Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-03 Thread Tiago de Paula Peixoto 
On 03.03.2017 12:38, P-M wrote:
> This now compiles and works on one of my machines. My other machine now
> complains about libicudata.so.56:
> 
> Traceback (most recent call last):
>   File "", line 1, in 
>   File
> "/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/__init__.py",
> line 111, in 
> dl_import("from . import libgraph_tool_core as libcore")
>   File
> "/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/dl_import.py",
> line 61, in dl_import
> exec(import_expr, local_dict, global_dict)
>   File "", line 1, in 
> ImportError: libicudata.so.56: cannot open shared object file: No such file
> or directory
> 
> This may be an anaconda issue but I am not sure. Do you have any thoughts on
> this? I will open a ticket for this so we can close this thread down.

This is not a bug in graph-tool. The linker cannot find that library. You
have to find where that is, and put its path into the LD_LIBRARY_PATH
environment variable. Or pass it as "-Wl,-rpath=", as explained in the
documentation.


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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-03 Thread P-M 
This now compiles and works on one of my machines. My other machine now
complains about libicudata.so.56:

Traceback (most recent call last):
  File "", line 1, in 
  File
"/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/__init__.py",
line 111, in 
dl_import("from . import libgraph_tool_core as libcore")
  File
"/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/dl_import.py",
line 61, in dl_import
exec(import_expr, local_dict, global_dict)
  File "", line 1, in 
ImportError: libicudata.so.56: cannot open shared object file: No such file
or directory

This may be an anaconda issue but I am not sure. Do you have any thoughts on
this? I will open a ticket for this so we can close this thread down.



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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-02 Thread P-M 
Similar error on a different sysyem. I ran ./configure CXXFLAGS="-std=gnu++14
-Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda2/bin/python2.7"
CAIROMM_LIBS="-L/home/pmj27/anaconda2/include/cairomm-1.0/cairomm"
--enable-openmp --with-boost=/home/pmj27/anaconda2 so didn't have any
CPPFLAGS

During make it crashes at the same spot it seems ( screengrab3.dat

 
). I am running boost 1.63.0 conda-forge.



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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-02 Thread P-M 
It seems to still fail I fear. The screen output is huge but in the attached
file ( screengrab1.zip

 
) you seem to be able to find the relevant error between lines 6824 and
7952.



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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-02 Thread P-M 
Great, thanks! Here is the output of "make V=1 2>&1 | tee ./screengrab.dat"
rerunning it after the error had occured ( screengrab.dat

 
). If you would like the output for an entirely new compilation let me know
and I shall get that to you, it might just take a little while longer to
run.



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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-02 Thread Tiago de Paula Peixoto 
On 02.03.2017 16:21, P-M wrote:
> That is strange indeed. I have downgraded to the anaconda version of boost
> (v1.60) and boost-python (v1.60) by sseefeld. The configure commands are
> unchanged as ./configure --prefix=$HOME/.local
> --with-boost=/home/pmj27/anaconda2 CXX="g++-5" CXXFLAGS="-std=gnu++14
> -Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda2/bin/python2.7"
> CPPFLAGS="-I/home/pmj27/anaconda2/include"
> LDFLAGS="-L/home/pmj27/anaconda2/lib" --enable-openmp which seems to still
> run happily ( config.log
> 
>  
> ) but during make this boost configuration also complains, albeit
> differently ( screengrab.dat
> 
>  
> ). Is there any way of narrowing down the root of the error?

Can you give me the full output of 'make V=1'?


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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-02 Thread Tiago de Paula Peixoto 
On 02.03.2017 16:21, P-M wrote:
> That is strange indeed. I have downgraded to the anaconda version of boost
> (v1.60) and boost-python (v1.60) by sseefeld. The configure commands are
> unchanged as ./configure --prefix=$HOME/.local
> --with-boost=/home/pmj27/anaconda2 CXX="g++-5" CXXFLAGS="-std=gnu++14
> -Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda2/bin/python2.7"
> CPPFLAGS="-I/home/pmj27/anaconda2/include"
> LDFLAGS="-L/home/pmj27/anaconda2/lib" --enable-openmp which seems to still
> run happily ( config.log
> 
>  
> ) but during make this boost configuration also complains, albeit
> differently ( screengrab.dat
> 
>  
> ). Is there any way of narrowing down the root of the error?
> 

Yes, the problem has to do with the order of the CPPFLAGS. I will be pushing
a fix to git soon.


