On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote:
Hi,
I have been trying to run Gromacs 4.5.3 parallel simulations using
openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this
version of Gromacs.
I don't understand what (you think) you mean. You can use thread-based
parallelism for processors that share common silicon, or MPI-based
parallelism if a network connection is involved, but not both. The
latter is named mdrun_mpi by default.
Our system administrator told me that all mpi related options have
been turned on while installing Gromacs. With either commands:
mdrun -np X -deffnm topol -N X (run in an 8-cpu node)
This won't run in parallel at all. mdrun ignores -np and -N
or
mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes
depending on availability)
This will get you the symptoms below, but -N is still ignored.
I get X identical simulations instead of a parallel run. If X=4, I get
4 identical simulations (the same simulation ran 4 times) instead of 1
parallel simulation in 4 processors. The performance difference
between a single-processor run and the X=4 run are also similar (no
marked difference in the time it takes to finish the simulation).
Has anyone encountered this problem?
You're using a serial mdrun. Use a parallel mdrun.
Mark
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