Re: [graph-tool] general "did not match C++ signature" error

[bloodymeli]

Hi,

It seems there is no  LDFLAGS option in the configure. I'm using graph-tool
2.20.

Best,
Eli

On Sun, Feb 5, 2017 at 7:56 PM, Tiago Peixoto [via Main discussion list for
the graph-tool project] <ml-node+s982480n4026992...@n3.nabble.com> wrote:

> Try passing
>
> LDFLAGS="-L/usr/local/epd/lib/"
>
> to configure while compiling. Also, do not forget to set LD_LIBRARY_PATH
> as
> I said, before trying to import the library.
>
> On 05.02.2017 17:13, bloodymeli wrote:
>
> > Dear Tiago,
> >
> > Thanks for the tip.
> > Please see the attached log file. As far as I know, there were no flags
> > added, but perhaps the epd setup script  (setup.csh) was first
> initialized.
> > The EPD python is the python interpreter I would like to use.
> >
> > Best,
> > Eli
> >
> > On Sun, Feb 5, 2017 at 6:09 PM, Tiago Peixoto [via Main discussion list
> for
> > the graph-tool project] <[hidden email]
> > > wrote:
> >
> > On 05.02.2017 14:08, bloodymeli wrote:
> > > Thanks!
> > >
> > > This is indeed strange, as the library is installed to
> > >
> > 
> > /usr/local/epd/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
>
> > >
> > > but compiled against:
> > > libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0
> > (0x738ce000)
> > >
> > > How do I specify which libpython to use?
> >
> >
> > This should be detected automatically when ./configure is run. The
> specific
> > python interpreter can be overridden by setting the PYTHON
> environment
> > variable to ./configure.
> >
> > But your symptom can also be caused by your custom python library
> (which
> > seems to be installed in the nonstandard path /usr/local/epd) not
> being set
> > in the linker's path. This could be fixed by doing something like:
> export
> > LD_LIBRARY_PATH=/usr/local/epd/lib/
> >
> > But these are just some guesses, since you gave us very little
> information.
> > Ideally, you would give us all parameters you passed to ./configure
> during
> > compilation, as well as the contents to config.log.
> >
> > Best,
> > Tiago
> >
> > --
> > Tiago de Paula Peixoto <[hidden email]
> > <http:///user/SendEmail.jtp?type=node=4026990=0>>
> >
> >
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> >
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> > >
> >
> >
> > 
> > 
>
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Re: [graph-tool] general "did not match C++ signature" error

[bloodymeli]

Dear Tiago,

Thanks for the tip.
Please see the attached log file. As far as I know, there were no flags
added, but perhaps the epd setup script  (setup.csh) was first initialized.
The EPD python is the python interpreter I would like to use.

Best,
Eli

On Sun, Feb 5, 2017 at 6:09 PM, Tiago Peixoto [via Main discussion list for
the graph-tool project] <ml-node+s982480n4026990...@n3.nabble.com> wrote:

> On 05.02.2017 14:08, bloodymeli wrote:
> > Thanks!
> >
> > This is indeed strange, as the library is installed to
> > /usr/local/epd/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
>
> >
> > but compiled against:
> > libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0
> (0x738ce000)
> >
> > How do I specify which libpython to use?
>
>
> This should be detected automatically when ./configure is run. The
> specific
> python interpreter can be overridden by setting the PYTHON environment
> variable to ./configure.
>
> But your symptom can also be caused by your custom python library (which
> seems to be installed in the nonstandard path /usr/local/epd) not being
> set
> in the linker's path. This could be fixed by doing something like: export
> LD_LIBRARY_PATH=/usr/local/epd/lib/
>
> But these are just some guesses, since you gave us very little
> information.
> Ideally, you would give us all parameters you passed to ./configure during
> compilation, as well as the contents to config.log.
>
> Best,
> Tiago
>
> --
> Tiago de Paula Peixoto <[hidden email]
> <http:///user/SendEmail.jtp?type=node=4026990=0>>
>
>
> ___
> graph-tool mailing list
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>
>
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setup.csh (302 bytes) 
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Re: [graph-tool] general "did not match C++ signature" error

[bloodymeli]

Thanks!

This is indeed strange, as the library is installed to 
/usr/local/epd/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so

but compiled against:
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x738ce000)

How do I specify which libpython to use?



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[graph-tool] general "did not match C++ signature" error

[bloodymeli]

