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

[Mark Abraham]

Hi,

You should only attempt this if the machines running MPI have homogeneous
hardware, otherwise the faster ones just wait for the slower ones. So,
assuming you have two near-identical machines, you can do a diff of the
single-node and dual-node log files and observe what mdrun is probably
complaining about in the two cases.

Mark

On Fri, Oct 17, 2014 at 5:05 PM, Rytis Slatkevičius <rytis.s at gmail.com>
wrote:

> 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
> > > > --
> > > > Gromacs Users mailing list
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