Hi there,
In a emailed titled "Amber with MPI (GNU and Intel) on Mac SL" I reported my
issues with Intel and OMPI and they are exactly what seen here.
Alan
On Wed, May 5, 2010 at 01:35, Ben Roberts <roberts.qtp.ufl.edu> wrote:
>
> On 4/5/2010, at 5:45 p.m., Ben Roberts wrote:
>
> > Unfortunately, I've just switched back to using 11.1.084, and I still get
> the same complaints. I don't know how I could have overlooked them earlier.
> >
> > A bigger problem I ran into with the 11.1.088 was that MPI executables
> failed rather comprehensively (in the sense that nothing at all worked -
> everything segfaulted). So I'm seeing if downgrading fixed that problem too.
> If not, I'll at least see if I can find out what's going on, though I
> suspect nothing good or easy to track down.
>
> Nope, downgrading didn't fix the problem with the parallel programs, to
> wit, the following:
>
> ./Run.sff: Program error
> make[2]: *** [sff_test] Error 1
> Running test to do simple minimization with shake
> (this tests the molecular mechanics interface)
>
> [qtpclnt070:22754] *** Process received signal ***
> [qtpclnt070:22754] Signal: Segmentation fault (11)
> [qtpclnt070:22754] Signal code: Address not mapped (1)
> [qtpclnt070:22754] Failing at address: 0x362e6cb68
> [qtpclnt070:22754] *** End of error message ***
> [qtpclnt070:22755] *** Process received signal ***
> [qtpclnt070:22755] Signal: Segmentation fault (11)
> [qtpclnt070:22755] Signal code: Address not mapped (1)
> [qtpclnt070:22755] Failing at address: 0x362e6cb68
> [qtpclnt070:22755] *** End of error message ***
>
> and analogous messages for other parts of AmberTools parallel and Amber
> parallel.
>
> Nor did compiling OpenMPI with --with-memory-manager=none, per a suggestion
> I found online.
>
> I'll look further into this. If the problem seems to be Amber code-related,
> I'll move this part of the discussion to amber-developers. If on my system,
> I plan on doing a follow-up post here for discovery by other inquiring
> users, along with a post at the Amber on Mac blog detailing what needs to be
> done.
>
> Ben
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>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed May 05 2010 - 01:30:03 PDT
