[gmx-users] about parallel run

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 15 01:54:16 CET 2008

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 :-)


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