graph-tool April 2011

graph-tool@skewed.de

7 participants
9 discussions

Segmentation fault using shortest_distance
by Juan Manuel Tirado 20 Mar '16

20 Mar '16

Hi Tiago, I am trying to calculate the shortest distances of a graph after applying a filter. I have a code that looks like this: g=gt.load_graph("myGraph.xml",format="xml") #for later use distances = gt.shortest_distance(g) #extract the components of the graph comp = g.label_components(g) #This splits the graph in several components #I want to calculate the shortest distances #for the component 2 for example filtering = g.new_vertex_property("boolean") for v in g.vertices(): if comp[v]==2: filtering[v]=True else: filtering[v]=False #set the vertex filter g.set_vertex_filter(filtering) distances_comp=gt.shortest_distance(g) The last line of code rises a segmentation fault. I have plotted the graph with the filtered graph and its correct, also I can calculate the local_clustering_coefficient without problems. Am I doing something wrong? Is there any other way to filter the graph and calculate the shortest distances? Is this a bug? Thanks so much, Juan

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Parallel Processing
by Derek Ditch 21 Nov '13

21 Nov '13

I want to use graph-tool using the multiprocessing library in Python 2.6. I keep running into issues though with trying to share a full graph object. I can store the graph in a multiprocessing.Namespace, but it doesn't keep the dicts of properties. Example: def initNS( ns ): _g = Graph( directed = False) ns.graph = _g ns.edge_properties = { 'genres': _g.new_edge_property("vector<string>"), 'movieid': _g.new_edge_property("int"), } ns.vertex_properties = { 'personid': _g.new_vertex_property("int32_t") } """ Build property maps for edges and vertices to hold our data The graph vertices represent actors whereas movies represent edges """ # Edges _g.edge_properties["genres"] = ns.edge_properties['genres'] _g.edge_properties["movieid"] = ns.edge_properties['movieid'] # Vertices _g.vertex_properties["personid"] = ns.vertex_properties['personid'] ns.graph = _g ########## This initializes 'ns', which is a multiprocessing.Namespace. The problem is that for example, ns.edge_properties[ * ] tells me that the type isn't pickle-able. I tried to just skip that and use the _g.edge_properties to access it, but those dicts aren't carried over to the different process in the pool. Presumably b/c they aren't pickle-able. Any thoughts about how to fix this? (For those interested, I'm attempting to use the IMDbPy library to do some graph analysis on the relationships among actors and movies. Each process has it's own db connection and trying to populate the graph with actor and movie information in parallel since it's a pretty large and dense graph. Somewhere in the neighborhood of 250,000+ vertices for just a depth of three relationships) Thanks, -- Derek

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Graph drawing: overlay possible?
by Sebastian Weber 11 Aug '11

11 Aug '11

Hi! I was wondering if it is possible to overlay two drawings of the same graph where I use different color-coded vertex sizes? Theses colors would need to be transparent and the graph layout must match in each drawing. Is there an easy way of doing so with graph-tool? Thanks! Regards, -- Sebastian Weber Group of Cell Communication and Control Freiburg Institute for Advanced Studies - FRIAS School of Life Sciences - LIFENET Albert-Ludwigs-Universität Freiburg Albertstr. 19 79104 Freiburg T.: +49-761-203-97237 Fax:+49-761-203-97334

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Re: [graph-tool] New version of graph-tool and portfiles for MacOS X
by Tiago Peixoto 28 Apr '11

28 Apr '11

Hi Rune, RuneMikkelsen wrote: > > The new function > label_largest_component() > is not working for me. > When I try: > graph_tool.topology.label_largest_component(g2) > It says: 'module' object has no attribute 'label_largest_component' > > The old function > graph_tool.topology.label_components(g2) > works just fine... > > Any help is appreciated :) > Are you sure you are using the right version? I'm definitely seeing the function here... :-) By the way, your message got stuck on the online nabble forum, and did not go through the mailing list, since you are not subscribed. Note that I do not read the forum very often, so I may miss a message if you post only to the forum. If you only want to read the forum, you can subscribe anyway and request not to receive any mail. Cheers, Tiago ----- -- Tiago de Paula Peixoto <tiago(a)skewed.de> -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

