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

Rytis Slatkevičius rytis.s at gmail.com
Fri Oct 17 15:20:41 CEST 2014


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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