[gmx-users] SMP/Parallel mdrun
gmx3 at hotmail.com
Thu Nov 27 10:49:44 CET 2008
> Date: Thu, 27 Nov 2008 02:49:10 +0000
> From: ijstokes at crystal.harvard.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] SMP/Parallel mdrun
> Hi Mark,
> Mark Abraham wrote:
> > Terminology - GROMACS is not threaded, but uses MPI processes for
> > parallelism.
> Yes, I gathered that.
> >> I have an MPI-compiled version of gromacs v4.0 and am attempting to
> >> get parallel execution on a 2x2 core AMD Opteron system via:
> >> $ lamboot
> >> $ mdrun -np 4 -s ../1WOM.tpr -v -N 4
> > -N does nothing, and -np is no longer accepted - as you'd know from
> > reading mdrun -h, right?
> That is a bit of a condecending way of putting it. If I knew -N did
> nothing and -np was no longer accepted, then of course I would not have
> used them. In fact, I was reading the documentation from a file called
> "manual-4.0.pdf" which stated:
> If you have a single machine with multiple processors you don’t have to
> use the mpirun com-
> mand, but you can do with an extra option to mdrun:
> % mdrun -np 8 -s topol -v -N 8
> so that is where I took the example from. I think this PDF was linked
> from the gromacs "documentation" section of the website.
Ah, I was not aware of this small section in the manual.
This information was already outdated about a decade ago.
I will remove it.
Note that mdrun also does not have the option -N.
(for some reason, which I still do not know, mdrun does
not check it command line options, unlike all other Gromacs
> > Like most MPI parallel codes, you need to use mpirun. If your lam
> > environment is correctly configured, then I think you will not need
> > -np 4 as an argument to mpirun.
> > Also, probably you are actually running a non-MPI gromacs, since by
> > default, using --enable-mpi will suffix mdrun to be mdrun_mpi.
> Doesn't look like it:
> $ ./configure --prefix=/opt/osg-shared/se/app/site --with-pic --enable-mpi
> $ make
> $ make install
> $ ls /opt/osg-shared/se/app/site/bin/ | grep mdrun
> Anyway, thanks for your suggestions because I now have it working via:
> $ mpirun -np 4 /opt/osg-shared/se/app/site/bin/mdrun -s ../1WOM.tpr -v -N 4
> and I see 4 processes running at 100% and an estimated run time 25% of
> the serial version.
> Ian Stokes-Rees, Research Associate
> SBGrid, Harvard Medical School
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