[gmx-users] Segmentation fault

[Erik Lindahl]

Alan Wilter Sousa da Silva wrote:

> Hi,
>         I've upgraded a MDK 7.2 linux box to Mandrake 8.0, but to my
> despair gromacs (version 3.0.5 rpm) stoped working.  Every program from
> gromacs package that I try to run stops with 'segmentation fault'. So I
> figured out that some library could not working well.  Then I decided to
> compile gromacs (version tar.gz 3.0.5).  Compilation worked well but I
> still have the same problem.  However I tested the compile version in
> another linux box (full MDK 8.0, not upgraded) and my compilation workred
> pretty well.
>         I think that issue should be sent to the
> gromacs-development-list but I don't take part there.  I believe there's
> some very important file or library to gromacs corrupted which is not
> described as a prerequisite since it must be present in the default linux
> installation.  But everything seems to work well at the upgraded computer,
> only gromacs is presenting problem!
>
>         So, could someone give me a light over this shadow of doubts?

Well, I don't know about mandrake, but most other linux distributions
are binary compatible within when you make minor upgrades (8.0 to 8.1) but
major version changes (7.2 to 8.0) usually breaks at least some of the
binary compatibility. So, I'm not surprised it broke when you upgraded the
system, but I don't know why a recompile didn't help :-)

Apart from the standard system libraries (libc, libm, libnsl, all the X
stuff,etc.)
we only need fftw, and lam if you want to run in parallel. Mandrake might
come with its own version of fftw that probably works, but again it might not
-
that's why we recommend to use the version we have on our homepage. Or
compile it from source - it's straighforward.

I guess the update program should bring your installation more or less in
sync
with a fresh 8.0 install, so unless you have made any major changes to the
7.2
installation this sounds like a bug in the Mandrake updater?

You could try to turn off all features in the configure script to see if that
helps,
but I doubt it will since everything works on the fresh 8.0 install. :-/

Cheers,

Erik