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

[Rytis Slatkevičius]

I am not mixing OpenMP with MPI; it runs one process per core and all are
communicating via Open MPI. Mixing these was indeed even slower.

--
Pagarbiai / Sincerely
Rytis Slatkevičius
+370 670 77777

On Fri, Oct 17, 2014 at 5:42 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> i heard that mixing mpi and open mp together is bad idea (run more slow),
> unless the simulation has large number of atoms, and use many cpu.
>
> May be comparing gromacs running on a single computer, with and without
> openmp will show a difference in speed.
>
> On Fri, Oct 17, 2014 at 10:05 AM, 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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