The import working means that Python can find the Python component of graph tool.
The error you get has to do with boost Python not finding, for a call internal to the Python component, a corresponding function in the C++ component that matches it's argument types.
Thus, this happens if any of the pieces involved do not match. A common cause is version mismatch.
Ldd is useful to check some of those: the versions of libraries linked to the C++ component.
In your led output I see
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ffff38ce000)
Thus it seems to be the case that the package got compiled against Python 2.6, yet got installed for Python 2.7 .
Cheers
ale
On Sunday, January 29, 2017, bloodymeli <
bloodymeli@gmail.com> wrote:
Hi,
Graph-tool was manually compiled on a local cluster (based on RedHat) by a
network admin. The python command
import graph_tool
works fine, but almost every other command results in an error related to
"did not match C++ signature":
For example,
gtGraph=graph_tool.load_graph("yeast.graphml")
(attached) results in:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/epd/lib/python2.7/site-packages/graph_tool/__init__.py",
line 2702, in load_graph
g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp)
File "/usr/local/epd/lib/python2.7/site-packages/graph_tool/__init__.py",
line 2320, in load
ignore_ep, ignore_gp)
Boost.Python.ArgumentError: Python argument types in
GraphInterface.read_from_file(GraphInterface, str, NoneType, str, list,
list, list)
did not match C++ signature:
read_from_file(graph_tool::GraphInterface {lvalue},
std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, boost::python::api::object,
std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, boost::python::list, boost::python::list,
boost::python::list)
Following some other posts in the mailing list, I've applied the ldd command
and:
ldd
/usr/local/epd/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
linux-vdso.so.1 => (0x00007ffff7ffe000)
libboost_iostreams.so.1.59.0 => /usr/lib64/libboost_iostreams.so.1.59.0
(0x00007ffff5c46000)
libboost_python.so.5 => /usr/lib64/libboost_python.so.5
(0x00007ffff59f5000)
libboost_regex.so.1.59.0 => /usr/lib64/libboost_regex.so.1.59.0
(0x00007ffff56df000)
libboost_coroutine.so.1.59.0 => /usr/lib64/libboost_coroutine.so.1.59.0
(0x00007ffff54d4000)
libCGAL.so.12 =>
/usr/local/cgal-releases-CGAL-4.9/build/release/lib/libCGAL.so.12
(0x00007ffff52af000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x00007ffff5087000)
libstdc++.so.6 =>
/usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libstdc++.so.6
(0x00007ffff4cf8000)
libm.so.6 => /lib64/libm.so.6 (0x00007ffff4a74000)
libc.so.6 => /lib64/libc.so.6 (0x00007ffff46e0000)
libgcc_s.so.1 =>
/usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libgcc_s.so.1
(0x00007ffff44c9000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007ffff42b8000)
libz.so.1 => /usr/local/epd/lib/libz.so.1 (0x00007ffff409a000)
librt.so.1 => /lib64/librt.so.1 (0x00007ffff3e91000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ffff3c74000)
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ffff38ce000)
libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007ffff2788000)
libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007ffff23f2000)
libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007ffff20a0000)
libboost_context.so.1.59.0 => /usr/lib64/libboost_context.so.1.59.0
(0x00007ffff1e96000)
libboost_thread.so.1.59.0 => /usr/lib64/libboost_thread.so.1.59.0
(0x00007ffff1c74000)
libboost_chrono.so.1.59.0 => /usr/lib64/libboost_chrono.so.1.59.0
(0x00007ffff1a6d000)
libboost_system.so.1.59.0 => /usr/lib64/libboost_system.so.1.59.0
(0x00007ffff1869000)
libmpfr.so.1 => /usr/lib64/libmpfr.so.1 (0x00007ffff161c000)
libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007ffff13c1000)
/lib64/ld-linux-x86-64.so.2 (0x0000003f14800000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007ffff11bc000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007ffff0fb9000)
yeast.graphml
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026983/yeast.graphml>
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