[gmx-users] Re: gromacs 4.0 parallelization

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 9 03:50:12 CET 2009

Justin A. Lemkul wrote:
> 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 Gromacs.

And additionally, I should read better before replying.  The --enable-mpi option 
is not an mpirun or mdrun option.  It must be invoked when configuring Gromacs. 
  Please be sure to read the instructions here:




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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