Thanks to all the people who gave me suggestions on how to build Gromacs
under Pathscale/Infiniband. I did succeed in building it, the trick was
to use
CFLAGS=-O3
which was mentioned on the Pathscale site http://www.pathscale.com/
building_code/gromacs.html
for an older version of Gromacs.
I'm locked into the Pathscale compilers at this point because our
nodes have Pathscale
IB, drivers, and compilers, and reconfiguring them is not an option
right now.
I'll definitely try the suggestion about disabling Fortran next. At
this point I do
have a working version of Gromacs on IB, so it's a little lower
priority. My current
build on the Infiniband/Opteron nodes gives pretty great performance.
I ran the d.dppc benchmark on several types of nodes including the
Infiniband;
if anyone is interested the results are at
http://biowulf.nih.gov/apps/gromacs/bench-3.3.1.html
Consistent superscaling (up to 10processors with Infiniband);
interesting!
Susan.
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