graph-tool December 2012

graph-tool@skewed.de

6 participants
10 discussions

graph-tool can't find Graphviz renderer
by Mikhail Spivakov 07 Apr '16

07 Apr '16

Hello! I've got graphviz installed with python and python27 bindings. However, when I do: graph_draw(ug, vprops={"label": ug.vertex_index}, output="two-nodes.pdf", layout="fdp") I get the following error: graph G { graph [outputorder=edgesfirst, mode=major, overlap=true, ratio=fill, size="5.905512,5.905512", start=3019255687130444316]; node [label="\N", shape=circle, width="0.105", height="0.105", style=filled, color="#2e3436", fillcolor="#a40000"]; edge [arrowsize="0.3", color="#2e3436", penwidth="1.0"]; graph [bb="0,0,425,425"]; 0 [label=0, width="0.47", height="0.47", pos="330,101"]; 1 [label=1, width="0.47", height="0.47", pos="93,324"]; 0 -- 1 [pos="318,113 277,152 147,274 106,312"]; } Error: renderer for pdf is unavailable Out[8]: <PropertyMap object with key type 'Vertex' and value type 'vector<double>', for Graph 0x5ff3f90, at 0x6001290> At the same time, if I save the above dot expression as test1.dot and run the following command from the command line: $ dot -Tpng test1.dot -o graph1.png I get a beautiful graph1.png. Graphviz is installed in a non-standard location as I don't have admin rights. However, the graphviz folder is in LD_LIBRARY_PATH and gv.py is in PYTHONPATH. Would very much appreciate your advice on what else graph-tool might need to find the libraries and/or how to test it better. Many thanks, Mikhail

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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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Undefined symbol drawing function
by sasho.j.markov 20 Apr '15

20 Apr '15

Hi New to the graph-tool. Build it from src on Fedora 16 (64) . Built with cairomm enabled . Try to run as per the quick start , however when executing graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, ... output_size=(200, 200), output="two-nodes.pdf") i get undefined symbol _ZN5Cairo7ContextC1EP6_cairob However the symbol above is defined in : libcairomm-1.0.so see below nm command results nm /usr/local/lib/libcairomm-1.0.so | grep -i _ZN5Cairo7ContextC1EP6_cairob 0000000000014b90 T _ZN5Cairo7ContextC1EP6_cairob Interestingly the library libgraph_tool_draw.so has indeed have the undefined symbol U _ZN5Cairo7ContextC1EP6_cairob but does not depend on the cairomm libarary - see the ldd output . unless the library is dynamically load i do not understand why Any advise appreciated- regards Sasho ldd /usr/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so linux-vdso.so.1 => (0x00007fffc46da000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f99fd6cd000) libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007f99fd30e000) libboost_iostreams.so.1.49.0 => /usr/local/lib/libboost_iostreams.so.1.49.0 (0x00007f99fd0f6000) libboost_python.so.1.49.0 => /usr/local/lib/libboost_python.so.1.49.0 (0x00007f99fceaa000) libboost_regex.so.1.49.0 => /usr/local/lib/libboost_regex.so.1.49.0 (0x00007f99fcbc8000) libCGAL.so.9 => /usr/local/lib/libCGAL.so.9 (0x00007f99fc9a5000) libexpat.so.0 => /usr/local/lib/libexpat.so.0 (0x00007f99fc77c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f99fc54d000) libm.so.6 => /lib64/libm.so.6 (0x00007f99fc2c9000) libc.so.6 => /lib64/libc.so.6 (0x00007f99fbf11000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f99fbcfb000) /lib64/ld-linux-x86-64.so.2 (0x00000030cea00000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f99fbadf000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f99fb8db000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f99fb6d7000) libz.so.1 => /lib64/libz.so.1 (0x00007f99fb4c0000) librt.so.1 => /lib64/librt.so.1 (0x00007f99fb2b8000) libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x00007f99fb0b3000) libboost_thread.so.1.49.0 => /usr/local/lib/libboost_thread.so.1.49.0 (0x00007f99fae98000) libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007f99fac41000) -- 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.

3 3

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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max_cardinality_matching heuristic
by Daniel Müllner 19 Dec '12

19 Dec '12

Hi all, in which sense is the algorithm in graph_tool.topology.max_cardinality_matching with the heuristic=True switch a heuristic and not exact? As I understand, it might not return a maximum-cardinality matching even if there is one. But what about the edge weights? Does it always return a minimum-weight matching (respectively maximum-weight with minimize=False)? Or is this not guaranteed? Note that there are pitfalls to this question: eg. if all edge weights are equal to one, then the optimal min-weight matching is empty if I do not insist on max-cardinality. Can someone enlighten me what the heuristic actually optimizes? Cardinality or weights? Both (in which sense) or none (what's it good for, then)? And does it always find the optimum for one of those two criteria? Best, Daniel -- Daniel Müllner Stanford University Department of Mathematics 450 Serra Mall, Building 380 Stanford, CA 94305 USA e-mail: muellner(a)math.stanford.edu http://math.stanford.edu/~muellner

2 3

Cannot access vertices of a GraphView
by Daniel Müllner 18 Dec '12

18 Dec '12

Dear experts, when I build a GraphView, I cannot access the vertices of an edge. Here is a minimal example: import graph_tool as gt import graph_tool.topology as gtt G = gt.Graph(directed=False) G.add_vertex(4) for s,t in [(0,1), (2,3), (0,2)]: G.add_edge(G.vertex(s), G.vertex(t)) match, is_maximal = gtt.max_cardinality_matching(G) GV = gt.GraphView(G, efilt=match) for edge in GV.edges(): source = GV.vertex_index(edge.source()) print(source) I get the following error message: Traceback (most recent call last): File "gt_test.py", line 16, in <module> source = GV.vertex_index(edge.source()) ... ... File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line 181, in _type_alias raise ValueError("invalid property value type: " + type_name) ValueError: invalid property value type: unsigned long Any idea what's wrong here, and more importantly: how to fix it? Best regards, Daniel -- Daniel Müllner Stanford University Department of Mathematics 450 Serra Mall, Building 380 Stanford, CA 94305 USA e-mail: muellner(a)math.stanford.edu http://math.stanford.edu/~muellner

