromacs. I have setup a protein MD simulation in a 
>> cluster, I'm using 6 computers with 2 CPUs each one.
>> After gromacs begun running I had 12 trajectory files in the folder 
>> the output is written:
>> md.trr
>> #md.trr.1#
>> #md.trr.2#
>> ................
>> #md.trr.11#
>> It seems like the trajectory is replicated by each CPU the simulation 
>> is running on.
>> All files has the same size, and grows  simultaneously as the 
>> simulation advances.
>> Is that a normal thing??
>> Can I delete the #* files??
> I infer from your results that you've run 12 single-processor 
> simulations from the same working directory. GROMACS makes backups of 
> files when you direct it to write to an existing file, and these are 
> numbered as #filename.index#. Your 12 simulations are all there, but 
> you can't assume that those files with number 5 are all from the same 
> simulation, because of the possibility of filesystem asynchronicities 
> in creating the files.
> If you're trying to run 12 single-processor simulations in the same 
> working directory, then you need to rethink your strategy. If you're 
> trying to do something else, then you also need to rethink :-)
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before 
> posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list