Shawn T. Brown wrote:
Hello, I am trying to port GROMACS 3.3.1 to the CRAY XT3, which is
essentially an Opteron machine with the PGI compilers. I can get
everything to compile, but when I run mdrun, I am “randomly” getting
segmentation faults. This seems to happen no matter what input file I
use. It happens in init_forcerec (line 1001), in add_gbond, and in
solvent_check. Some times it runs fine. I am configuring with the
following command:
./configure --with-fft=fftw3 --disable-nice --enable-mpi
--program-suffix="_xt3" --enable-float --with-external-blas
--with-external-lapack --disable-threads
--prefix=/usr/local/packages/gromacs-3.3.1
I am wondering if anyone else has seen these types of problems and knows
how to fix them. I have tried compiling the code without optimization,
to no avail.
Thanks in advance,
Shawn
Hi Shawn, last time I tested the PGI compiler gave at most equal
performance as the gcc compilers. I presume you could try compiling with
gcc.
From your mail it is not clear whether the problems occurs in parallel
or in sequential execution of mdrun. Anyway it is of course difficult to
debug remotely, e.g. line 1001 is force.c does not look very suspect.
Shawn T. Brown
/Senior Scientific Support Specialist/
*Pittsburgh** Supercomputing Center*
Carnegie Mellon University
Pittsburgh Supercomputing Center
Rm #369
Pittsburgh, PA 15213
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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