[Debichem-devel] Bug#644397: Bug#644397: Bug#644397: gromacs: pdb2gmx, version 4.5.5, fails with 'Illegal instruction' on i686, 3.0.0.1-686-pae (testing)

[Nicholas Breen]

On Sat, Oct 08, 2011 at 08:26:37PM +0200, groenedraeck wrote:
> $ apt-get source --build gromacs > log.20111007 2>&1

When building that package, it's also possible to both turn on debugging (i.e.
turn off binary stripping at the end) and disable compiler optimization.  The
latter might help avoid the bug, and the former should help identify what
exactly is causing the failure.  A command such as:

 $ DEB_BUILD_OPTIONS=noopt,debug apt-get source --build (etc.)

will enable both options.  I would be curious to learn if that changes the bug
behavior in any way.  Unfortunately I have no access to Duron hardware and
cannot test these myself.



> When finished, the log was inspected for apparent errors. The log
> file frequently contained a MPI implementation error:
> > -- Using manually set binary suffix: "_mpi.mpich"
> > -- Using manually set library suffix: "_mpi.mpich"
> > CMake Warning at CMakeLists.txt:192 (MESSAGE):
> >
> >
> >             There are known problems with some MPI implementations:
> >                        OpenMPI version < 1.4.1
> >                        MVAPICH2 version <= 1.4.1

These are harmless, it issues those warnings regardless of the OpenMPI version
on the system (your installation is probably using 1.4.3), and pdb2gmx doesn't
use MPI anyhow.

Best,


-- 
Nicholas Breen
nbreen at ofb.net