[gmx-users] gromacs 4.0 parallelization

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 7 00:24:34 CET 2009

milad ekramnia wrote:
> Dear gromacs users I am working with gromacs 4.0 and my system is a protein
> under tension solvated in water under Lincs constraint .when I run my mdrun
> over n nodes by mpirun I'll get n-1 trajectory files (also the same happen
> for all other output files ) which as it appears all are identical. as far as
> I know each file shall represent a separate part of the box but when I
> analyze the trrs the results are identical ( e.g for g_gyrate task ) I want
> to now if they are exactly the same ? if yes , can I prevent the rest of them
> from being biult up ?

It sounds like, instead of one single MPI process, you're getting a number of 
identical (serial) runs.  Did you --enable-mpi when you configured mdrun?


> thanks


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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