On 14/12/2010 11:14 AM, Te, Jerez A., Ph.D. wrote:
Hi Mark,
Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The
gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using "mdrun -np 8 -s
topol -v -N 8" in running a single machine with multiple (8) processors and "mpirun -p
goofus,doofus,fred 10 mdrun -s topol -v -N 30" to run three machines with ten processors each.
You probably already know this but I am confused as to whether these commands are correct in
running parallel simulations (thus the assumption that mdrun_mpi is no longer applicable in gromacs
4.5.3). So far I have not been successful in running parallel simulations (as I mentioned before
the two options above would only start X identical serial processes). My bottom line is I want to
run Gromacs simulation in parallel (regardless of whether it is running on one silicon with a
number of processors or on different machines or nodes with a specified number of processors).
I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using the
--enable-mpi option because currently our gromacs executable bin does not have
mdrun_mpi. Our system administrator said that all mpi-related options have been
enabled in compiling gromacs and still the mdrun_mpi is not found as one of the
exe files. Please help.
I echo Justin's comments.
"all mpi-related options" seems suspicious. There's only one,
--enable-mpi. Obviously you need a correctly-configured MPI compiler and
environment for it to work
Mark
Thanks,
JT
-----Original Message-----
From: [email protected] on behalf of Mark Abraham
Sent: Mon 12/13/2010 4:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3
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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