Tom Joseph wrote:
Providing a backtrace or two would really help. Given the exact same
input files and run conditions, does it sometimes segfault and sometimes
not? Does this happen on a login node (full glibc and such) or just the
compute nodes (POSIX subset)?
Separately, is it a better idea to use fftw2 since it supports MPI?
No, gromacs now does the parallel FFT itself, and fftw3 is slightly faster.
(Hopefully soon my Teragrid access will extend to bigben, so I'm
especially interested in this...)
--Tom
On Apr 17, 2006, at 10:06 PM, 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
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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