Package: libopenmpi1.6 Version: 1.6.5-10 Severity: normal File: /usr/lib/libmpi.so.1
Dear Maintainer, * What led up to the situation? I was trying to install QBox http://eslab.ucdavis.edu/software/qbox/index.htm. I compiled it, but it segfaults when I run it with mpirun -np 1 ./qb qb needs a variety of packages that require MPI, so openmpi was installed using apt-get by installing the dependencies for QBox. Oddly enough, QBox doesn't segfault when I run it without mpirun. I made a simple program to reproduce the behavior. # cat mpitest.c #include <mpi.h> int main(int argc, char **argv) { MPI_Init(&argc, &argv); MPI_Finalize(); } * What exactly did you do (or not do) that was effective (or ineffective)? Here are the steps needed to reproduce the behavior. faerun:/tmp# mpicc -o mpitest mpitest.c faerun:/tmp# mpirun -np 1 /tmp/mpitest [faerun:20716] *** Process received signal *** [faerun:20716] Signal: Segmentation fault (11) [faerun:20716] Signal code: (128) [faerun:20716] Failing at address: (nil) [faerun:20716] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf8d0) [0x7f7b39bef8d0] [faerun:20716] [ 1] /usr/lib/x86_64-linux-gnu/libhwloc.so.5(+0x244c5) [0x7f7b39e244c5] [faerun:20716] [ 2] /usr/lib/x86_64-linux-gnu/libhwloc.so.5(+0xc1c7) [0x7f7b39e0c1c7] [faerun:20716] [ 3] /usr/lib/x86_64-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1ab) [0x7f7b39e0d15a] [faerun:20716] [ 4] /usr/lib/libmpi.so.1(opal_hwloc_unpack+0xc7) [0x7f7b3a34e107] [faerun:20716] [ 5] /usr/lib/libmpi.so.1(opal_dss_unpack_buffer+0x6e) [0x7f7b3a3497ce] [faerun:20716] [ 6] /usr/lib/libmpi.so.1(opal_dss_unpack+0xae) [0x7f7b3a34a6de] [faerun:20716] [ 7] /usr/lib/libmpi.so.1(orte_util_nidmap_init+0x2b1) [0x7f7b3a315591] [faerun:20716] [ 8] /usr/lib/openmpi/lib/openmpi/mca_ess_env.so(+0x1b29) [0x7f7b380b9b29] [faerun:20716] [ 9] /usr/lib/libmpi.so.1(orte_init+0x193) [0x7f7b3a2fdc63] [faerun:20716] [10] /usr/lib/libmpi.so.1(ompi_mpi_init+0x166) [0x7f7b3a2b81d6] [faerun:20716] [11] /usr/lib/libmpi.so.1(MPI_Init+0x16a) [0x7f7b3a2d095a] [faerun:20716] [12] /tmp/mpitest() [0x400708] [faerun:20716] [13] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f7b39851b45] [faerun:20716] [14] /tmp/mpitest() [0x400619] [faerun:20716] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 20716 on node faerun exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- faerun:/tmp# /tmp/mpitest faerun:/tmp# * What was the outcome of this action? Note the segfault listed above. * What outcome did you expect instead? I expected mpitest to run without segfaulting. Note, running mpitest without mpirun doesn't segfault. Using mpirun should allow me to run using multiple threads. faerun:/tmp# dpkg --list '*openmpi*' Desired=Unknown/Install/Remove/Purge/Hold | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) ||/ Name Version Architecture Description +++-=====================-===============-===============-=============================================== ii libblacs-openmpi1 1.1-33 amd64 Basic Linear Algebra Comm. Subprograms - Shared ii libopenmpi-dev 1.6.5-10 amd64 high performance message passing library -- hea un libopenmpi1 <none> <none> (no description available) rc libopenmpi1.3 1.4.5-1 amd64 high performance message passing library -- sha ii libopenmpi1.6 1.6.5-10 amd64 high performance message passing library -- sha un libopenmpi2 <none> <none> (no description available) ii libscalapack-openmpi1 1.8.0-12.1 amd64 Scalable Linear Algebra Package - Shared libs. un octave-openmpi-ext <none> <none> (no description available) ii openmpi-bin 1.6.5-10 amd64 high performance message passing library -- bin ii openmpi-checkpoint 1.6.5-10 amd64 high performance message passing library -- che ii openmpi-common 1.6.5-10 all high performance message passing library -- com un openmpi-dev <none> <none> (no description available) un openmpi-libs0 <none> <none> (no description available) un yorick-mpy-openmpi <none> <none> (no description available) -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 3.10-2-amd64 (SMP w/4 CPU cores) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Init: systemd (via /run/systemd/system) Versions of packages libopenmpi1.6 depends on: ii libc6 2.19-18 ii libcr0 0.8.5-2.2 ii libgcc1 1:5.1.1-9 ii libgfortran3 5.1.1-9 ii libhwloc5 1.11.0-1 ii libibverbs1 1.1.8-1.1 ii libltdl7 2.4.2-1.11 ii libquadmath0 5.1.1-9 ii libstdc++6 5.1.1-9 libopenmpi1.6 recommends no packages. libopenmpi1.6 suggests no packages. -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
