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From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2007-11-07 08:09:14


I'm not familiar with DOCK or Debian, but you will definitely have
problems if you mix-n-match MPI implementations. Specifically, the
mpi.h files are not compatible between MPICH and Open MPI.

Additionally, you may run into problems if you compile your app with
one version of Open MPI and then run it with another. We have not
[yet] done anything in terms of binary compatibility between versions.

On Nov 7, 2007, at 8:05 AM, Francesco Pietra wrote:

> I wonder whether any suggestion can be offered about segmentation
> fault
> occurring on running a docking program (DOCK 6.1, written in C) on
> Debian Linux
> amd64 etch, i.e. dual opterons machine. Running DOCK6.1 parallel was
> OK until
> yesterday. I vaguely remember that before these problems I carried
> out a
>
> apt-get upgrade
>
> and something was done for OpenMPI.
>
> DOCK 6.1 was compiled:
>
> ./configure gnu parallel
> MPICH_HOME=/usr/local
> export MPICH_HOME
> make dock
>
> by pointing MPICH (for which DOCK 6.1 is configured, to my
> installation of
> OpenMPI 1.2.3
>
> In my .bashrc:
>
> DOCK_HOME=/usr/local/dock6
> PATH=$PATH:$DOCK_HOME/bib; export DOCK_HOME PATH
>
> MPI_HOME=/usr/local
> export MPI_home
>
>
> which mpicxx
> /usr/local/bin/mpicxx
>
>
>
> updatedb
> locate mpi.h
> /usr/include/sc/util/group/memmtmpi.h
> /usr/include/sc/util/group/messmpi.h
> /usr/dock6/src/dock/base_mpi.h
> /usr/local/include/mpi.h
> /usr/local/openmpi-1.2.3/ompi/include/mpi.h
> /usr/local/openmpi-1.2.3/ompi/include/mpi.h.in
> /usr/local/openmpi-1.2.3/ompi/mpi/f77/prototypes_mpi.h
> -------
>
> On these basis, running:
>
> mpirun -np 4 dock6.mpi -i dock.in -o dock.out
>
> the process halted with error message:
>
> Initialing MPI routines ....
> [deb64:03540] *** Process received signal ***
> [deb64:03540] Signal: Segmentation fault (11)
> [deb64:03540] Signal code: Address not mapped (1)
> [deb64:03540] Failing at address: 0x2b9ef5691000
> dock6.mpi[3540]: segfault at 00002b9ef56910000 rip 0000000000447b1b
> rsp
> 00007fff43c137b0 error 6
> [deb64:03540] [0] /lib/libthread.so.0 [0x2b9e681bc410]
> [deb64:03540] [1] dock6.mpi (_ZN60rient12match_ligandER7DOCKMol+0x40b)
> [0x447b1b]
> [deb64:03540] [2] dock6.mpi (main+0xaf5) [0x42cc75]
> [deb64:03540] [3] dock6.mpi /lib/libc.so.6(__libc_start_main+0xda)
> [0x2b9e682e14ca]
> [deb64:03540] [4] dock6.mpi (__gxx_personality_v0+0xc2) [0x41b4ea]
> [deb64:03540] *** End of error message ***
> mpirun noticed that jpb rank 0 with PID 3537 on node deb64 exited on
> signal 15
> (Terminated).
> 3 additional processes aborted (not shown)
>
>
> Thanks
> francesco pietra
>
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-- 
Jeff Squyres
Cisco Systems