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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