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From: Francesco Pietra (chiendarret_at_[hidden])
Date: 2007-11-07 08:20:11


Hi Jeff:
I understand that my question was posed in extremely vague terms. Though,
pointing MPICH to the installation of OpenMPI was suggested by the author of
DOCK and it performed perfectly for a long while, until yesterday. Perhaps,
could you please instruct me how to verify beyond doubt if the "apt-get update"
has modified the version of OpenMPI that was originally installed (1.2.3)? On
its side, Debian Linux is a perfectly standard Linux.

francesco

--- Jeff Squyres <jsquyres_at_[hidden]> wrote:

> 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
>
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