Could be this that cause the segfault. On Fri, Jan 29, 2016 at 7:21 PM, Eric <eric.audemard@umontreal.ca> wrote:
Thanks for your offer, but I can't reproduce this segmentation fault on small script/example. I let you know if I found a way.
When I check libgraph_tool_core.so with ldd: linux-vdso.so.1 => (0x00007ffdd6d57000) libpython2.7.so.1.0 => /soft/bioinfo/linux_RH6/python-2.7.6/lib/libpython2.7.so.1.0 (0x00007ff7cbc49000) libboost_iostreams.so.5 => /usr/lib64/libboost_iostreams.so.5 (0x00007ff7cba10000) libboost_python.so.5 => /usr/lib64/libboost_python.so.5 (0x00007ff7cb7bf000) libboost_regex.so.5 => /usr/lib64/libboost_regex.so.5 (0x00007ff7cb4cb000) libboost_coroutine.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_coroutine.so.1.59.0 (0x00007ff7cb2be000) libCGAL.so.11 => /u/eaudemard/bin/lib/libCGAL.so.11 (0x00007ff7cb095000) libexpat.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/libexpat.so.1 (0x00007ff7cae6c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007ff7cac5a000) libstdc++.so.6 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libstdc++.so.6 (0x00007ff7ca948000) libm.so.6 => /lib64/libm.so.6 (0x00007ff7ca6c4000) libc.so.6 => /lib64/libc.so.6 (0x00007ff7ca32f000) libgcc_s.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libgcc_s.so.1 (0x00007ff7ca119000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff7c9efc000) libdl.so.2 => /lib64/libdl.so.2 (0x00007ff7c9cf7000) libutil.so.1 => /lib64/libutil.so.1 (0x00007ff7c9af4000) libz.so.1 => /lib64/libz.so.1 (0x00007ff7c98de000) libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ff7c9537000) libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007ff7c91e5000) libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007ff7c8e4f000) libboost_context.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_context.so.1.59.0 (0x00007ff7c8c43000) libboost_thread.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_thread.so.1.59.0 (0x00007ff7c8a21000) libboost_chrono.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_chrono.so.1.59.0 (0x00007ff7c881b000) libboost_system.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_system.so.1.59.0 (0x00007ff7c8617000) librt.so.1 => /lib64/librt.so.1 (0x00007ff7c840f000) libmpfr.so.4 => /u/eaudemard/bin/lib/libmpfr.so.4 (0x00007ff7c81b0000) libgmp.so.10 => /u/eaudemard/bin/lib/libgmp.so.10 (0x00007ff7c7f39000) libboost_thread-mt.so.5 => /usr/lib64/libboost_thread-mt.so.5 (0x00007ff7c7d24000) libboost_system-mt.so.5 => /usr/lib64/libboost_system-mt.so.5 (0x00007ff7c7b21000) /lib64/ld-linux-x86-64.so.2 (0x0000003756800000) libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007ff7c69d5000)
Some libboost are linked with the good version of boost but some others are linked an oldest version (1.41). I try to fixe this with the option "--with-boost-python=" of configure but it doesn't work: ./configure --prefix=/u/eaudemard/bin/ --with-python-module-path=/u/eaudemard/bin/lib/python2.7/site-packages/ --with-boost=/soft/bioinfo/linux_RH6/boost-1.59.0/ --with-boost-libdir=/soft/bioinfo/linux_RH6/boost-1.59.0/lib/
--with-boost-python=/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 ... checking for boostlib >= 1.54.0... yes checking whether the Boost::Python library is available... yes checking for exit in -l/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0... no
You need this library installed (v 1.59.0)? Probably you it's called libboost-python, search your package repo.
checking for exit in
-lboost_python-/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0... no checking for exit in -lboost_python... yes
ls -l /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 -rwxr-xr-x. 1 adsoft users 404020 Oct 19 13:39 /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0
After this i try apm -e of the old version and this time the configure don't find "boost_python" checking for boostlib >= 1.54.0... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no configure: error: No usable boost::python found
Have you an idea on that point ?
Regards, Eric.
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