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

[Mark Abraham]

That benchmark is using the group scheme, which started to lose parallel
efficiency with Infiniband at around 1000 atoms/core, but YMMV greatly.
That number will go up for gigabit ethernet. There's no point sharing the
workload if the communication latency becomes comparable with the compute
time, of course.

Mark

On Fri, Oct 17, 2014 at 5:36 PM, Rytis Slatkevičius <rytis.s at gmail.com>
wrote:

> 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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