[gmx-users] XT3 porting
tom-lists at jambon.ll.cx
Tue Apr 18 04:43:49 CEST 2006
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?
(Hopefully soon my Teragrid access will extend to bigben, so I'm
especially interested in this...)
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,
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