Opened 10 years ago
Last modified 9 years ago
#11521 closed defect
Memleak when resolving the action of Integers on an Elliptic Curve — at Version 53
Reported by: | jpflori | Owned by: | robertwb |
---|---|---|---|
Priority: | major | Milestone: | sage-5.5 |
Component: | coercion | Keywords: | sd35 |
Cc: | jpflori, nthiery | Merged in: | |
Authors: | Simon King | Reviewers: | |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | #11900 #715 | Stopgaps: |
Description (last modified by )
The following piece of code leaks memory.
sage: K = GF(1<<55,'t')
sage: a = K.random_element()
sage: while 1:
....: E = EllipticCurve(j=a); P = E.random_point(); 2*P;
The problem seems to occur while resolving the action of ZZ on E.
It does not happen if:
- one does not change the curve in the loop
- does P+P instead of a multiplication
Apply
Change History (54)
comment:1 Changed 10 years ago by
comment:2 Changed 10 years ago by
- Component changed from memleak to coercion
- Owner changed from rlm to robertwb
So this could be just #715 .
comment:3 Changed 10 years ago by
This is definitely #715.
Resetting the coercion cache and calling gc.collect() deletes the cached elements.
I guess weak refs should be used in the different TripleDict? objects of !CoercionModel_cache_maps.
So this should be closed as duplicate/won't fix.
comment:4 Changed 10 years ago by
- Status changed from new to needs_review
comment:5 Changed 10 years ago by
Jean-Pierre, why did you change the status to "needs review"? There is no patch to review.
Also, how to you reset the coercion cache? I would be interested if you have a workaround for the memory leak in:
for p in prime_range(10^8): k = GF(p)
Paul
comment:6 follow-up: ↓ 17 Changed 10 years ago by
As far as I'm concerned, this is nothing but a concrete example of the vague #715. So I guess I put it to "needs review" so that it could be closed as "duplicate/won't fix". Not sure it was the right way to do it.
I seem to remember that I had some workarounds to delete some parts of the cache (so that I could perform my computations), but not all of them. In fact there are several dictionnaries hidden in different places. It was quite a while ago, but I'll have another look at it at some point. Anyway, using weak references for all these dictionnaries seems to be a quite non trivial task. Moreover it should also not slow things down too much to be viable...
comment:7 Changed 10 years ago by
for the computations I need to perform, which need to create about 200000 prime fields, this memory leak makes it impossible to perform it with Sage, which eats all the available memory.
I would be satisfied if I had a magic command to type to explicitly free the memory used by
every k=GF(p)
.
Paul
comment:8 follow-up: ↓ 22 Changed 10 years ago by
I'm having a look at your problem right now. Here are some hints to study the problem, mostly stolen from #10548.
I put it here for the record, and so that i can go faster next time.
First, if I only create the finite fields and do nothing with them, I do not seem to get a memleak. Some fields are not garbage collected immediately, but calling gc.collect() does the trick.
sage: import gc sage: for p in prime_range(10**5): ....: k = GF(p) ....: sage: del p, k sage: gc.collect() 1265 sage: from sage.rings.finite_rings.finite_field_prime_modn import FiniteField_prime_modn as FF sage: L = [x for x in gc.get_objects() if isinstance(x, FF)] sage: len(L) 1 sage: L [Finite Field of size 2]
Of course I guess you actually do something with your finite fields.
So here is a small example causing the fields to stay cached.
sage: import gc sage: for p in prime_range(10**5): ....: k = GF(p) ....: sage: del p, k sage: gc.collect() 0
The zero here is bad and indeed
sage: from sage.rings.finite_rings.finite_field_prime_modn import FiniteField_prime_modn as FF sage: L = [x for x in gc.get_objects() if isinstance(x, FF)] sage: len(L) 9592
If you want to know where it comes from you can use the objgraph python module (on my debian I just installed the python-objgraph package, updated sys.path in Sage to include '/usr/lib/python2.6/dist-packages')
sage: sys.path.append('/usr/lib/python2.6/dist-packages') sage: import inspect, objgraph sage: objgraph.show_backrefs(L[-1],filename='/home/jp/br.png',extra_ignore=[id(L)])
And look at the png or use
sage: brc = objgraph.find_backref_chain(L[-1],inspect.ismodule,max_depth=15,extra_ignore=[id(L)]) sage: map(type,brc) [<type 'module'>, <type 'dict'>, <type 'dict'>,... sage: brc[0] <module 'sage.categories.homset'...
