Anyone able to scan if I'm using the library correctly? Or any other tips ? The MWE is provided through a download link.

Much appreciated!

On Wed, Jun 30, 2021 at 10:17 PM Mathias Versichele <> wrote:
Fair point. I managed to find some time to make a MWE. Here's the link to a zip file containing both the input data (network and costs as csv dumps from our postgres db) and the code:

To use: just run "python". The last line calculates a shortest path tree until 60mins for cost structure "49" (these are costs associated with car travel, the specific id has no meaning). Because this is only Belgium, mem usage when I run this is manageable (under 1Gb).

In general my question is: can this code be made more performant, both in terms of mem and speed ? Am I right in using GraphViews for each cost structure, where the view only contains the edges which have costs associated with them ? Does this make gt.shortest_distance() faster ?

The most production-critical part of the code here is point_drivetimes(). Any gain there in calculation time would be very valuable. The loading of the network and cost structure only need to happen once, so can be a bit slower.

Thx for helping me !

On Tue, Jun 22, 2021 at 9:43 AM Tiago de Paula Peixoto <> wrote:
Dear Mathias,

It is not reasonable to expect us to make this kind of evaluation just
from partial code. As with anything, we need a minimal working example
to be able to say something concrete.

I would recommend you to try to separate the pandas dataframe
manipulation from the graph-tool side in order to determine which is
consuming more memory.


Am 22.06.21 um 09:24 schrieb Mathias Versichele:
> Hi all. Anyone can provide me with some insights here ? I know it's
> quite an open question here, and it might take some effort of course.
> Would anyone be available/willing to do an actual code audit of the code
> that I have ? This would be compensated of course. Feel free to contact
> me to discuss.
> Kind regards
> On Tue, Jun 15, 2021 at 8:45 PM Mathias Versichele
> < <>> wrote:
>     Hi, I've been using graph-tool for the last year or so for
>     calculating shortest-path trees on large-scale road networks. We
>     used to do this in a postgres database with the pgrouting extension,
>     but were continually confronted with unacceptable startup costs. The
>     switch to a python module using graph-tool has considerably sped up
>     our routing queries, but we are suffering from this service using
>     too much memory. I have the feeling I might be using graph-tool in a
>     wrong way, but before I dive into that, it would be good to know
>     what is the expected memory footprint for my use case.
>     Take for example a road network with 30Mio edges and 31 Mio nodes
>     (the combined road network of Belgium, Netherland, France and
>     Germany in OSM). For this road network, I need to calculate shortest
>     paths using different edge weights (edge property map). What would
>     be a  very rough estimate how much memory this would use ? For the
>     network only + per edge-property-map. In our setup, there would be
>     one edge-property-map with edge weights per country. We're currently
>     seeing usage of over 50Gb easily, spiking even higher when we're
>     loading extra cost structures or networks. Is that expected ? Or am
>     I experiencing memory leaks somewhere ?
>     How I'm using graph-tool right now:
>     *1) loading network*
>     /nw = dataframe with edges info in the structure: startnode-id,
>     endnode-id, edge-id, country/
>     G = gt.Graph(directed=True)
>     G.ep["edge_id"] = G.new_edge_property("int")
>     G.ep["country_id"] = G.new_edge_property("int16_t")
>     eprops = [G.ep["edge_id"], G.ep["country_id"]]
>     n = G.add_edge_list(nw.to_numpy(), hashed=True, eprops=eprops)
>     G.vertex_properties["n"] = n
>     *2) loading edge costs: I'm using GraphViews*
>     *
>     *
>     /countries = list of country-codes/
>     edge_filter = np.in1d(G.ep["country_id"].a, [get_country_id(c) for c
>     in countries])*
>     *
>     GV = gt.GraphView(G, efilt=edge_filter)
>     edges = GV.get_edges([GV.edge_index])
>     sources = G.vertex_properties["n"].a[edges[:,0]]
>     targets = G.vertex_properties["n"].a[edges[:,1]]
>     idxs = edges[:,2]
>     /db_costs = pandas dataframe with structure: source, target, cost
>     /
>     sti = np.vstack((idxs,sources,targets)).T
>     sti_df = pd.DataFrame({'idx': sti[:, 0], 'source': sti[:, 1],
>     'target': sti[:, 2]})
>     m = pd.merge(sti_df, db_costs, on=['source', 'target'], how='left',
>     sort=False)[['idx', 'c']]
>     wgts_list = m.sort_values(by=['idx']).T.iloc[1].to_numpy()
>     wgts_list = np.where(wgts_list==np.nan, np.iinfo(np.int32).max,
>     wgts_list)
>     wgts = GV.new_edge_property("int32_t")
>     wgts.fa = wgts_list
>     wgts.fa = np.where(wgts.fa==-2147483648, np.iinfo(np.int32).max,
>     wgts.fa)
>     GV.edge_properties[cs_ids_str] = wgts
>     GV2 = gt.GraphView(GV, efilt=wgts.fa != np.inf)
>     *3) I then use GV2 for calculating Dijkstra and such...*
>     I could of course work on an MWE of some sorts. But would be very
>     nice to get an estimate on mem footprint, and to see if I'm doing
>     sth really silly in the code above.
>     Thx!
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