Could be this that cause the segfault.
On Fri, Jan 29, 2016 at 7:21 PM, Eric <[email protected]> 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. > > > > > -- > View this message in context: > http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Segmentation-fault-when-I-try-to-access-to-a-vertex-tp4026392p4026394.html > Sent from the Main discussion list for the graph-tool project mailing list > archive at Nabble.com. > _______________________________________________ > graph-tool mailing list > [email protected] > http://lists.skewed.de/mailman/listinfo/graph-tool >
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