Opened 7 years ago

Last modified 7 years ago

#15507 closed enhancement

Static sparse graphs on > 65536 vertices — at Version 9

Reported by: ncohen Owned by:
Priority: major Milestone: sage-6.1
Component: graph theory Keywords:
Cc: SimonKing, dcoudert, stumpc5 Merged in:
Authors: Nathann Cohen Reviewers:
Report Upstream: N/A Work issues:
Branch: public/15507 (Commits, GitHub, GitLab) Commit: 16b4b265b784192dab04950e8bd57060917d73a9
Dependencies: Stopgaps:

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Description (last modified by vdelecroix)

On Sage-devel [1], Christian reported an humiliating error message :

sage: graphs.PathGraph(70000).diameter()       
ValueError: The graph backend contains more than 65535 nodes

This is because Sage's "static_sparse_graphs" are stored on unsigned short fields (and thus to 65536 vertices), and though this is a meaningful limitation for Sage's code to compute the "all pairs shortest path" (the distance between all pairs of vertices, i.e. a n2 matrix of integers), it does not make any sense to refuse to compute the diameter of such graphs.

Soooooooooo this patch changes these "unsigned short" to 32-bits unsigned integers (and note more, because that already doubles the memory requires), which is also good to have when Simon is about to use the same data structure for combinatorial graphs, which can be huge.

I have to mention that this does not make "diameter" answer very fast either on instances with more than 65536 vertices :-/

sage: %time graphs.PathGraph(70000).diameter()
CPU times: user 132.41 s, sys: 0.16 s, total: 132.57 s
Wall time: 133.42 s

But at least we can build them T_T

What this patch does:

  • change the type of the static_sparse_graph data structure from ushort to uint32_t, as well as the functions that use it
  • change the all_pairs_shortest_path_BFS function to first compute the distance on a int * array of length n. The values are then copied into the n^2 matrix of ushort if necessary. That's a loss of time, but it's either this or rewriting two versions of the function :-/
  • remove a useless degree variable in the same function
  • Some simplifications from place to place in the code



Change History (9)

comment:1 Changed 7 years ago by ncohen

  • Branch set to public/15507
  • Description modified (diff)
  • Status changed from new to needs_review

comment:2 Changed 7 years ago by ncohen

  • Description modified (diff)

comment:3 Changed 7 years ago by git

  • Commit set to fd4b4a5f81e6186b49ec270574393a4784ea45dd

Branch pushed to git repo; I updated commit sha1. New commits:

fd4b4a5trac #15507: Static sparse graphs on > 65536 vertices

comment:4 Changed 7 years ago by stumpc5

Thanks for working on that - how do I find your branch, it doesn't seem to be valid, and I just fetched and do not see any branch containing "15507".

Cheers, C.

comment:5 Changed 7 years ago by stumpc5

Ah, there it is...

I still don't feel super comfortable, it more feels like git is using me rather than how it should be. E.g., in #15228 I don't know how to kick the patchbot. I also do not know how to get rid of branches I checked out once. Anyway, I will look at your changes now.

Best, C.

Last edited 7 years ago by stumpc5 (previous) (diff)

comment:6 Changed 7 years ago by git

  • Commit changed from fd4b4a5f81e6186b49ec270574393a4784ea45dd to 16b4b265b784192dab04950e8bd57060917d73a9

Branch pushed to git repo; I updated commit sha1. New commits:

16b4b26trac #15507: Static sparse graphs on > 65536 vertices

comment:7 Changed 7 years ago by ncohen

(sorry, I updated the branch since, as there were two broken doctests left. Some integers were printed as 1L instead of 1 T_T)


comment:8 Changed 7 years ago by stumpc5

Out of curiosity: why do you now use public/ticketnumber after using u/ncohen/ticketnumber before?

I cannot judge if you created any problems anywhere in the code, but I guess you know what you are doing...

I just ran the doctest on all of graphs, and the only error I see is AttributeError in doctesting framework which is also there without having your changes applied.

I didn't see any new doctest for the code testing the diameter for something bigger, line the line graph of 70000 vertices. Don't you think it would be nice to have such an example in the code?

Cheers, Christian

comment:9 Changed 7 years ago by vdelecroix

  • Description modified (diff)

The syntax checker was around... in order to read n2 you should write n caret 2 caret.

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