Thanks for the quick reply! I might be even better off just installing
Linux, I've tried it on a virtual instance and it was more or less just an
apt-get install on Ubuntu which is quite a bit easier :)
I was wondering: the specific graphs I'm looking for are induced isomorphic
subgraphs. G can be any undirected graph, and subgraph S is a chorless
cycle (i.e. a 'ring' with n vertices).
I specifically want to find all (unique) vertex induced subgraphs of S in
G, or in other words all chordless subgraphs of length n in G.
With
vm, em = gt.subgraph_isomorphism(S,G)
I can find subgraphs, but they are not neccesarily vertex induced: the
found isomorphic subgraph (lets call them F) can have more edges than S
I can see two ways to detect if the found subgraph F is isomorphic to S
1. (for this specific case) check if the number of edges in S == number
of edges in F - as they are cyclic this works
2. check with gt.isomorphism(S,F)
Only: how do I get F?
I use vmask, emask = gt.mark_subgraph(G,S, vm[i], em[i]) in a loop as in
http://projects.skewed.de/graph-tool/doc/topology.html#graph_tool.topology.subgraph_isomorphism,
but after masking G.set_vertex_filter(vmask) still gt.isomorphism(S,G) ==
False
How do I generate a new graph from the output of
gt.subgraph_isomorphism(S,G) which has all vertices and edges of F but no
more (i.e. how do I define F as a graph which will possibly give
gt.isomorphism(F,S) == True when this is the case).
Or should I be able to check the number of edges in the filtered version of
G as per my method 1? How?
Thanks for your assistance!
Jelle Veraa
On 3 January 2013 11:42, Tiago Peixoto [via Main discussion list for the
graph-tool project] <[email protected]> wrote:
> Hi there,
>
> It seems the configure script cannot find some libraries:
>
> c:/users/jelle.veraa/dropbox/ke-works-jelleveraa/random/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe:
>
> cannot find -lbz2
> c:/users/jelle.veraa/dropbox/ke-works-jelleveraa/random/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe:
>
> cannot find -lexpat
>
> and it screws up finding extra link flags for python:
>
> configure:17030: checking python extra linking flags
> configure:17037: result: None
> configure:17044: checking consistency of all components of python
> development environment
> configure:17070: gcc -o conftest.exe -g -O2 -Ic:\Python27\include
> conftest.c -lm -Lc:\Python27\Lib\config -lpython27 None >&5
> gcc.exe: error: None: No such file or directory
>
> Make sure all the necessary libraries are installed in the correct
> path. For the last bug, the check is done in m4/ax_python_devel.m4:
>
> if test -z "$PYTHON_EXTRA_LDFLAGS"; then
> PYTHON_EXTRA_LDFLAGS=`$PYTHON -c "import
> distutils.sysconfig; \
> conf = distutils.sysconfig.get_config_var; \
> print (conf('LINKFORSHARED'))"`
> fi
>
> For some reason, it is printing 'None', instead of an empty string. This
> could be changed to something like,
>
> if test -z "$PYTHON_EXTRA_LDFLAGS"; then
> PYTHON_EXTRA_LDFLAGS=`$PYTHON -c "import
> distutils.sysconfig; \
> conf = distutils.sysconfig.get_config_var; \
> x = conf('LINKFORSHARED'); \
> x = x if x is not None else ''; \
> print (x)"`
> fi
>
> But this is unlikely to fix the problem, since I think it is very
> strange that this value points to None in the first place.
>
> It would be nice to have graph-tool working on windows, but it is a very
> weird platform, and I do not have access to a windows machine to
> understand all its idiosyncrasies.
>
> Cheers,
> Tiago
>
>
> On 01/02/2013 02:27 PM, Jelle Veraa wrote:
>
> > Dear all,
> >
> > Happy new year!
> >
> > Starting of with what I'd actually like to do (building the program is
> > of course a means to an end :) - I'd like to use the library for its
> > subgraph isomorphism algorithm specifically - should you be able to
> > provide me a binary of the library or know of another fast
> > implementation for subgraph isomorphism that might help me as well.
> >
> > I'm trying to install the library on a 64 bit Windows 7 machine running
> > 32 bit python 2.7.
> > Installing the dependencies (from binaries) works, but running ./config
> > from MinGW/MSys gives me an error. it exits with "Could not link test
> > program to Python. Maybe the main Python library has been installed in
> > some non-standard library path. If so, pass it to configure, via the
> > LDFLAGS environment variable.", but the solution seems less
> > straightforward - I've already tried all kinds of LDFLAGS versions
> > pointing towards my Python folder (at C:\Python27, or /c/Python27 in
> > MinGW).
> >
> > here is the log:
> > http://bpaste.net/show/82ASZHcSnWmGsBIglFEo/
> >
> > From line 2055/configure:16996 things start going wrong (a bit is posted
> > below). There is a reference to Lib\config, but the config directory
> > does not exist. Furthermore the output 'None' at configure:17037 is
> > injected into the command line for gcc.exe which also gives an error.
> >
> > I've been googling for an answer for some hours now bu no luck. I see
> > that you need python-dev on linux for instance, but I've got Windows so
> > 'apt-get python-dev' won't work :)
> >
> > Can anyone help me?
> >
> > thanks,
> > Jelle
> >
> > configure:16996: result: -Lc:\Python27\Lib\config -lpython27
> > configure:17003: checking for Python site-packages path
> > configure:17009: result: c:\Python27\Lib\site-packages
> > configure:17016: checking python extra libraries
> > configure:17023: result:
> > configure:17030: checking python extra linking flags
> > configure:17037: result: None
> > configure:17044: checking consistency of all components of python
> > development environment
> > configure:17070: gcc -o conftest.exe -g -O2 -Ic:\Python27\include
> > conftest.c -lm -Lc:\Python27\Lib\config -lpython27 None >&5
> > gcc.exe: error: None: No such file or directory
> >
> >
> > _______________________________________________
> > graph-tool mailing list
> > [hidden email] <http://user/SendEmail.jtp?type=node&node=4024890&i=0>
> > http://lists.skewed.de/mailman/listinfo/graph-tool
> >
>
> --
> Tiago de Paula Peixoto <[hidden
> email]<http://user/SendEmail.jtp?type=node&node=4024890&i=1>>
>
>
>
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