graph-tool July 2013

graph-tool@skewed.de

11 participants
17 discussions

What formula is used for std in vertex_average and edge_average?
by VaSa 16 Jul '20

16 Jul '20

I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average >>> t2=gt.Graph() >>> t2.add_vertex(2) >>> t2.add_edge(t2.vertex(0), t2.vertex(1)) >>> gt.vertex_average(t2, "in") (0.5, 0.35355339059327373) Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ? also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710 0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some relation to that. A little bigger graph. >>> t3=gt.Graph() >>> t3.add_vertex(5) >>> t3.add_edge(t3.vertex(0), t3.vertex(1)) >>> gt.vertex_average(t3, "in") (0.2, 0.17888543819998318) Now, we should have 0,1,0,0,0 series for vertex incoming degree. So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854 come from ? Reason, I am asking because, I have a large graph, where the average looks quite alright but the std makes no sense, as going by the histogram, degree values are quite a bit more distributed than the std would indicate. -- 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 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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graph-tool graphml and networkx
by tcb 17 Aug '15

17 Aug '15

Hi, I am trying to read the graphml output of graph-tool's graphml using networkx. https://github.com/networkx/networkx/issues/843 Unfortunately this does not work with any of the vector_* type property maps which graph-tool uses. Have you encountered this issue before? It seems the right thing to do might be to extend your graphml to hold the vector_* attributes as detailed: http://graphml.graphdrawing.org/primer/graphml-primer.html#EXT Is there some reason why it was done the way it is? How do you manage read/writing graphml data to other tools? In the meantime, it might be possible to hack some read support for graph-tool's xml into networkx. To this end, could you please advise how to parse the 'key1' data (should be two floats) <node id="n1"> <data key="key0">6</data> <data key="key1">0x1.5c71d0cb8d943p+3, 0x1.70db7f4083655p+3</data> </node> thanks - -- 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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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

Problem importing on Mac OS X 10.8, installed using MacPorts
by Uldis Bojars 07 Mar '14

07 Mar '14

Hi, When trying to import graph-tool the following error message is returned: >>> from graph_tool.all import * Fatal Python error: PyThreadState_Get: no current thread Could you help me solve this problem? graph-tool version py-graph-tool-2.2.18 was successfully installed using MacPorts but it fails during importing. Thanks, Uldis

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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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gt.astar_search 'zero' and 'infinity' parameter type interpretation is wrong
by Guillaume Lemaître 25 Jul '13

25 Jul '13

Documentation (http://projects.skewed.de/graph-tool/doc/search_module.html#graph_tool.sear…) says that both 'zero' and 'infinity' parameters type should be int or float. To me this is wrong, their type should be the one used to represent costs. A confirmation of that is that I used to work with 2.2.17 version. While moving to 2.2.24, I encounter a bug that has been introduced in 2.2.18 version (commit 016d8244a24b3dba812ce2bb305e2e1f09e85154) In my application, 'cost_map' and 'dist_map' are both created with graph.new_vertex_property("object") 'zero' and 'infinity' are two specific Cost() instances, which is a type with a __init__ function that don't take any other argument than the regular 'self' one). The call to astart_search is like this: gt.astar_search (g=MyGraph, source=MyGraph.vertex(0), weight = MyGraph.new_edge_property("object"), visitor=MyVisitor, dist_map = MyGraph.new_vertex_property("object"), cost_map = MyGraph.new_vertex_property("object"), pred_map = MyGraph.new_vertex_property("int"), zero = CostZero, infinity = CostInfinity, implicit = true) While it used to work with 2.2.17, now my application crashes in search/__init__.py, at the beginning of the astart_function, more precisely the instruction in the following "try" section: try: zero = _python_type(dist_map.value_type())(zero) except OverflowError: zero = (weight.a.max() + 1) * g.num_vertices() zero = _python_type(dist_map.value_type())(zero) I don't get why we try here to convert 'zero' (and right after this, 'infinity') whereas it already has the correct type. What did I miss? -- 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.

2 4

Configure error Installing graph-tool on Ubuntu 12.04 from source
by msah 24 Jul '13

24 Jul '13

I am trying to install locally on ubuntu 12.04. I have installed all the dependencies as well. I got the following error: I have set all the flags but I still get the LDFLAGS error. I configure as: ./configure --prefix=/lab/app/python/python_mohammad/my_py/ CXXFLAGS="-I/lab/app/python/python_mohammad/my_py/include/python2.7" CFLAGS="-I/lab/app/python/python_mohammad/my_py/include/python2.7" PYTHON="/lab/app/python/python_mohammad/my_py/bin/python2.7" LDFLAGS="-L/lab/app/python/python_mohammad/my_py/include/python2.7/" PYTHON=/lab/app/python/python_mohammad/my_py/bin/python --with-boost="/lab/app/python/python_mohammad/my_py/lib" PYTHON_LDFLAGS="-L/lab/app/python/python_mohammad/my_py/include/python2.7/ -lpython2.7" And the error is: ================ Detecting python ================ checking whether /lab/app/python/python_mohammad/my_py/bin/python version is >= 2.6... yes checking for /lab/app/python/python_mohammad/my_py/bin/python version... 2.7 checking for /lab/app/python/python_mohammad/my_py/bin/python platform... linux2 checking for /lab/app/python/python_mohammad/my_py/bin/python script directory... ${prefix}/lib/python2.7/site-packages checking for /lab/app/python/python_mohammad/my_py/bin/python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for python2.7... /lab/app/python/python_mohammad/my_py/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.3'... yes checking for the distutils Python package... yes checking for Python include path... -I/lab/app/python/python_mohammad/my_py/include/python2.7 checking for Python library path... -L/lab/app/python/python_mohammad/my_py/include/python2.7/ -lpython2.7 checking for Python site-packages path... /lab/app/python/python_mohammad/my_py/lib/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... no configure: error: in `/lab/app/python/python_mohammad/graph-tool-2.2.24': 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. ============================================================================ See `config.log' for more details -------------------------- Please help! I attached the log file here <http://pastebin.com/RNqzrjRj> . -- 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.

2 3

Bi- or tri-partite layout
by John Reid 23 Jul '13

23 Jul '13

Hi, I have a tripartite graph. I.e. one with 3 layers. Nodes in the first later are only connected to nodes in the second layer. Similarly nodes in the third layer are only connected to the nodes in the second layer. I'd like to try and layout the graph. I was imagining something where the nodes in each layer are positioned in the same horizontal or vertical plane but how to choose the ordering and spacing between the nodes in this plane? The number of edge cross-overs would be a good objective function to minimise. The three layers have about 700, 50 and 1500 nodes respectively. Does graph-tool offer me any layout options for this sort of graph? I don't mind implementing something if it is not too complicated. Thanks for any ideas, John.

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graph-tool July 2013