#6775 closed enhancement (fixed)
Create an interface for Disjoint Set data structure
Reported by: | slabbe | Owned by: | slabbe |
---|---|---|---|
Priority: | major | Milestone: | sage-4.3.3 |
Component: | combinatorics | Keywords: | disjoint set data structure |
Cc: | rlm | Merged in: | sage-4.3.3.alpha0 |
Authors: | Sébastien Labbé | Reviewers: | Robert Miller |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
I would like to have an easy to use disjoint-set data structure like the one described here:
http://en.wikipedia.org/wiki/Disjoint_set_data_structure
sage: d = DisjointSet(range(5)) sage: d {{0}, {1}, {2}, {3}, {4}} sage: d.union(3,4) sage: d {{0}, {1}, {2}, {3, 4}} sage: d.union(0,2) sage: d {{0, 2}, {1}, {3, 4}} sage: d.union(1,4) sage: d.find(3) 3 sage: d.find(4) 3
As suggested by Robert Miller on sage-devel, one could use what is defined in
sage/groups/perm_gps/partn_ref/data_structures_*
Attachments (2)
Change History (21)
comment:1 Changed 9 years ago by
- Summary changed from Having an easy to use Disjoint Set data structure to [with patch, needs work] Having an easy to use Disjoint Set data structure
comment:2 Changed 9 years ago by
- Milestone set to sage-4.1.2
comment:3 Changed 8 years ago by
- Owner changed from mhansen to slabbe
- Summary changed from [with patch, needs work] Having an easy to use Disjoint Set data structure to [with patch, needs work] Create an interface for Disjoint Set data structure
comment:4 follow-up: ↓ 5 Changed 8 years ago by
- You should probably declare things like
cdef class DisjointSet_of_integers(SageObject): cdef OrbitPartition *_nodes
and
cdef class DisjointSet_of_hashable(SageObject): cdef list _int_to_el cdef dict _el_to_int cdef DisjointSet_of_integers _d
in disjoint_set.pxd
instead of disjoint_set.pyx
. That'll make it easier to use these classes elsewhere.
- You should have
__del__
print something and see if it's even getting called. I would define__dealloc__
and see if that gets called instead. You're usingOP_dealloc
correctly.
comment:5 in reply to: ↑ 4 ; follow-up: ↓ 6 Changed 8 years ago by
- Cc rlm added
- Report Upstream set to N/A
- Status changed from needs_work to needs_review
- Summary changed from [with patch, needs work] Create an interface for Disjoint Set data structure to Create an interface for Disjoint Set data structure
I just replace the old patch and I solved the pickle problem.
Replying to rlm:
- You should probably declare things like
[snip]
in
disjoint_set.pxd
instead ofdisjoint_set.pyx
. That'll make it easier to use these classes elsewhere.
Done. Thanks for the comment. But is it really necessary since the function DisjointSet
is the function used as a constructor? Should I also add that one to the .pxd
?
- You should have
__del__
print something and see if it's even getting called. I would define__dealloc__
and see if that gets called instead. You're usingOP_dealloc
correctly.
The function __del__
was not called, but __dealloc__
is. Although, I am getting memory errors when using the __dealloc__
function. I put a pass
command in it and I get All test pass. Am I losing memory somewhere?
Needs review!
comment:6 in reply to: ↑ 5 Changed 8 years ago by
- Status changed from needs_review to needs_work
Replying to slabbe:
Replying to rlm:
- You should probably declare things like
[snip]
in
disjoint_set.pxd
instead ofdisjoint_set.pyx
. That'll make it easier to use these classes elsewhere.Done. Thanks for the comment. But is it really necessary since the function
DisjointSet
is the function used as a constructor?
It would make things easier for developers using this later on, who want to use some Cython with this object. The DisjointSet? function is a Python function, so it is irrelevant. I'm just talking about the class definitions.
- You should have
__del__
print something and see if it's even getting called. I would define__dealloc__
and see if that gets called instead. You're usingOP_dealloc
correctly.The function
__del__
was not called, but__dealloc__
is. Although, I am getting memory errors when using the__dealloc__
function. I put apass
command in it and I get All test pass. Am I losing memory somewhere?
Yes, because your dealloc isn't doing anything. You should replace pass
with OP_dealloc(self._nodes)
.
comment:7 Changed 8 years ago by
The patch trac_6775-with_dealloc-sl.patch puts back the dealloc. I now get a mysterious error :
slabbe@pol:~/sage-4.2/devel/sage-combinat/sage/sets$ sage -t disjoint_set.pyx sage -t "devel/sage-combinat/sage/sets/disjoint_set.pyx" A mysterious error (perhaps a memory error?) occurred, which may have crashed doctest. [2.3 s] exit code: 768 ---------------------------------------------------------------------- The following tests failed: sage -t "devel/sage-combinat/sage/sets/disjoint_set.pyx" Total time for all tests: 2.3 seconds
Today I was not able to reproduce the same problem in the command line. Is there a way to get more informations on such a failed test?
