January 2018 - graph-tool - archives.skewed.de

Parallelization issues on all_shortest_paths
by Percy 10 Jan '18

10 Jan '18

Greetings, Tiago! I am trying to use the multiprocess module in Python to accelerate my simulations. Specifically, I use the following code to parallelly calculate k-shortest paths for a set of node pairs, self.valid_paths[v] = pool.map(lambda x: gt.all_shortest_paths(self.g,source = v_index, target = x),[self.g.vertex_index[c] for c in self.Cloudlet]), where self.Cloudlet is a predefined node list. However, python reports the pickling issues self.valid_paths[v] = pool.map(lambda x: gt.all_shortest_paths(self.g,source = v_index, target = x),[self.g.vertex_index[c] for c in self.Cloudlet]) File "/home/percy/anaconda2/lib/python2.7/site-packages/multiprocess/pool.py", line 251, in map return self.map_async(func, iterable, chunksize).get() File "/home/percy/anaconda2/lib/python2.7/site-packages/multiprocess/pool.py", line 567, in get raise self._value RuntimeError: Pickling of "graph_tool.libgraph_tool_core.Vertex" instances is not enabled (http://www.boost.org/libs/python/doc/v2/pickle.html) Is there anything I am missing? My OS is 16.04, python 2.7.14, graph-tool is from Ostrokach's Anaconda. Thanks for your reply Best, Percy -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Vertices on the periphery
by Snehal Shekatkar 09 Jan '18

09 Jan '18

Dear Tiago, For some graph drawing, I would like to identify the vertices on the periphery after the node positions have been generated (for example, by sfdp_layout). Is there any way to do this? Thank you Snehal Sent with [ProtonMail](https://protonmail.com) Secure Email.

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graph_draw crashes with directed graph
by Evangelos Petsalis 05 Jan '18

05 Jan '18

Hi, I am trying to create a simple NxM graph where each vertex is connected to all of its immediate neighbors with directed edges. When I use graph_draw to see the graph it crashes if I define the graph to be directed, but works fine when the graph is not. Interestingly enough, the problem seems to disappear for very small size graphs (e.g. 5x5) I am using version 2.26 on an Ubuntu 16.04 system. See bellow a snippet of code that recreates the problem. Thanks, Vaggelis import gi gi.require_version('Gtk', '3.0') from graph_tool.all import * if __name__ == '__main__': dt_dict = {} g = Graph(directed=False) dict_v_name_to_v = {} g.vertex_properties["name"] = g.new_vertex_property("string") g.vertex_properties["pos"] = g.new_vertex_property("vector<double>") g.vertex_properties["coords"] = g.new_vertex_property("vector<double>") vp = g.vertex_properties ep = g.edge_properties N_LAT = 20 N_LON = 20 # Vertices for i in range(0, N_LAT): for j in range(0, N_LON): v_name = str(i) + '_' + str(j) v = g.add_vertex() dict_v_name_to_v[v_name] = v vp["name"][v] = v_name vp['pos'][v] = [float(i), float(j)] # vp['coords'][v] = (lat_ar[i], lng_ar[j]) # vp['elev_in_m'][v] = el_ar[i, j] # Edges for j in range(1, N_LON - 1): # long jm1 = j - 1 jp1 = j + 1 for i in range(1, N_LAT - 1): # lat ip1 = i + 1 im1 = i - 1 print(str((i, j))) v_i_jm1 = dict_v_name_to_v[str(i) + '_' + str(jm1)] v_i_j = dict_v_name_to_v[str(i) + '_' + str(j)] v_i_jp1 = dict_v_name_to_v[str(i) + '_' + str(jp1)] v_ip1_jm1 = dict_v_name_to_v[str(ip1) + '_' + str(jm1)] v_ip1_j = dict_v_name_to_v[str(ip1) + '_' + str(j)] v_ip1_jp1 = dict_v_name_to_v[str(ip1) + '_' + str(jp1)] v_im1_jm1 = dict_v_name_to_v[str(im1) + '_' + str(jm1)] v_im1_j = dict_v_name_to_v[str(im1) + '_' + str(j)] v_im1_jp1 = dict_v_name_to_v[str(im1) + '_' + str(jp1)] e_i_jm1 = g.add_edge(v_i_j, v_i_jm1) e_i_jp1 = g.add_edge(v_i_j, v_i_jp1) e_ip1_jm1 = g.add_edge(v_i_j, v_ip1_jm1) e_ip1_j = g.add_edge(v_i_j, v_ip1_j) e_ip1_jp1 = g.add_edge(v_i_j, v_ip1_jp1) e_im1_jm1 = g.add_edge(v_i_j, v_im1_jm1) e_im1_j = g.add_edge(v_i_j, v_im1_j) e_im1_jp1 = g.add_edge(v_i_j, v_im1_jp1) graph_draw(g, pos=g.vertex_properties['pos'], # vertex_text=g.vertex_properties["name"], update_layout=False) -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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