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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