graph-tool March 2018

graph-tool@skewed.de

6 participants
14 discussions

homebrew/science was deprecated. This tap is now empty as all its formulae were migrated.
by Kimon 22 Mar '18

22 Mar '18

I get this error when I try to follow the installation instructions here: https://git.skewed.de/count0/graph-tool/wikis/installation-instructions I know this is not related to graph-tool, but this problem brakes one of the easy installation option that graph-tool had for Mac. Please let me know if anyone has an easy fix. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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exporting graph to svg fails
by Alexandre Bovet 09 Mar '18

09 Mar '18

Hi, I cannot export graphs to svg files with graph_draw(). Exporting to pdf or png works fine. With svg, it raises an ExpatError: File "/home/alex/graphtoolenv/lib/python3.6/site-packages/graph_tool/draw/cairo_draw.py", line 1197, in graph_draw img = IPython.display.SVG(data=out.getvalue()) File "/home/alex/graphtoolenv/lib/python3.6/site-packages/IPython/core/display.py", line 599, in __init__ self.data = data File "/home/alex/graphtoolenv/lib/python3.6/site-packages/IPython/core/display.py", line 717, in data x = minidom.parseString(svg) File "/usr/lib64/python3.6/xml/dom/minidom.py", line 1968, in parseString return expatbuilder.parseString(string) File "/usr/lib64/python3.6/xml/dom/expatbuilder.py", line 925, in parseString return builder.parseString(string) File "/usr/lib64/python3.6/xml/dom/expatbuilder.py", line 223, in parseString parser.Parse(string, True) ExpatError: no element found: line 1, column 0 Any idea of the reason why it fails? My graph-tool version is ''2.26 (commit b89e6b4e, Thu Nov 9 14:55:43 2017 +0000)'' manually compiled with Python3.6 on arch linux with "core/expat 2.2.5-1" and "multilib/lib32-expat 2.2.2-1". Thanks Regards, Alex

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Compiling Graphtool 2.26 on Ubuntu 16.04 32-bit fails with memory error
by Evangelos Petsalis 04 Mar '18

04 Mar '18

Hi, I am trying to compile GT v2.26 on 32-bit image of Ubuntu 16.04. Everything works fine until somewhere in the middle of the process I get the following error, indicating the machine is out of virtual memory. I have a 4gig swap file and a 32 GB or memory so it's highly unlikely that this is not enough. I have successfully compiled GT multiple time on a 64-bit machine, so I was wondering if there are any compatibility issues with 32-bit architectures. Thanks in advance, Vaggelis Making all in inference make[4]: Entering directory '/media/sf_shared/graph-tool-2.26/src/graph/inference' CXX layers/graph_blockmodel_layers_imp.lo In file included from layers/graph_blockmodel_layers_imp.cc:25:0: layers/../blockmodel/graph_blockmodel.hh: In lambda function: layers/../blockmodel/graph_blockmodel.hh:300:29: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ layers/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::remove_vertices(Vlist&)’: layers/../blockmodel/graph_blockmodel.hh:666:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ layers/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::add_vertices(Vlist&, Blist&)’: layers/../blockmodel/graph_blockmodel.hh:759:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ virtual memory exhausted: Cannot allocate memory Makefile:793: recipe for target 'layers/graph_blockmodel_layers_imp.lo' failed make[4]: *** [layers/graph_blockmodel_layers_imp.lo] Error 1 make[4]: Leaving directory '/media/sf_shared/graph-tool-2.26/src/graph/inference' Makefile:751: recipe for target 'all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory '/media/sf_shared/graph-tool-2.26/src/graph' Makefile:422: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/media/sf_shared/graph-tool-2.26/src' Makefile:603: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/media/sf_shared/graph-tool-2.26' Makefile:490: recipe for target 'all' failed make: *** [all] Error 2 -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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creating and filtering multilayer-networks
by M. Vigouroux 04 Mar '18

04 Mar '18

Good morning T.Paula Piexoto and first of all : thank you for the great job you’v already done with graph-tool. I am physicist and I am trying to deal with multilayer large (|E|=10^6) graphs. This largeness is basically the reason why i get seduced by graph-tool. I am trying to find a way to *creat* and *filter* graphs G(E,V,D) according to the dimension D of sets of nodes and keep edges between them to perform common mono-layer graph’s operations with it. <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> Multilayered-network with dimension D in (1,2,3,4), each layers C(D) are linked with each other with edges. (Reference : https://en.wikipedia.org/wiki/Multidimensional_network ) I’m asking myself if you have designed such a thing in graph-tool and if, maybe, you have some examples to show how to do that. I hope I didn’t missed this case in the documentation you have provided… Best regards M. Vigouroux -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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graph-tool March 2018