[gmx-users] Re: gromacs 4.0 parallelization

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 9 03:47:01 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 ?
> my mdrun command line is : mpirun -n 4 mdrun_mpi -v -s topol.tpr

Is -n the appropriate option?  Some MPI implementations are different (-np, -N, 
etc), and/or you may need to supply a hostfile.

> and the grommp command is: grompp_mpi -v -c minimized.gro  -p topol.top  -f pull.mdp  -n index.ndx  
> I also added --enabled-mpi to my mdrun command line but it didn't work .

If you did "--enabled-mpi" then that is incorrect, and you probably didn't 
actually compile with MPI support.  The proper configuration option is 
"--enable-mpi" so you should check that you did not make a typo when installing 


> 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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