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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-01 Thread Tiago de Paula Peixoto 
On 01.03.2017 18:21, P-M wrote:
> `conda list` returns `boost 1.63.0 
> np112py27_6conda-forge`. That should be about as up-to-date as it gets.

This is strange. I have the same version, and I cannot reproduce the error.


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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-03-01 Thread Tiago de Paula Peixoto 
On 01.03.2017 16:20, P-M wrote:
> Does anybody know what this is caused by/how I could solve it?

Which boost version do you have installed?

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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-28 Thread P-M 
I have updated cgal to 4.7 so that now works and after applying the
libreadline workaround it compiles and installs but I still get C++
signature mismatches. 

I have ripped off Anaconda entirely, re-installed it, installed the latest
Boost in it using only one source to make sure all packages are compatible
(conda-forge). Running "./configure --prefix=$HOME/.local CXX="g++-5"
CXXFLAGS="-std=gnu++14 -Wno-unused-local-typedefs"
PYTHON="/home/pmj27/anaconda2/bin/python2.7"
CPPFLAGS="-I/home/pmj27/anaconda2/include"
LDFLAGS="-L/home/pmj27/anaconda2/lib" --enable-openmp" seems to work and
completes succesfully, however, the configuration summary prints "Boost CPP
flags: -I/usr/include" which is not what I want and which I guess is causing
my later problems?

 CONFIGURATION SUMMARY

Using python version:   2.7.13
Python interpreter: /home/pmj27/anaconda2/bin/python2.7
Installation path: 
/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool

C++ compiler (CXX): g++-5
C++ compiler version:   5.4.0

Prefix: /home/pmj27/.local
Pkgconfigdir:   ${libdir}/pkgconfig

Python CPP flags:   -I/home/pmj27/anaconda2/include/python2.7
Python LD flags:-L/home/pmj27/anaconda2/lib -lpython2.7
Boost CPP flags:-I/usr/include
Boost LD flags: -lboost_iostreams -lboost_python -lboost_regex
-lboost_coroutine
Numpy CPP flags:   
-I/home/pmj27/anaconda2/lib/python2.7/site-packages/numpy/core/include
Sparsehash CPP flags:
CGAL CPP flags: -I/usr/include
CGAL LD flags:  -L/usr/lib -lCGAL -lCGAL_Core -lgmp
Expat CPP flags:-I/usr/include
Expat LD flags: -L/usr/lib -lexpat
Cairomm CPP flags:  -std=c++11 -I/usr/include/cairomm-1.0
-I/usr/lib/x86_64-linux-gnu/cairomm-1.0/include -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/sigc++-2.0 -I/usr/lib/x86_64-linux-gnu/sigc++-2.0/include
Cairomm LD flags:   -lcairomm-1.0 -lcairo -lsigc-2.0
OpenMP compiler flags:  -fopenmp
OpenMP LD flags:
Extra CPPFLAGS: -I/home/pmj27/anaconda2/include
Extra CXXFLAGS: -fopenmp -O3 -fvisibility=default
-fvisibility-inlines-hidden -Wno-deprecated -ftemplate-depth-250  -DNDEBUG
-Wall -Wextra -ftemplate-backtrace-limit=0 -std=gnu++14
-Wno-unused-local-typedefs
Extra LDFLAGS:  -L/home/pmj27/anaconda2/lib

Using OpenMP:   yes
Using sparsehash:   yes
Using cairo:yes


Is there any way of telling why it keeps defaulting back to using the boost
in /usr/include and a way of making sure it doesn't do so? The  config.log

  
is attached.