Although, adding a print statement in the __init__
gives more information in the failed tests. I am getting the result below. Changing the print statement from one __init__
to another changes the place where the memory error occur.
... ********************************************************************** File "/home/slabbe/sage-4.2/devel/sage-combinat/sage/sets/disjoint_set.pyx", line 744: sage: d = DisjointSet(range(5)) Expected nothing Got: DisjointSet_of_hashable.__init__ called ********************************************************************** File "/home/ ------------------------------------------------------------ Unhandled SIGSEGV: A segmentation fault occured in SAGE. This probably occured because a *compiled* component of SAGE has a bug in it (typically accessing invalid memory) or is not properly wrapped with _sig_on, line 760: sage: d = DisjointSet(range(5)) Expected nothing Got: DisjointSet_of_hashable.__init__ called ********************************************************************** File "/home/slabbe/sage-4.2/devel/sage-combinat/sage/sets/disjoint_set.pyx", line 781: sage: d = DisjointSet(range(5)) Expected nothing Got: DisjointSet_of_hashable.__init__ called ********************************************************************** ...
Will I get the same problem at the same place if I redo all the doctests in the same order as in the file by hand directly in the command line. Can I reproduce the problem is my actual question.
I think I also need to understand when exactly the __dealloc__
is called.
comment:8 Changed 8 years ago by
http://wiki.sagemath.org/ValgrindingSage
You may need to build a fresh version of Sage to use valgrind with it, see the above link for details. Once you get it built, and get your patch attached, you can run the doctest session in valgrind mode, and when it segfaults, valgrind will tell you what leaked.
comment:9 Changed 8 years ago by
PS - Make sure to do this on a Linux box :)
comment:10 Changed 8 years ago by
Finally, sage -t -verbose
gave me enough information to solve the problem. There was one doctest doing :
sage: DisjointSet(-1)
to illustrate that the argument must be non negative. The test arg < 0
was done inside the __init__
function of the class so that the attribute _nodes
was not initialized if an error was raised before. Then, __dealloc__
was trying to call OP_dealloc
on a non existing _nodes
: BOOM!
I moved the arg < 0
test in the DisjointSet
function and All tests passed : great !
I just uploaded the second patch.
comment:11 Changed 8 years ago by
I am now having problem building the documentation...
/home/slabbe/sage-4.3/devel/sage/doc/en/reference/sage/sets/disjoint_set.rst:6: (WARNING/2) error while formatting signature for sage.sets.disjoint_set.OP_represent: Could not parse cython argspec /home/slabbe/sage-4.3/devel/sage/doc/en/reference/sage/sets/disjoint_set.rst:6: (WARNING/2) error while formatting signature for sage.sets.disjoint_set.PS_represent: Could not parse cython argspec
I will look at this before changing the status to needs review
.
comment:12 Changed 8 years ago by
The docbuild problem comes from _sage_getargspec_cython
which fails because it doesn't handle the presence of commas inside default value of arguments of a function. In fact, both OP_represent
and PS_represent
do use commas in their default arguments...
sage: from sage.misc.sageinspect import _sage_getargspec_cython sage: _sage_getargspec_cython('def PS_represent(partition=5, splits=[444]):') (['partition', 'splits'], None, None, (5, [444])) sage: _sage_getargspec_cython('def PS_represent(partition=5, splits=[444,4]):') Traceback (most recent call last): ... ValueError: Could not parse cython argspec
One solution could be to avoid the presence of those two functions in the doc, but I don't know how to do this since they appear from the cython line
include '../groups/perm_gps/partn_ref/data_structures_pyx.pxi'
which includes everything in the file including PS_represent
and OP_represent
which are not needed for disjoint_set.pyx
. Is it possible to include only what we need?
I think this problem concerns something independant from this ticket (another ticket could be open for the comma problem). So I change the status of this ticket to needs review
.
comment:13 Changed 8 years ago by
- Status changed from needs_work to needs_review
Needs review! (Both patches together).
comment:14 Changed 8 years ago by
Are you still having the same problems building the documentation?
If you are, then you should know that both OP_
and PS_
-represent
are functions which are only intended to illustrate a point. In fact, you could change their default arguments to None
and simply feed in the original arguments in the doctests, since that is their only purpose.
comment:15 Changed 8 years ago by
Good point. I followed your suggestion and I folded both precedent patches.
Needs review!
comment:16 Changed 8 years ago by
- Reviewers set to Robert Miller
- Status changed from needs_review to positive_review
Good work!
comment:17 Changed 8 years ago by
- Type changed from defect to enhancement
comment:18 Changed 8 years ago by
- Merged in set to sage-4.3.3.alpha0
- Resolution set to fixed
- Status changed from positive_review to closed
I just added a patch. I have two issues :
__del__
function to call theOP_dealloc
, but I not sure it is proper...