gmane.comp.science.graph.graph-tool.general

Re: Building on OSX 10.8 with brew, Anaconda Python distribution

Tiago de Paula Peixoto — 2013-05-21T07:08:53

Hm... This is strange. Could you please send me the _full_ build output, with the entire error message?

You really get absolutely no difference switching boost versions?

Cheers,
Tiago

Re: Building on OSX 10.8 with brew,Anaconda Python distribution

Eric Jonas — 2013-05-21T00:05:37

Alas, I tried, and still somehow get the exact same error. The config
output is  https://gist.github.com/ericmjonas/5616481 . And this is
with both clang and with the brew-installed g++-4.7, as the ticket
seemed to suggest might be the problem.

On Mon, May 20, 2013 at 2:22 PM, Tiago de Paula Peixoto <tiago< at >skewed.de> wrote:

Re: Building on OSX 10.8 with brew, Anaconda Python distribution

Tiago de Paula Peixoto — 2013-05-20T21:22:50

Try disabling sparsehash by passing --disable-sparsehash to the
configure script.

Take a look at the following ticket for further explanation: https://projects.skewed.de/graph-tool/ticket/125

Cheers,
Tiago

Building on OSX 10.8 with brew,Anaconda Python distribution

Eric Jonas — 2013-05-20T17:42:18

Hey guys! I'm trying to build graph-tool and I'm using:
OSX 10.8
brew
The latest Anaconda python distribution from Continuum.

When building the blockmodel I'm getting the following error:

graph_blockmodel.hh:910: error: no matching function for call to
'get(const boost::tuples::tuple<boost::UndirectedAdaptor<boost::filtered_graph<boost::adj_list<long
unsigned int>, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned
char, boost::adj_edge_index_property_map<long unsigned int> > >,
graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned
char, boost::typed_identity_property_map<long unsigned int> > > >
boost::tuples::null_type, boost::tuples::null_type,
boost::tuples::null_type, boost::tuples::null_type,
boost::tuples::null_type, boost::tuples::null_type>&)'

The (now complex) configure command I'm using is:
LDFLAGS=-L/usr/local/opt/boost149/lib
CPPFLAGS="-I/usr/local/opt/boost149/include
-I/usr/local/include/sparsehash" CC=gcc-4.7
PKG_CONFIG_PATH=/opt/X11/lib/pkg

Re: importing graph_tool

2013-05-17T19:25:52

Thanks Tiago for response.

When I compile there is not other significant processes in background. 
Before compilation there is no more than 700MB used by other processes.

Just in case I attach my configure.log.

In free time I will try to compile it with clang.


Kris

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Re: importing graph_tool

Tiago de Paula Peixoto — 2013-05-17T16:37:06

Hi there,

On 05/17/2013 12:19 PM, piwonski.kris< at >gmail.com wrote:

This is a bug... It should be to import the module with graph filtering
disabled. I'll submit a fix to it.



It should be possible to compile graph-tool under 4GB RAM... Did you
make sure no other process was using significant amount of memory, such
as the browser and such?

Optionally, you can use the clang compiler. It uses significantly less
memory than GCC (around half or so).

Cheers,
Tiago

importing graph_tool

2013-05-17T10:19:01

Hi guys,

when I import graph_tool I get an error.
It complains  graph filtering was disabled at compile time.
Well, I can't set it enable because for some reason compiling with flag 
enabled drains out my memory.
I have 4GB RAM and I am using Arch. I get package from AUR repository and 
made makepkg on it(I had to modify it slightly to get rid of openmp and 
graph-filtering).



My stack trace from ipython:


In [1]: from graph_tool.all import *
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-1-100bbe2bc9d9> in <module>()
----> 1 from graph_tool.all import *

/usr/lib/python2.7/site-packages/graph_tool/__init__.py in <module>()
   2010                     e.__class__.__doc__ = _edge_doc
   2011 
-> 2012 init_edge_classes()
   2013 
   2014 # some shenanigans to make it seem there is only a single edge class

/usr/lib/python2.7/site-packages/graph_tool/__init__.py in 
init_edge_classes()

Another Windows 7 64-bit user attempting to getgraph-tool running

Brian Ball — 2013-05-02T21:07:54

I am encountering the same errors others have:

configure:16482: checking for main in -lbz2
configure:16501: g++ -o conftest.exe -Wall -Wextra  -ftemplate-depth-150
-Wno-deprecated -Wno-unknown-pragmas -O3 -fvisibility=default
-fvisibility-inlines-hidden -Wno-unknown-pragmas   conftest.cpp -lbz2  -lm
c:/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe:
cannot find -lbz2

configure:16522: checking for main in -lexpat
configure:16541: g++ -o conftest.exe -Wall -Wextra  -ftemplate-depth-150
-Wno-deprecated -Wno-unknown-pragmas -O3 -fvisibility=default
-fvisibility-inlines-hidden -Wno-unknown-pragmas   conftest.cpp -lexpat
-lm  >&5
c:/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe:
cannot find -lexpat

And finally:

configure:17109: checking consistency of all components of python
development environment
configure:17135: gcc -o conftest.exe -g -O2  -Ic:\Python2.7\include
conftest.c -lm  -Lc:\Python2.7\Lib\config -lpython27 None  >&5
gcc.exe: error: None: No such file or direct

Re: Graph I/O & pickle

Tiago de Paula Peixoto — 2013-04-30T13:29:33

This has been fixed now in the git version...