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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-24 Thread Tiago de Paula Peixoto 
On 24.02.2017 17:15, P-M wrote:
> I have noticed that too. Does the output of `make` get routed to a file like
> it does for config.log? Or would I need to use console redirection? 

You need to redirect.

> The system cgal seems to be version 4.7-4. The conda version is cgal 4.5 by
> ostrokach

It seems like 4.5 is too old. Version 4.7 should work, however.


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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-24 Thread P-M 
I have noticed that too. Does the output of `make` get routed to a file like
it does for config.log? Or would I need to use console redirection? 

The system cgal seems to be version 4.7-4. The conda version is cgal 4.5 by
ostrokach



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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-24 Thread P-M 
Applying the work around and using the system readline means ./configure now
seems to run without errors.

When running make I get an error however revolving around CGAL. Do you know
what might be causing them?

In file included from
/usr/include/CGAL/Periodic_3_Delaunay_triangulation_traits_3.h:30:0,
 from graph_triangulation.cc:55:
/home/pmj27/anaconda2/include/CGAL/Periodic_3_triangulation_traits_3.h:33:9:
error: redefinition of ‘class CGAL::Traits_with_offsets_adaptor’
   class Traits_with_offsets_adaptor {
 ^
In file included from
/usr/include/CGAL/Periodic_3_Delaunay_triangulation_traits_3.h:27:0,
 from graph_triangulation.cc:55:
/usr/include/CGAL/Traits_with_offsets_adaptor.h:31:9: error: previous
definition of ‘class CGAL::Traits_with_offsets_adaptor’
   class Traits_with_offsets_adaptor {
 ^
In file included from
/usr/include/CGAL/Periodic_3_Delaunay_triangulation_traits_3.h:30:0,
 from graph_triangulation.cc:55:
/home/pmj27/anaconda2/include/CGAL/Periodic_3_triangulation_traits_3.h:96:7:
error: redefinition of ‘class CGAL::Periodic_3_construct_point_3’
 class Periodic_3_construct_point_3 : public Construct_point_3_base
   ^
In file included from
/usr/include/CGAL/Periodic_3_Delaunay_triangulation_traits_3.h:28:0,
 from graph_triangulation.cc:55:
/usr/include/CGAL/Periodic_3_construct_point_3.h:31:7: error: previous
definition of ‘class CGAL::Periodic_3_construct_point_3’
 class Periodic_3_construct_point_3 : public Construct_point_3_base
   ^
In file included from
/home/pmj27/anaconda2/include/boost/type_traits/ice.hpp:15:0,
 from
/home/pmj27/anaconda2/include/boost/python/detail/def_helper.hpp:9,
 from
/home/pmj27/anaconda2/include/boost/python/class.hpp:29,
 from /home/pmj27/anaconda2/include/boost/python.hpp:18,
 from ../../../src/graph/numpy_bind.hh:22,
 from graph_triangulation.cc:72:
/home/pmj27/anaconda2/include/boost/type_traits/detail/ice_or.hpp:17:71:
note: #pragma message: NOTE: Use of this header (ice_or.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
   ^
In file included from
/home/pmj27/anaconda2/include/boost/type_traits/ice.hpp:16:0,
 from
/home/pmj27/anaconda2/include/boost/python/detail/def_helper.hpp:9,
 from
/home/pmj27/anaconda2/include/boost/python/class.hpp:29,
 from /home/pmj27/anaconda2/include/boost/python.hpp:18,
 from ../../../src/graph/numpy_bind.hh:22,
 from graph_triangulation.cc:72:
/home/pmj27/anaconda2/include/boost/type_traits/detail/ice_and.hpp:18:72:
note: #pragma message: NOTE: Use of this header (ice_and.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
^
In file included from
/home/pmj27/anaconda2/include/boost/type_traits/ice.hpp:17:0,
 from
/home/pmj27/anaconda2/include/boost/python/detail/def_helper.hpp:9,
 from
/home/pmj27/anaconda2/include/boost/python/class.hpp:29,
 from /home/pmj27/anaconda2/include/boost/python.hpp:18,
 from ../../../src/graph/numpy_bind.hh:22,
 from graph_triangulation.cc:72:
/home/pmj27/anaconda2/include/boost/type_traits/detail/ice_not.hpp:17:72:
note: #pragma message: NOTE: Use of this header (ice_not.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
^
In file included from
/home/pmj27/anaconda2/include/boost/type_traits/ice.hpp:18:0,
 from
/home/pmj27/anaconda2/include/boost/python/detail/def_helper.hpp:9,
 from
/home/pmj27/anaconda2/include/boost/python/class.hpp:29,
 from /home/pmj27/anaconda2/include/boost/python.hpp:18,
 from ../../../src/graph/numpy_bind.hh:22,
 from graph_triangulation.cc:72:
/home/pmj27/anaconda2/include/boost/type_traits/detail/ice_eq.hpp:17:71:
note: #pragma message: NOTE: Use of this header (ice_eq.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
   ^
In file included from
/home/pmj27/anaconda2/include/CGAL/Periodic_3_Delaunay_triangulation_3.h:29:0,
 from graph_triangulation.cc:56:
/home/pmj27/anaconda2/include/CGAL/Periodic_3_triangulation_3.h: In
instantiation of ‘CGAL::Periodic_3_triangulation_3::Vertex_handle
CGAL::Periodic_3_triangulation_3::periodic_insert(const Point&,
const Offset&, CGAL::Periodic_3_triangulation_3

Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-24 Thread Tiago de Paula Peixoto 
On 24.02.2017 16:11, P-M wrote:
> That resolved the numpy issue. Now I get another error message though:
> 
> configure: creating ./config.status
> config.status: creating Makefile
> gawk: symbol lookup error: /home/pmj27/anaconda2/lib/libreadline.so.6:
> undefined symbol: PC
> config.status: error: could not create Makefile
> 
> I have attached the  config.log
> 
>   
> again. Doing some googling this is an issue others have observed too with
> anaconda (https://github.com/ContinuumIO/anaconda-issues/issues/152 ). Is
> this something addressable within graph-tool or by providing configure flags
> or is this something that needs to be solved within anaconda?

This is not a graph-tool problem at all. You should try some of the
workarounds described in the anaconda issue.


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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-24 Thread P-M 
That resolved the numpy issue. Now I get another error message though:

configure: creating ./config.status
config.status: creating Makefile
gawk: symbol lookup error: /home/pmj27/anaconda2/lib/libreadline.so.6:
undefined symbol: PC
config.status: error: could not create Makefile

I have attached the  config.log

  
again. Doing some googling this is an issue others have observed too with
anaconda (https://github.com/ContinuumIO/anaconda-issues/issues/152 ). Is
this something addressable within graph-tool or by providing configure flags
or is this something that needs to be solved within anaconda?

Best,

Philipp



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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-24 Thread Tiago de Paula Peixoto 
On 24.02.2017 12:17, P-M wrote:
> I am getting that impression too. Unfortunately the newest git verison
> produces the same error as far as I can tell.  config.log
> 
>   
> is attached again.

Can you please try once more?


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Re: [graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-23 Thread P-M 
The odd thing though is that graph-tool is compiled against
/home/pmj27/anaconda2/bin/python2.7. The anaconda boost is installed through
conda so should also be linked against that. I can try and tell configure
explicitely to take its boost libraries from /home/pmj27/anaconda2/lib/. As
far as I can tell all the library files reside in that folder. What would I
need to specify for that? (My proficiency isn't great enough to piece it
together from the manual unfortuantely.) As far as I can tell by the output
reproduced by ldd
/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
though the boost libraries used by graph-tool are the anaconda boost
libraries as they reside in /home/pmj27/anaconda2/lib/ so it isn't clear to
me if that would change much. Or am I missing a vital piece here? 



