kalav...@gmx.net wrote:
Hi,
I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the
intel compiler suit 12.0.2, still leading to segmentation faults. As
suggested, I tried lots of combinations of different forcefields, water
types and *.pdb's. Non of them was successful, so my segmentation fault
is reproducible. Even the delivered tutorial/test cases stopped with a
segmentation fault.
It would probably be useful to compile with debugging support (CFLAGS=-g) and
run pdb2gmx through a debugger like gdb. That way you can track down exactly
what's happening.
As a last step, I will try to compile gromacs with CMake. If there are
any alternatives you would suggest me to conduct, don't hesitated to let
me know.
That might be worth a try, but it would also be useful to grab the latest
release-4-5-patches to see if this is the same issue as
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060685.html or a
different one.
The readdir_r() issue hasn't been fixed yet (since bug 739 is still open -
http://redmine.gromacs.org/issues/739), but at least working with the latest
development version might provide some clues if there's something else that's
been fixed along the way.
-Justin
Cheers,
M.Kalavera
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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