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 "", line 1, in 
  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,
std::allocator >, boost::python::api::object,
std::__cxx11::basic_string,
std::allocator >, 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 =>  (0x77ffe000)
libboost_iostreams.so.1.59.0 => /usr/lib64/libboost_iostreams.so.1.59.0
(0x75c46000)
libboost_python.so.5 => /usr/lib64/libboost_python.so.5
(0x759f5000)
libboost_regex.so.1.59.0 => /usr/lib64/libboost_regex.so.1.59.0
(0x756df000)
libboost_coroutine.so.1.59.0 => /usr/lib64/libboost_coroutine.so.1.59.0
(0x754d4000)
libCGAL.so.12 =>
/usr/local/cgal-releases-CGAL-4.9/build/release/lib/libCGAL.so.12
(0x752af000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x75087000)
libstdc++.so.6 =>
/usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libstdc++.so.6
(0x74cf8000)
libm.so.6 => /lib64/libm.so.6 (0x74a74000)
libc.so.6 => /lib64/libc.so.6 (0x746e)
libgcc_s.so.1 =>
/usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libgcc_s.so.1
(0x744c9000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x742b8000)
libz.so.1 => /usr/local/epd/lib/libz.so.1 (0x7409a000)
librt.so.1 => /lib64/librt.so.1 (0x73e91000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x73c74000)
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 
(0x738ce000)
libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x72788000)
libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x723f2000)
libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x720a)
libboost_context.so.1.59.0 => /usr/lib64/libboost_context.so.1.59.0
(0x71e96000)
libboost_thread.so.1.59.0 => /usr/lib64/libboost_thread.so.1.59.0
(0x71c74000)
libboost_chrono.so.1.59.0 => /usr/lib64/libboost_chrono.so.1.59.0
(0x71a6d000)
libboost_system.so.1.59.0 => /usr/lib64/libboost_system.so.1.59.0
(0x71869000)
libmpfr.so.1 => /usr/lib64/libmpfr.so.1 (0x7161c000)
libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x713c1000)
/lib64/ld-linux-x86-64.so.2 (0x003f1480)
libdl.so.2 => /lib64/libdl.so.2 (0x711bc000)
libutil.so.1 => /lib64/libutil.so.1 (0x70fb9000)

yeast.graphml

  



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[graph-tool] Some clarifications regarding directness

[bloodymeli]

Hi,

Consider the following GraphML file (attached).
According to the GraphML file, it represents an undirected graph.
Therefore, I would expect that as I set it to directed graph:
gtGraph=gt.load_graph("yeast.graphml")
gtGraph.set_directed(1)

I would obtain two directed edges for every undirected edge. In particular,
the in degree of every node should be equal to the out degree. However, this
is not the case, for example:
v=gtGraph.vertex(1834)

v.in_degree()
Out[3]: 5

v.out_degree()
Out[4]: 2

I'm a bit puzzled. 
A) Is the source file corrupted?
B) When I set the directedness flag to 1, am I guaranteed that every
undirected edge would be converted to two directed edges? If not, how can I
perform this operation (A = A + A', assuming the adjacency matrix is
triangular) or validate it?

yeast.graphml

  



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Re: [graph-tool] RedHat Installation Assistance

[bloodymeli]

Thank you once again.
I apologize for re-consulting, but our IT manager failed to install again
(arghh).
I'm forwarding his message:

I set the environment to use the newer python and numpy, and corrected the
boost library to work with it.
Configure worked OK but now make failed in searching cairommconfig.h

  CXX  graph_cairo_draw.lo
graph_cairo_draw.cc:37:27: fatal error: cairommconfig.h: No such file or
directory
compilation terminated.

cairommconfig.h exists: /usr/include/cairomm-1.0/cairomm/cairommconfig.h
as a part of the installed cairomm-devel.

I didn't find a way to tell the configure from where to take the cairomm
header files.
Please ask the developer.

The log files attached.



Best,
Eli

On Mon, Dec 5, 2016 at 7:36 PM, Tiago Peixoto [via Main discussion list for
the graph-tool project] <ml-node+s982480n4026899...@n3.nabble.com> wrote:

> On 05.12.2016 17:58, bloodymeli wrote:
> > Thanks! I'll ask the manager to update the numpy installation. However,
> he
> > might be reluctant to do so due to breaking other dependencies. I guess
> this
> > is the reason he tried to link with the local numpy-1.8.1-2. It's there
> a
> > way to link/compile with the epd copy ( at
> >   usr/local/epd/lib/python2.7/site-packages/numpy)  rather than the
> system
> > numpy?
>
> Yes, you have to specify its directory with the option --with-numpy=DIR
> passed to ./configure.
>
> Best,
> Tiago
>
> --
> Tiago de Paula Peixoto <[hidden email]
> <http:///user/SendEmail.jtp?type=node=4026899=0>>
>
>
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Re: [graph-tool] RedHat Installation Assistance

[bloodymeli]

Thanks! I'll ask the manager to update the numpy installation. However, he
might be reluctant to do so due to breaking other dependencies. I guess
this is the reason he tried to link with the local numpy-1.8.1-2. It's
there a way to link/compile with the epd copy ( at
usr/local/epd/lib/python2.7/site-packages/numpy)  rather than the system
numpy?

On 5 Dec 2016 17:44, "Tiago Peixoto [via Main discussion list for the
graph-tool project]" <ml-node+s982480n4026897...@n3.nabble.com> wrote:

On 05.12.2016 16:16, bloodymeli wrote:
> Via the RedHat rpm - numpy-1.4.1-9 is installed.

This is the problem. graph-tool requires numpy version 1.7 or above.

Numpy 1.4 is already over 6 years old.

