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
