Opened 10 years ago
Closed 9 years ago
#7966 closed enhancement (fixed)
Giving some punch to distance computations
Reported by: | ncohen | Owned by: | rlm |
---|---|---|---|
Priority: | major | Milestone: | sage-4.3.4 |
Component: | graph theory | Keywords: | |
Cc: | Merged in: | sage-4.3.4.alpha0 | |
Authors: | Nathann Cohen | Reviewers: | Paul Zimmermann |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
This patch creates a function shortest_path_all_vertices in c_graphs which, given a vertex v, computes a shortest path for each other vertex.
With small other modifications, it improves the speed of many functions ( which were all calling each other )
Before :
sage: g = graphs.RandomGNP(50,.3) sage: %timeit g.shortest_path_lengths(0) 100 loops, best of 3: 3.72 ms per loop sage: %timeit g.average_distance() 10 loops, best of 3: 383 ms per loop sage: %timeit g.wiener_index() 10 loops, best of 3: 384 ms per loop sage: %timeit g.szeged_index() 10 loops, best of 3: 325 ms per loop sage: %timeit g.eccentricity() 10 loops, best of 3: 189 ms per loop sage: g.sparse6_string() ':q_OW_CCBb?WcOL@@`_{CGDB@pCGIF``@[WQK_`?w_QIDoo_WSJEBWGOKIDbG?CZ?@@Owwb?@?o_SOMba@X?bA@`OpKhBB@p?kX@Caq@YAACAphWn@B@po{j?@`?o_]QIeGOWMGDCqheEDB@pXMAEBa@GscYLoo__QJEBaxcvBECAPWqYNQ`gwgTKERX}?@@@@Gg[QHdBXt@?BAa@WmYNGWo[OLFCQhqCLFCRPky]POow_SLGCRHw}ca@_w_SLHCq`_u[OGg?GEDBAP_{iUJeBiYKGCbPp_qYMFbyLIea``WoYMFcA`SkXMGS[?MIFCahgw\\NP`Ww]VLfSskYMHDApcs[NHSy`R?A@pOkWMGcb@oy]TjGGKOJIEBh|QjUOox?mWLEryHIh___WOaRIDr@cu[MhTauCCBa@Gk]PHdax_w]NhCq\\Sm'
After
sage: %timeit g.shortest_path_lengths(0) 10 loops, best of 3: 430 µs per loop sage: %timeit g.average_distance() 10 loops, best of 3: 22 ms per loop sage: %timeit g.wiener_index() 10 loops, best of 3: 22.1 ms per loop sage: %timeit g.szeged_index() 10 loops, best of 3: 41.5 ms per loop sage: %timeit g.eccentricity() 10 loops, best of 3: 22 ms per loop
Nathann
Attachments (1)
Change History (7)
comment:1 Changed 10 years ago by
- Status changed from new to needs_review
comment:2 Changed 10 years ago by
comment:3 Changed 9 years ago by
- Reviewers set to Paul Zimmermann
- Status changed from needs_review to needs_work
The speedups are great, but I got one extra failure (against 4.3.3 on Fedora 12):
sage -t graphs/base/c_graph.pyx File "/usr/local/sage-4.3.3/sage/devel/sage-trac/sage/graphs/base/c_graph.pyx",\ line 1427: sage: all([ len(paths[v]) == 0 or len(paths[v])-1 == g.distance(0,v) for v \ in g]) Exception raised: Traceback (most recent call last): File "/usr/local/sage-4.3.3/sage/local/bin/ncadoctest.py", line 1231, in \ run_one_test self.run_one_example(test, example, filename, compileflags) File "/usr/local/sage-4.3.3/sage/local/bin/sagedoctest.py", line 38, in r\ un_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compil\ eflags) File "/usr/local/sage-4.3.3/sage/local/bin/ncadoctest.py", line 1172, in \ run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_43[7]>", line 1, in <module> all([ len(paths[v]) == Integer(0) or len(paths[v])-Integer(1) == g.dist\ ance(Integer(0),v) for v in g])###line 1427: sage: all([ len(paths[v]) == 0 or len(paths[v])-1 == g.distance(0,v) for v \ in g]) KeyError: 20
Please could you look at this?
comment:4 Changed 9 years ago by
- Status changed from needs_work to needs_review
At first, the function associated a path from v to each other vertex, possibly empty if there was none. Then I noticed the other functions in Sage expected the dictionary to only contain keys corresponding to the vertices reachable from v (which was sound, too), and changed the original function, forgetting the docstrings... Fixed now !
And I also removed the (commented) loop which was associating empty paths when needed...
Thank you again ! :-)
Nathann
Changed 9 years ago by
comment:5 Changed 9 years ago by
- Status changed from needs_review to positive_review
with the new patch c_graph.pyx
works again:
[zimmerma@coing sage]$ sage -t graphs/base/c_graph.pyx sage -t "devel/sage-7966/sage/graphs/base/c_graph.pyx" [2.5 s] ---------------------------------------------------------------------- All tests passed! Total time for all tests: 2.5 seconds
Thus a positive review.
Paul
comment:6 Changed 9 years ago by
- Merged in set to sage-4.3.4.alpha0
- Resolution set to fixed
- Status changed from positive_review to closed
Small modification to distance_graph too:
Before :
After
Nathann