Hi John,
Does everything segfault instantly? Even say:
mpirun -np 2 /path_to_sander/sander.MPI
Which when run from an empty directory should report that it cannot find
'mdin'.
If this is the case then I would suspect 1 of 2 problems:
1) Your mpirun does not match the mpi instance you are building with. Thus
the code is segfaulting at mpi_init.
2) You do not have enough stack space. Try ulimit -s unlimited (Or as high
as you can make it).
If it is failing on a specific job or at a specific point in the code we
would need more info to be able to look further.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Beale, John
> Sent: Thursday, April 01, 2010 11:53 AM
> To: AMBER Mailing List
> Subject: [AMBER] Segmentation Fault
>
> I am getting a segmentation fault when I try to run sander.MPI on an
> SGI with mpirun. This used to work, and I haven't any idea of what has
> changed to cause this problem. I thought that if I completely
> recompiled
> Amber 10 it might solve the problem, but it didn't. Can anyone suggest
> what I might do next to troubleshoot the segmentation fault?
>
>
>
> John
>
>
>
>
>
>
>
>
>
>
>
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Received on Thu Apr 01 2010 - 12:30:02 PDT
