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 <jsquy...@cisco.com> 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 > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam protection around > > http://mail.yahoo.com > > _______________________________________________ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > Cisco Systems > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
