[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0

Justin A. Lemkul jalemkul at vt.edu
Mon May 9 20:31:50 CEST 2011

Kalavera at 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.


> Cheers,
> M.Kalavera


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list