1 0

New version of graph-tool and portfiles for MacOS X
by Tiago de Paula Peixoto 27 Apr '11

27 Apr '11

Hi, I just released a new version of graph-tool (2.2.12), which has a couple of bug fixes and better support for MacOS X. I've also added a portfile in the download section of the website, so that people can easily install it on MacOS X with macports. I've tested it and it seems to work fine, as long as the Apple version of GCC is used (with macports GCC from FSF I get strange segfaults). Please report any problems, and enjoy! Cheers, Tiago -- Tiago de Paula Peixoto <tiago(a)skewed.de>

3 7

label vertices
by Emad Fadhal 22 Apr '11

22 Apr '11

Hi i would like to know the code that change the label of vertices form index (0,1,3,... n-1) to different names (PDC,HOD,KNF,...n-1)?

2 1

Install on Mac OX
by paulo lopes 16 Apr '11

16 Apr '11

Hi I have a problem running the ./install, i looked the log file but i do not know what could be the problem. ersions/2.7/lib/python2.7/site-packages checking python extra libraries... -ldl -framework CoreFoundation checking python extra linking flags... -u _PyMac_Error Python.framework/Versions/2.7/Python checking consistency of all components of python development environment... no configure: error: 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. Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib" ============================================================================ ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them. ============================================================================ i already see in the mailing list a problem similar, but the solution is not the same (I guess). i'm new in this stuff, so i hope you can help me :) Paulo Lopes

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copy_graph in graph-tool?
by Sebastian Weber 14 Apr '11

14 Apr '11

Hey, I was wondering why compressing graphs to their largest component is so slow in comparison to doing this in C++ directly. The graph-tool way of doing by invoking remove_vertex_if or PurgeVertices are both not very fast. In former times I used copy_graph from boost to copy from a filtered graph object to a new graph object. I cannot find the respective function in graph-tool - is there a reason for that function missing? Ok, this double in-memory requirements, but from my experience things are a lot faster then. So in short: Could a copy_graph function be included in graph-tool? Thanks, -- Sebastian Weber Group of Cell Communication and Control Freiburg Institute for Advanced Studies - FRIAS School of Life Sciences - LIFENET Albert-Ludwigs-Universität Freiburg Albertstr. 19 79104 Freiburg T.: +49-761-203-97237 Fax:+49-761-203-97334

2 2

graph-tool installing and cygwin
by dd 02 Apr '11

02 Apr '11

Hi to all, I'm trying to configure, build and install graph-tool in a windows environment using CygWin. I already successfully installed all the dependencies reported in the graph-tool website. The problem arises while running "configure" script: when it tries to find a python version it comes to me the following error: checking for python... (cached) /cygdrive/c/Program Files/Python27/python checking for a version of Python >= '2.1.0'... configure: line 16603: /cygdrive/ c/Program: No such file or directory no configure: error: in `/cygdrive/c/Program Files/graph-tool-2.2.11': configure: error: This version of the AC_PYTHON_DEVEL macro doesn't work properly with versions of Python before 2.1.0. You may need to re-run configure, setting the variables PYTHON_CPPFLAGS, PYTHON_LDFLAGS, PYTHON_SITE_PKG, PYTHON_EXTRA_LIBS and PYTHON_EXTRA_LDFLAGS by hand. Moreover, to disable this check, set PYTHON_NOVERSIONCHECK to something else than an empty string. See `config.log' for more details I guess the problem is with my python root directory, that is "C:\Program Files\Python27" and contains a blank space, so when the script receives from the cygwin environment the path "/cygdrive/c/Program Files/Python27" it searches for "/cygdrive/c/Program" that doesn't exist. I don't know if my supposition is correct... in any case, can anybody please help me to deal with this problem? Thanks in advance, DD -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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graph-tool April 2011