[gmx-users] Not achieving any speedup using Open MPI
johnny.lu128 at gmail.com
Fri Oct 17 16:42:12 CEST 2014
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.
> On Fri, Oct 17, 2014 at 9:20 AM, Rytis Slatkevičius <rytis.s at gmail.com>
> > 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
> > 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
> > 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
> > 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
> > 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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