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

Da-Wei Li lidawei at gmail.com
Fri Oct 17 16:06:06 CEST 2014

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 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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