Hi,
I check and fixe all lib: ldd
~/bin/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
linux-vdso.so.1 => (0x00007ffc8f5ea000)
libpython2.7.so.1.0 =>
/soft/bioinfo/linux_RH6/python-2.7.6/lib/libpython2.7.so.1.0
(0x00007f0ff8088000)
libboost_iostreams.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_iostreams.so.1.59.0
(0x00007f0ff7e70000)
libboost_python.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0
(0x00007f0ff7c22000)
libboost_regex.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_regex.so.1.59.0
(0x00007f0ff7911000)
libboost_coroutine.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_coroutine.so.1.59.0
(0x00007f0ff7704000)
libCGAL.so.11 => /u/eaudemard/bin/lib/libCGAL.so.11 (0x00007f0ff74db000)
libexpat.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/libexpat.so.1
(0x00007f0ff72b2000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f0ff7077000)
libstdc++.so.6 =>
/soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libstdc++.so.6
(0x00007f0ff6d65000)
libm.so.6 => /lib64/libm.so.6 (0x00007f0ff6ae1000)
libc.so.6 => /lib64/libc.so.6 (0x00007f0ff674c000)
libgcc_s.so.1 =>
/soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libgcc_s.so.1
(0x00007f0ff6536000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0ff6319000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f0ff6114000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f0ff5f11000)
libz.so.1 => /lib64/libz.so.1 (0x00007f0ff5cfb000)
librt.so.1 => /lib64/librt.so.1 (0x00007f0ff5af2000)
libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007f0ff49a7000)
libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007f0ff4611000)
libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007f0ff42be000)
libboost_context.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_context.so.1.59.0
(0x00007f0ff40b3000)
libboost_thread.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_thread.so.1.59.0
(0x00007f0ff3e91000)
libboost_chrono.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_chrono.so.1.59.0
(0x00007f0ff3c8a000)
libboost_system.so.1.59.0 =>
/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_system.so.1.59.0
(0x00007f0ff3a87000)
libmpfr.so.4 => /u/eaudemard/bin/lib/libmpfr.so.4 (0x00007f0ff3827000)
libgmp.so.10 => /u/eaudemard/bin/lib/libgmp.so.10 (0x00007f0ff35b1000)
And the segmentation fault is deferent (with gdb):
(gdb) bt
#0 0x000000339ee4406a in vfprintf () from /lib64/libc.so.6
#1 0x000000339ee69609 in vsprintf () from /lib64/libc.so.6
#2 0x000000339ee4f2b8 in sprintf () from /lib64/libc.so.6
#3 0x0000000000464451 in PyString_FromFormatV (format=0x530a57 "",
vargs=0x7fffff3ff8e0) at Objects/stringobject.c:370
#4 0x000000000046491b in PyString_FromFormat (format=<value optimized out>)
at Objects/stringobject.c:410
#5 0x000000000046f0ae in object_repr (self=0x6f51b10) at
Objects/typeobject.c:2996
#6 0x00000000004522a5 in PyObject_Repr (v=0x6f51b10) at
Objects/object.c:381
#7 0x0000000000452668 in internal_print (op=0x6f51b10, fp=0x339f18e7a0,
flags=<value optimized out>, nesting=0) at Objects/object.c:305
#8 0x000000000044ccbd in dict_print (mp=0x44c993830, fp=0x339f18e7a0,
flags=<value optimized out>) at Objects/dictobject.c:1063
#9 0x00000000004525a3 in internal_print (op=0x44c993830, fp=0x339f18e7a0,
flags=1, nesting=0) at Objects/object.c:315
#10 0x000000000042f9d9 in file_PyObject_Print (v=<value optimized out>,
f=0x7ffff7fae150, flags=1) at Objects/fileobject.c:110
#11 PyFile_WriteObject (v=<value optimized out>, f=0x7ffff7fae150, flags=1)
at Objects/fileobject.c:2574
#12 0x00000000004a70d9 in PyEval_EvalFrameEx (f=<value optimized out>,
throwflag=<value optimized out>) at Python/ceval.c:1770
#13 0x00000000004a9ab5 in fast_function (f=<value optimized out>,
throwflag=<value optimized out>) at Python/ceval.c:4107
#14 call_function (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:4042
#15 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized
out>) at Python/ceval.c:2666
#16 0x00000000004a9ab5 in fast_function (f=<value optimized out>,
throwflag=<value optimized out>) at Python/ceval.c:4107
#17 call_function (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:4042
#18 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized
out>) at Python/ceval.c:2666
The version of /lib64/libc.so come from CentOS 6:
glibc-2.17-106.el7_2.1.x86_64 (compiled with gcc 4.4.7)
We update your OS in 2 weeks, but do you know if this version can create an
segmentation fault ? Or have you an other idea ?
Regards,
Eric.
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