Hi Stephan, I've used graph tool to compute a lot of shortest paths and used a dumb solution of just throwing it into multiprocessing module from python (with some lru_cache tricks). If you have enough memory and you don't call the main procedure often (seems to be the case?) then the overhead of multiprocessing becomes insignificant. A benefit is that this is pretty easy to code and scales perfectly to more cores (until you run out of memory).
Best, Aleks On Wed, Nov 24, 2021 at 3:32 PM Monecke, Stephan <[email protected]> wrote: > > Hi Tiago and the list, > > > > my algorithm is still _infeasibly_ slow and > 90 % of the run-time results > from shortest_path(). > > > Do you have any idea on how this could be sped up? > > > I have the graph G, the set of all nodes V and a sub-set B ⊂ V. > > > I want to calculate or approximate the mean shortest distance between all > pairs V\B x V\B but on the complete graph - or in other words, calculate the > mean of all pairs shortest distance ( mean(shortest_distance()) ) but exclude > n∈B from being source or target. > > Sub-sampling would be okay as well. > > > I currently don't see a way to do this fast with graph-tool besides writing a > custom function but that probably exceeds my capacities. Am I missing > something? Do you have any ideas? > > > Ideal would be something like a multi-threaded shortest_distance(g=G, > source=V\B, target=V\B, weights=G.edge_properties['weight'], samples=N) with > N pairs random sub-sampling and source / target being lists. > > > > Thanks a ton! > > Stephan > > ________________________________ > Von: Monecke, Stephan <[email protected]> > Gesendet: Donnerstag, 18. November 2021 14:59 > An: Main discussion list for the graph-tool project > Betreff: [graph-tool] Re: All Pairs Shortest Path with limitations > > This works like a charm! > > With it, I'm down to 228 ms ± 1.31 ms from 3.6 s ( 82.9 ms ± 2.45 ms for > shortest_distance(G) ). > > It's still very very expensive as it's 2.75 times APSP but approaching > reasonability. The costly remaining part is the manual B x B.* > > I tried to speed it up by the approximation to limit G to B since I know that > B is connected but graph-tool segfaults right away (I wrote another ticket > for that). :/ > > If anyone else has any ideas on how to speed this up, I'd be very grateful! > > > Cheers, > Stephan > > - - - o - - - > > *Since the graph is directed, we have the following: Say V is the set of all > vertices and B a subset of V I want to exclude as sources / targets from > APSP. Then the set of points is > (V\B) x (V\B) = [ (V x V) \ [ (V x B) + (B x V) ] ] U (B x B). > > Or in graph-tool terms: > - (V x V): shortest_distance(G) > - (B x V): shortest_distance(G, b, _) for b in B > - (V x B): shortest_distance(GraphView(G, reversed=True), b, _) for b in B > - (B x B): shortest_distance(G, u, v) for u,v in B x B > > > > > Von: Stephan Monecke <[email protected]> > Gesendet: Mittwoch, 17. November 2021 20:24 > An: Main discussion list for the graph-tool project > Betreff: [graph-tool] Re: All Pairs Shortest Path with limitations > > 🥳 I didn't know that existed! > > Thanks a ton, I'm really looking forward to test it out tomorrow! > > Cheers, > Stephan > -- > Sent from my mobile device. Please excuse my brevity. > > Am 17. November 2021 19:27:37 MEZ schrieb Tiago de Paula Peixoto > <[email protected]>: > >Am 17.11.21 um 19:22 schrieb Monecke, Stephan: > >> The main reason is that shortest_distance() has a "single source, all > >> targets" mode but no "single target, all sources" mode (the reverse) - as > >> soon as "source" is empty, it defaults to APSP, neglecting "target". > >> > > > >Of course it does. Just reverse the graph with: > > > > GraphView(g, reversed=True) > > > > > _______________________________________________ > graph-tool mailing list -- [email protected] > To unsubscribe send an email to [email protected] > > _______________________________________________ > graph-tool mailing list -- [email protected] > To unsubscribe send an email to [email protected] > _______________________________________________ > graph-tool mailing list -- [email protected] > To unsubscribe send an email to [email protected] _______________________________________________ graph-tool mailing list -- [email protected] To unsubscribe send an email to [email protected]