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Optimizing distance computation in a periodic space.
by Guillaume Gay 17 Dec '12

17 Dec '12

Hi list. I am using graph-tool to model an /apical junctions/ network, based on the model by Farhadifar et al. <http://www.sciencedirect.com/science/article/pii/S0960982207023342>. In short, it corresponds to the outer surface of the cells in a particular region of the embryo, where each cell is represented by a polygon. Topology of the network changes due to cell division and cell death. The physical model involves the local minimization of an energy depending on the local geometry. I got a working model, but the energy optimization is time consuming. I think that this is due to the way I compute the components of the vector formed by each edge of the graph, by iterating over the edges., eg: |for edgein graph.edges(): v0, v1 = edge.source(), edge.target() deltax[edge] = x[v1] - x[v0] deltay[edge] = y[v1] - y[v0]| This is further complicated (to a little extent) by periodic conditions to the coordinate systems, and some other details, but I think this is the core issue. I have the feeling I can do better, perhaps by using the adjacency matrix? This would be particularly interesting as the graph topology doesn't change for a given optimization. Any advice is welcome, thanks! Guillaume

3 11

Color Space?
by Chris Diehl 10 Dec '12

10 Dec '12

Hello, I've got a quick question: how are the colors parameterized? Is it expecting CMYK? Thanks, Chris

2 1

Installing using MacPorts under OSX Lion
by Chris Diehl 09 Dec '12

09 Dec '12

By some small miracle, I managed to get the installation to work on my MacBook Pro for work. I'm still struggling with my MacBook Air. Wondering if anyone has any suggestions. Here's what I'm seeing. $ sudo port install py27-graph-tool---> Computing dependencies for py27-graph-tool ---> Fetching archive for py27-graph-tool ---> Attempting to fetch py27-graph-tool-2.2.18_2.darwin_11.x86_64.tbz2 from http://packages.macports.org/py27-graph-tool ---> Attempting to fetch py27-graph-tool-2.2.18_2.darwin_11.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/py27-graph-… ---> Attempting to fetch py27-graph-tool-2.2.18_2.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/py27-graph-tool ---> Fetching distfiles for py27-graph-tool ---> Attempting to fetch graph-tool-2.2.18.tar.bz2 from http://distfiles.macports.org/py-graph-tool ---> Verifying checksum(s) for py27-graph-tool ---> Extracting py27-graph-tool ---> Configuring py27-graph-tool Error: org.macports.configure for port py27-graph-tool returned: configure failure: command execution failed Please see the log file for port py27-graph-tool for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-graph-tool/py27-graph-tool/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port py27-graph-tool failed Digging into the log file, I see the place where things go off the rails. :info:configure Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-graph-tool/py27-graph-tool/work/graph-tool-2.2.18" && ./configure --prefix=/opt/local --with-boost=/opt/local :info:configure Exit code: 1 :error:configure org.macports.configure for port py27-graph-tool returned: configure failure: command execution failed :debug:configure Error code: NONE :debug:configure Backtrace: configure failure: command execution failed while executing "$procedure $targetname" :info:configure Warning: targets not executed for py27-graph-tool: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install :notice:configure Please see the log file for port py27-graph-tool for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-graph-tool/py27-graph-tool/main.log Running those commands myself, I see the following from the configure statement: ... ================ Detecting python ================ checking for a Python interpreter with version >= 2.6... python checking for python... /opt/local/bin/python checking for python version... 2.7 checking for python platform... darwin checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for python2.7... (cached) /opt/local/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.1'... yes checking for the distutils Python package... yes checking for Python include path... -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 checking for Python library path... -L/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config -lpython2.7 checking for Python site-packages path... /Library/Python/2.7/site-packages checking python extra libraries... -ldl -framework CoreFoundation checking python extra linking flags... -u _PyMac_Error /System/Library/Frameworks/Python.framework/Versions/2.7/Python checking consistency of all components of python development environment... yes =========================== Using python version: 2.7.1 =========================== checking for boostlib >= 1.38.0... yes checking whether the Boost::Python library is available... no configure: error: No usable boost::python found I tried uninstalling and reinstalling boost different ways and to no avail. Definitely out of ideas. Any pointers would be greatly appreciated! Chris

2 2

Drawing large graphs
by alepulver 03 Dec '12

03 Dec '12

Hello, I've started using graph-tool mainly because it's faster than networkx. Recently I tried analyzing Wordnet by constructing a graph from all synsets and polysemy relations between them; it has 117659 nodes and 549414 edges. When I run statistics such as degree average, local clustering average and pseudo diameter they only take a few seconds. On the other hand, if I try to draw it with graph_draw it takes 6 hours (using 4 cores, and about 24hs of combined CPU time) or graphviz_draw (which I haven't run for more than an hour). Initially I thought the bottleneck was in using labels (which I removed afterwards), then in the layout algorithm (before confirming that random layout takes only a few seconds), and finally outputting pixels instead of vectors (svg instead of png), but none of them seemed to have to do with it. Also, saving the graph also takes just a few seconds. I have uploaded it in xml.gz format here (it's 6.4MB): http://www.sendspace.com/file/zc7yrh If you have any suggestions please let me know. Thanks in advance, Alejandro -- 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 December 2012