[gmx-developers] some notes on compiling the current gmx cvs sources on cray xt3

Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
Wed May 17 03:32:01 CEST 2006

hi everybody,

im currently trying to get the current gmx development cvs sources
compiled on a cray xt3 (basically an opteron cluster with an embedded
kernel and a special low-lentency network).
the catch is, that one has to basically cross-compile, which only
seems to work, when i edit the configure file to default to cross-compilation.
otherwise ./configure will not finish and create the makefiles etc...

while trying several options, i noticed that a) you cannot currently compile
serially and b) there are a number of c++ style comments in the c-code
that have PGI's pgcc choke heavily (gcc is more forgiving). a patch that
attempts to fix both problems is attached.

as already reported by shawn brown elsewhere, the gcc compiled code
tends to crash
in different places (e.g. segfault in add_gbond(), mpi error in splitter.c).

the PGI compiled binary seems to work, however, and for the DPPC
benchmark input it has a speed increase even for large numbers of
nodes (just with standard settings and no i/o buffer hacks etc, that
should help the code to scale even more on this machine). the same
code checkout with the same optimization compiled on a dual-opteron
myrinet cluster running the identical input scales out at 8 processors...

32 nodes:
               NODE (s)   Real (s)      (%)
       Time:    274.000    274.000    100.0            4:34
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    161.963     15.477      3.153      7.611

64 nodes:
               NODE (s)   Real (s)      (%)
       Time:    191.000    191.000    100.0            3:11
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    232.514     22.285      4.524      5.306

96 nodes:
               NODE (s)   Real (s)      (%)
       Time:    155.000    155.000    100.0              2:35
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    286.292     27.540      5.574      4.306

best regards,
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.
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