Cheers,
Tiago

Re: Graph I/O & pickle

Anatol Wegner — 2013-04-29T16:47:00

Ok, thanks.
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Re: Graph I/O & pickle

Tiago de Paula Peixoto — 2013-04-29T15:51:08

Ok, this looks like a bug. It works fine in Python 3, but I cannot test
with Python 2.7 right now. Could you please put this in a ticket in the
website, so that I don't forget to fix it?

Cheers,
Tiago

Re: Graph I/O & pickle

Anatol Wegner — 2013-04-29T14:18:42

The script:
 >>> mt=load_graph('m.xml')
 >>> import pickle
 >>> f=open('graph','w')
 >>> pickle.dump(mt,f)
 >>> f.close()
 >>> g=open('graph','r')
 >>> m=pickle.load(g)
Traceback (most recent call last):
   File "<pyshell#11>", line 1, in <module>
     m=pickle.load(g)
   File "/usr/lib/python2.7/pickle.py", line 1378, in load
     return Unpickler(file).load()
   File "/usr/lib/python2.7/pickle.py", line 858, in load
     dispatch[key](self)
   File "/usr/lib/python2.7/pickle.py", line 1217, in load_build
     setstate(state)
   File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 
1789, in __setstate__
     self.load(stream, "xml")
   File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 
1518, in load
     props = self.__graph.ReadFromFile("", file_name, fmt)
TypeError: No registered converter was able to produce a C++ rvalue of 
type std::string from this Python object of type unicode
 >>>

thanks for the fast reply

Anatol
_______________________________________________
gr

Re: Graph I/O & pickle

Tiago de Paula Peixoto — 2013-04-29T12:27:46

I've never benchmarked this extensively, but I do believe that either
graphml or gml should be the fastest.


I'd need more information, such a very simple script where this
happens... What python version are you using?

Cheers,
Tiago

Graph I/O & pickle

Anatol Wegner — 2013-04-29T12:16:13

Hi all,
In general which graph format is fastest when writing/reading graphs? I 
am also getting errors when I load pickled and cpickled graphs...That is 
something like:

"TypeError: No registered converter was able to produce a C++ rvalue of 
type std::string from this Python object of type unicode"

Cheers,

Anatol

Re: versions and errors

Rodrigo Agerri — 2013-04-29T09:15:07

Thanks!

Rodrigo


On Mon, Apr 29, 2013 at 9:48 AM, Tiago de Paula Peixoto <tiago< at >skewed.de>wrote:

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Re: versions and errors

Tiago de Paula Peixoto — 2013-04-29T07:48:04

Hi,

On 04/28/2013 11:01 PM, Rodrigo Agerri wrote:

The behaviour of the internal graph property maps changed exactly in
version 2.2.19. Here is the commit:

http://git.skewed.de/graph-tool/commit/?id=14b91f60ce6fcb4d834b85eee49408f7be50b0d7

In the current versions, the dictionary returns the map values, not the
property map object themselves, so that one does not need to keep
passing the graph object as key any longer, which was redundant.

Cheers,
Tiago

versions and errors

Rodrigo Agerri — 2013-04-28T21:01:01

Hello,

I am using Debian and I have two versions of graph-tool available. I have a
program we would like to distribute using graph-tool but it turns out that
it runs fine with version graph-tool_2.2.19-1 but it does not with
version 2.2.23-1.

 File "process.py", line 168, in <module>
    main()
  File "process.py", line 126, in main
    processor.process_text((input_text, parse_tree))
  File "process.py", line 100, in process_text
    self.reset_graph()
  File "process.py", line 37, in reset_graph
    self.graph = self.graph_builder.new_graph()
  File
"/home/ragerri/pythoncode/corefgraph-en-opener/corefgraph/graph/graph_builder.py",
line 92, in new_graph
    GraphWrapper.set_properties(graph=graph,
graph_properties={'graph_builder': self})
  File
"/home/ragerri/pythoncode/corefgraph-en-opener/corefgraph/graph/utils.py",
line 82, in set_properties
    graph.graph_properties[name][graph] = property_value
TypeError: 'NoneType' object does not support item assignment

This error does not arise if I remove [gra

Re: Installation on Fedora 18

2013-04-26T06:25:27

Thanks, but for noobs like me, I would highly appreciate installation 
procedure via distribution. I would update you with my progress in 
installing graph-tool
On Wednesday, April 24, 2013 2:28:22 PM UTC+6, mij.raf...< at >gmail.com wrote:

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Re: Installation on Fedora 18

Tiago de Paula Peixoto — 2013-04-24T14:17:18

Compiling graph-tool on fedora is no different than in any other
distro. Just unpack the tarball and run:

        ./configure
        make
        make install

The last step should be run as root. If all the dependencies are
correctly installed, it should just work. However, it will take a little
while to compile, and eat some of your RAM (~4 GB).

It is in my TODO list to include fedora packages, but I never find time
to do it.

Cheers,
Tiago

--
Tiago de Paula Peixoto <tiago< at >skewed.de>

Installation on Fedora 18

2013-04-24T08:28:22

Can anyone give step by step installation procedure, directed towards noob, 
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Re: Generate random graph from given degree sequence

Matthias Ekman — 2013-04-17T13:26:49

Thanks Tiago!

On Tuesday, 16 April 2013 22:49:26 UTC+2, Tiago Peixoto wrote:
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