Hi
in a system upgrade and subsequent lammps rebuild I’ve started to see repeated/regular segmentation faults. Anyone else seeing similar behavior? It seems to go away if I rebuild with gcc optimization turned off.
thanks,
Reese
ps the specifics
backtrace:
[bn07:134838] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x7ffbb37ad5e0]
[bn07:134838] [ 1] /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/openmpi/mca_btl_vader.so(+0x4798)[0x7ffba4e09798]
[bn07:134838] [ 2] /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/libopen-pal.so.40(opal_progress+0x2c)[0x7ffbb2e8deec]
[bn07:134838] [ 3] /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x6e5)[0x7ffb9fde6715]
[bn07:134838] [ 4] /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/libmpi.so.40(PMPI_Send+0xe2)[0x7ffbb425a7e2]
[rjones@…8054… Pyr]$ lmp_mpi
LAMMPS (10 Oct 2018)
[rjones@…8054… Pyr]$ mpiexec --version
mpiexec (OpenRTE) 3.1.2
[rjones@…8054… Pyr]$ ldd ~/bin/lmp_mpi
linux-vdso.so.1 => (0x00007ffe931ea000)
libfftw3.so.3 => /opt/spack/c7.3/base6/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/fftw-3.3.7-eion3j2muqd4e775kpvvw5kpoua3vpvr/lib/libfftw3.so.3 (0x00007fc90f384000)
libmpi_cxx.so.40 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/libmpi_cxx.so.40 (0x00007fc90f169000)
libmpi.so.40 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/libmpi.so.40 (0x00007fc90ee6d000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc90eb4e000)
libm.so.6 => /lib64/libm.so.6 (0x00007fc90e84c000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fc90e635000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fc90e419000)
libc.so.6 => /lib64/libc.so.6 (0x00007fc90e056000)
libopen-rte.so.40 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/libopen-rte.so.40 (0x00007fc90dd9f000)
libopen-pal.so.40 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.2-4k3hzwk5diww5ehx5e3tc6nl7t5gknxk/lib/libopen-pal.so.40 (0x00007fc90dad9000)
librt.so.1 => /lib64/librt.so.1 (0x00007fc90d8d1000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fc90d6cd000)
libhwloc.so.5 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/hwloc-1.11.9-dbujvxxzoz27e5ioypd3popnmb4p7gkd/lib/libhwloc.so.5 (0x00007fc90d48e000)
libnuma.so.1 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/numactl-2.0.11-cjrsk2xfdu6avit3uw5zx2mqffptsjcr/lib/libnuma.so.1 (0x00007fc90d282000)
libudev.so.1 => /lib64/libudev.so.1 (0x00007fc90d26d000)
libpciaccess.so.0 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libpciaccess-0.13.5-5chyfxo6gpmcf74gpv3sqni2aa6v5x57/lib/libpciaccess.so.0 (0x00007fc90d064000)
libxml2.so.2 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libxml2-2.9.8-okofegeulrhnfyzu6sldwacn3gbpfjj4/lib/libxml2.so.2 (0x00007fc90ccfd000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fc90caf9000)
libz.so.1 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/zlib-1.2.11-64vg6e4evdrlqgx7iicwhu2hs7lv6gpz/lib/libz.so.1 (0x00007fc90c8e2000)
liblzma.so.5 => /opt/spack/c7.3/MPI-20180920/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/xz-5.2.4-agv5zlv7phi4ye3evlpv3t4ypgve4bpe/lib/liblzma.so.5 (0x00007fc90c6bc000)
/lib64/ld-linux-x86-64.so.2 (0x00005608337fb000)
libcap.so.2 => /lib64/libcap.so.2 (0x00007fc90c4b6000)
libdw.so.1 => /lib64/libdw.so.1 (0x00007fc90c26f000)
libattr.so.1 => /lib64/libattr.so.1 (0x00007fc90c069000)
libelf.so.1 => /lib64/libelf.so.1 (0x00007fc90be51000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007fc90bc41000)