----- "case" <case.biomaps.rutgers.edu> wrote:
> On Fri, May 14, 2010, Jan Schulze wrote:
> >
> > I have been compiling serial and parallel Amber 11 with gcc 4.5.0
> and
> > openmpi 1.3.3. The test suites of amber tools and serial amber are
> > successful and do not have any test failures. When testing parallel
> > amber with 2 processors, almost all tests are successful - three
> tests
> > show very small test differences.
>
> Others have reported seemingly similar problems; I'm hoping the NEB
> gurus
> can take a look at this, finding a machine that shows the problem.
> Other
> reports suggest that the hangs are "random" (i.e. not always in the
> same
> place).
For me, they always happen in the same place.
> For now, the prudent thing to do is to comment out the neb test cases
> in
> amber11/test/Makefile, and await bugfixes.
>
> It would help to know what OS you are using, and how you installed
> the
> compiler. gcc 4.5.0 was only released a month ago, so you may be one
> of the
> early testers here. Have you tried any other compilers, or any more
> recent
> version of openmpi? The reason I ask about more recent openmpi comes
> from
> bug reports at the openmpi site:
I am using Scientific Linux 5.2, but the compiler was built and tested by hand. I also tried gcc 4.3.2 (self-built). That gave big test errors for the serial version, so I did not try the parallel one. With OpenMPI 1.4.2 (and gcc 4.5.0) it's the stuck test case again.
I'll try the compat-gcc (v. 3.X) option for compiling OpenMPI, that was suggested in the other answer, and report back.
Best Regards,
Jan
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Received on Mon May 17 2010 - 05:00:03 PDT