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[graph-tool] Boost.Python.ArgumentError: Python argument types did not match C++ signature

2017-02-22 Thread P-M 
I have been trying to compile the recent git version of graph-tool against my
anaconda python. I do this using

sudo ./configure CXX="g++-5" CXXFLAGS="-std=gnu++14
-Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda2/bin/python2.7"
CAIROMM_LIBS="-L/home/pmj27/anaconda2/include/cairomm-1.0/cairomm"
--enable-openmp 

(if I skip the sudo it won't pick up boost for reasons not quite known to
me). I then run "sudo make -j20" followed by "make install". When opening
python and importing the module I however get the error message

Traceback (most recent call last):
  File "", line 1, in 
  File
"/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/__init__.py",
line 3323, in 
openmp_set_schedule("static", 0)
  File
"/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/__init__.py",
line 3320, in openmp_set_schedule
return libcore.openmp_set_schedule(schedule, chunk)
Boost.Python.ArgumentError: Python argument types in
graph_tool.libgraph_tool_core.openmp_set_schedule(str, int)
did not match C++ signature:
openmp_set_schedule(std::__cxx11::basic_string, std::allocator >, int)

My first thought was that graph-tool must be linking against an incorrect
version of boost. So, following the advice from other posts, I ran ldd
/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
. This returns:

linux-vdso.so.1 =>  (0x7fffc93ce000)
libpython2.7.so.1.0 => /home/pmj27/anaconda2/lib/libpython2.7.so.1.0
(0x7fbcd05ec000)
libboost_iostreams.so.1.63.0 =>
/home/pmj27/anaconda2/lib/libboost_iostreams.so.1.63.0 (0x7fbcd03c4000)
libboost_python.so.1.63.0 =>
/home/pmj27/anaconda2/lib/libboost_python.so.1.63.0 (0x7fbcd0175000)
libboost_regex.so.1.63.0 =>
/home/pmj27/anaconda2/lib/libboost_regex.so.1.63.0 (0x7fbccfe5a000)
libboost_coroutine.so.1.63.0 =>
/home/pmj27/anaconda2/lib/libboost_coroutine.so.1.63.0 (0x7fbccfc5)
libexpat.so.1 => /home/pmj27/anaconda2/lib/libexpat.so.1
(0x7fbccfa27000)
libstdc++.so.6 => /home/pmj27/anaconda2/lib/libstdc++.so.6
(0x7fbccf66b000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fbccf33c000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fbccef72000)
libgcc_s.so.1 => /home/pmj27/anaconda2/lib/libgcc_s.so.1
(0x7fbcced5b000)
libgomp.so.1 => /home/pmj27/anaconda2/lib/libgomp.so.1
(0x7fbcceb38000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x7fbcce91a000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7fbcce716000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
(0x7fbcce513000)
libz.so.1 => /home/pmj27/anaconda2/lib/./libz.so.1
(0x7fbcce2fc000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x7fbcce0f4000)
libicudata.so.56 => /home/pmj27/anaconda2/lib/./libicudata.so.56
(0x7fbccc711000)
libicui18n.so.56 => /home/pmj27/anaconda2/lib/./libicui18n.so.56
(0x7fbccc214000)
libicuuc.so.56 => /home/pmj27/anaconda2/lib/./libicuuc.so.56
(0x7fbccbe2f000)
libboost_context.so.1.63.0 =>
/home/pmj27/anaconda2/lib/./libboost_context.so.1.63.0 (0x7fbccbc26000)
libboost_thread.so.1.63.0 =>
/home/pmj27/anaconda2/lib/./libboost_thread.so.1.63.0 (0x7fbccba04000)
libboost_chrono.so.1.63.0 =>
/home/pmj27/anaconda2/lib/./libboost_chrono.so.1.63.0 (0x7fbccb7fd000)
libboost_system.so.1.63.0 =>
/home/pmj27/anaconda2/lib/./libboost_system.so.1.63.0 (0x7fbccb5fa000)
/lib64/ld-linux-x86-64.so.2 (0x55cf9c8bc000)

As far as I can tell all boost libraries are based on the anaconda boost
libraries. Does anybody have any ideas what might be going wrong?

Best,

Philipp



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