Issue will gt.topology.all_paths()

graph-tool
1

Hi,

I am running graph-too v2.18 on Ubuntu 15.10 and I was trying to to use the
all_paths() function but when I run the example code (or any other code for
that matter) I keep getting the following error:

Traceback (most recent call last):
  File "/usr/lib/python3.4/code.py", line 90, in runcode
    exec(code, self.locals)
  File "<input>", line 1, in <module>
  File "/usr/lib/python3/dist-packages/graph_tool/topology/__init__.py",
line 1732, in all_paths
    _prop("v", g, visited))
RuntimeError: This functionality is not available because boost::coroutine
was not found at compile-time

Did I compile the graph-tool the wrong way or is it a problem with the
function itself?

Regards,
Vaggelis

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2

As the error message indicates, the boost::coroutine library was not found
at compilation, and hence the algorithm was not compiled, since it requires it.

3

One of your previous posts indicated that there might be an issue with
Ubuntu and co-routine installation. Is this still valid?

http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Debian-package-and-boost-at-compile-time-td4026383.html

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4

This has been fixed in newer Ubuntu and Debian releases.

5

Is there a particular version that graph-tool requires? Because when I ran
configure I get the following:

....
checking whether the Boost::Coroutine library is available... yes
configure: WARNING: No usable boost::coroutine found! Some functionality
will be disabled in the library.
.....

My system has coroutine1.58

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6

This should be sufficient. It could be that the configure script is having
trouble detecting the correct name of the library (which varies across
distros). Try the following:

   ./configure --with-boost-coroutine=boost_coroutine

Best,
Tiago

7

That seems to do the trick.

Thanks

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8

Tiago,

Apologies for yet another email, but now the compilation fails with the
following error.
I tried modifying the LDFLAGS parameter with the suggested value but still
same error.
Any suggestions?

Thansk again for all the help,
Vaggelis

  CXX graph_blockmodel_overlap_vacate.lo
  CXX graph_inference.lo
  CXX int_part.lo
  CXX spence.lo
  CXXLD libgraph_tool_inference.la
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/
libboost_coroutine.a(exceptions.o): relocation R_X86_64_32 against `.bss'
can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libboost_coroutine.a:
error adding symbols: Bad value
collect2: error: ld returned 1 exit status
Makefile:556: recipe for target 'libgraph_tool_inference.la' failed
make[4]: *** [libgraph_tool_inference.la] Error 1
make[4]: Leaving directory '/media/sf_VB_SHARE/graph-
tool-2.18/src/graph/inference'
Makefile:741: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/media/sf_VB_SHARE/graph-tool-2.18/src/graph'
Makefile:412: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/media/sf_VB_SHARE/graph-tool-2.18/src'
Makefile:584: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/media/sf_VB_SHARE/graph-tool-2.18'
Makefile:471: recipe for target 'all' failed
make: *** [all] Error 2

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9

It seems like the boost::corountine library was compiled statically, instead
of dynamically. Check if there is a libboost_coroutine.so file in the lib
directory. If there is not, you have to re-compile boost making sure all
libraries are shared objects.