[gmx-users] Not achieving any speedup using Open MPI

[Rytis Slatkevičius]

Thanks; what do you think would be a good number of atoms to expect actual
speedup?

--
Pagarbiai / Sincerely
Rytis Slatkevičius
+370 670 77777

On Fri, Oct 17, 2014 at 5:05 PM, Da-Wei Li <lidawei at gmail.com> wrote:

> For a system with only ~20K atoms and you are using normal LAN, I feel your
> result is not unexpected.
>
> dawei
>
> On Fri, Oct 17, 2014 at 9:20 AM, Rytis Slatkevičius <rytis.s at gmail.com>
> wrote:
>
> > Hello,
> >
> > first of all: I am not a scientist, but rather an IT person trying to set
> > up Gromacs for fellow scientists. My goal is to set up Gromacs on several
> > local computers (connected with 1gbps LAN) and achieve some speedup of
> our
> > runs using MPI.
> >
> > I have installed Gromacs 5.0.2 from Debian repository (package
> > gromacs-openmpi). I can run Gromacs over multiple computers, I see
> > processes being spooled up, so MPI itself is working. However, I am not
> > seeing any speedup at all - in fact, I get a significant slowdown.
> >
> > When running on a rather old dualcore laptop, I can finish a d.lzm run
> from
> > http://www.gromacs.org/About_Gromacs/Benchmarks within 109s or so. If I
> > add
> > a quadcore machine into the mix, I would expect the computation to be
> much
> > faster - but instead I finish everything within 139 seconds! The quadcore
> > can finish the job in 45 seconds when running on its own without Open
> MPI.
> >
> > I can't wrap my head around what I am doing wrong. My command line is:
> >
> > mpirun --display-map --hostfile hosts mdrun_mpi -v -deffnm d.lzm -dlb yes
> >
> > Any help would be appreciated.
> >
> > --
> > Pagarbiai / Sincerely
> > Rytis Slatkevičius
> > +370 670 77777
> > --
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