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Re: [graph-tool] RedHat Installation Assistance

[bloodymeli]

Hi,

Here's the IT manager response :
Via the RedHat rpm - numpy-1.4.1-9 is installed.
Also under the local installation of python2.7,  numpy-1.8.1-2 is installed.
Regarding folders :

/usr/lib64/python2.6/site-packages/numpy

/usr/local/epd/lib/python2.7/site-packages/numpy

Once again, thanks for your help!

On 5 Dec 2016 15:46, "Tiago Peixoto [via Main discussion list for the
graph-tool project]" <ml-node+s982480n4026895...@n3.nabble.com> wrote:

> On 05.12.2016 13:40, bloodymeli wrote:
> > I'm attaching the corresponding information and filed I have received
> from
> > out IT manager.
>
> Thanks, but I still don't know what numpy version you have installed.
>
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Re: [graph-tool] RedHat Installation Assistance

[bloodymeli]

Thanks.
I'm attaching the corresponding information and filed I have received from
out IT manager. 

The system info is :

# uname -a
Linux admin 2.6.32-431.5.1.el6.x86_64 #1 SMP Fri Jan 10 14:46:43 EST 2014
x86_64 x86_64 x86_64 GNU/Linux
# cat /etc/issue
Red Hat Enterprise Linux Server release 6.5 (Santiago)
Kernel \r on an \m


Setup before the configure :

export CAIROMM_CFLAGS=-O
export CAIROMM_LIBS=/usr/lib64/libcairomm-1.0.so
export PYCAIRO_HEADER=/usr/include/pycairo
source /usr/local/gcc5.3/setup.sh

where :
# cat  /usr/local/gcc5.3/setup.sh

#!/bin/sh
# Setup for GCC 5.3

export DIR=/usr/local/gcc5.3
export PATH=$DIR/bin:$PATH
export LD_LIBRARY_PATH=$DIR/lib64:$DIR/lib:$LD_LIBRARY_PATH
export LD_RUN_PATH=$LD_LIBRARY_PATH

The log files are in the attached zip file. 

Thanks ahead! logsofgraphtool2_19installation.zip

  




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[graph-tool] RedHat Installation Assistance

[bloodymeli]

Dear All,

I have requested out IT manager to install graph-tool on our local cluster
(based on RedHat).
He changed the "configure" link to point to the corresponding directories,
and the "configure" operation seemed to completed successfully. 
However, the make operation failed with the corresponding message:


In file included from ./../graph_python_interface.hh:48:0,
 from graph_motifs.cc:26:
./../numpy_bind.hh: In function ‘boost::python::api::object
wrap_vector_owned(const std::vector<_RealType>&)’:
./../numpy_bind.hh:83:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in
this scope
 PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
  ^
./../numpy_bind.hh:83:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared
in this scope
 PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
  ^
./../numpy_bind.hh:84:25: error: ‘NPY_ARRAY_OWNDATA’ was not declared in
this scope
 NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE);
 ^
./../numpy_bind.hh:84:45: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in
this scope
 NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE);
 ^
./../numpy_bind.hh:84:64: error: there are no arguments to
‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration
of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive]
 NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE);
^
./../numpy_bind.hh:84:64: note: (if you use ‘-fpermissive’, G++ will accept
your code, but allowing the use of an undeclared name is deprecated)
./../numpy_bind.hh: In function ‘boost::python::api::object
wrap_vector_not_owned(std::vector<_RealType>&)’:
./../numpy_bind.hh:101:33: error: ‘NPY_ARRAY_ALIGNED’ was not declared in
this scope
 PyArray_ENABLEFLAGS(ndarray,NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
 ^
./../numpy_bind.hh:101:53: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared
in this scope
 PyArray_ENABLEFLAGS(ndarray,NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
 ^
./../numpy_bind.hh:102:25: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in
this scope
 NPY_ARRAY_WRITEABLE);
 ^
./../numpy_bind.hh:102:44: error: there are no arguments to
‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration
of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive]
 NPY_ARRAY_WRITEABLE);
^
./../numpy_bind.hh: In function ‘boost::python::api::object
wrap_multi_array_owned(const boost::multi_array&)’:
./../numpy_bind.hh:122:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in
this scope
 PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
  ^
./../numpy_bind.hh:122:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared
in this scope
 PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
  ^
./../numpy_bind.hh:123:25: error: ‘NPY_ARRAY_OWNDATA’ was not declared in
this scope
 NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE);
 ^
./../numpy_bind.hh:123:45: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in
this scope
 NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE);
 ^
./../numpy_bind.hh:123:64: error: there are no arguments to
‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration
of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive]
 NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE);
^
./../numpy_bind.hh: In function ‘boost::python::api::object
wrap_multi_array_not_owned(boost::multi_array&)’:
./../numpy_bind.hh:137:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in
this scope
 PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
  ^
./../numpy_bind.hh:137:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared
in this scope
 PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS
|
  ^
./../numpy_bind.hh:138:25: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in
this scope
 NPY_ARRAY_WRITEABLE);
 ^
./../numpy_bind.hh:138:44: error: there are no arguments to
‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration
of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive]
 NPY_ARRAY_WRITEABLE);