So the culprit is "_cache" in sage.categories.homset which has a direct reference to the finite fields in its keys.
The clean solution woul be to used weakref in the keys (let's say something as WeakKeyDirectory? in python).
However, resetting cache should be a (potentially partial) workaround (and could kill your Sage?).
sage: sage.categories.homset.cache = {} sage: gc.collect() 376595
It also seems to be enough if I do "a = k.random_element(); a = a+a" in the for loop, but not if I add "a = 47*a+3".
I'm currently investigating that last case.
comment:9 Changed 10 years ago by
For info, using "k(47)*a+k(3)" is solved, so the problem left really comes from coercion and action of integers.
sage: cm = sage.structure. get_coercion_model() sage: cm.reset_cache()
does not help.
comment:10 Changed 10 years ago by
First, the second example above is missing the line "k(1);" in the for loop, otherwise it does nothing more than the first example.
Second, I guess the remaining references to the finite fields are in the different lists and dictionnaries of the integer ring named _coerce_from_list, _convert_from_list etc.
You can not directly access them from Python level, but there a function _introspect_coerce() (defined in parent.pyx) which returns them.
comment:11 Changed 10 years ago by
In fact, everything is in _*_hash.
And to conclude, I'd say that right now you can not directly delete entries in this dictionaries from the Python level.
So for minimum changes, you should eitheir avoid coercion, or make the dictionaries "cdef public" in parent.pxd to be able to explicitely delete every created entries (be aware that it could be written in different places for example in ZZ but also in QQ and CC and I don't know where...).
And I could also have missed other dictionaries used by Sage.
comment:12 Changed 10 years ago by
Jean-Pierre, I cannot reproduce that:
sage: sys.path.append('/usr/lib/python2.6/dist-packages') sage: import inspect, objgraph --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /users/caramel/zimmerma/Adm/Strass/SED/2011/<ipython console> in <module>() ImportError: No module named objgraph
Paul
comment:13 Changed 10 years ago by
Did you "apt-get install python-objgraph" on your system?
If yes, is it a version for python 2.6 ?
comment:14 Changed 10 years ago by
The path I gave above might also be different on your system...
As the package manager.
comment:15 follow-up: ↓ 16 Changed 10 years ago by
Any progress on your side?
If you found any other dicitonaries leading to cahing problems, it would be great to mention them here for the record.
Hence the day someone will finally decide to tackle ticket #715, it will speed up the search of the culprit.
comment:16 in reply to: ↑ 15 Changed 10 years ago by
Replying to jpflori:
Any progress on your side?
no time so far. I will look at this during the SageFlint? days in December, unless someone else has some time before.
Paul
comment:17 in reply to: ↑ 6 Changed 9 years ago by
Replying to jpflori:
As far as I'm concerned, this is nothing but a concrete example of the vague #715. So I guess I put it to "needs review" so that it could be closed as "duplicate/won't fix". Not sure it was the right way to do it.
If you think it should be closed, then I think you should set the milestone to duplicate/wontfix. Otherwise, it is probably better to change the status back to 'new'.
comment:18 Changed 9 years ago by
with Sage 4.7.2 I get the following:
sage: for p in prime_range(10^5): ....: K = GF(p) ....: a = K(0) ....: sage: import gc sage: gc.collect() 0 sage: from sage.rings.finite_rings.finite_field_prime_modn import \ ....: FiniteField_prime_modn as FF sage: L = [x for x in gc.get_objects() if isinstance(x, FF)] sage: len(L), L[0], L[len(L)-1] (9592, Finite Field of size 2, Finite Field of size 99767)
thus whenever we use the finite field we get a memleak.
(If I remove the a=K(0)
line, I get only two elements in L, for p=2 and p=99991.)
Paul
comment:19 Changed 9 years ago by
comment:20 Changed 9 years ago by
I think we have a different problem here.
The finite fields themselves should be cached. The cache (see GF._cache
) uses weak references, which should be fine.
Also, there are special methods zero_element
and one_element
which should do caching, because zero and one are frequently used and should not be created over and over again.
However, it seems that all elements of a finite field are cached - and that's bad!
sage: K = GF(5) sage: K(2) is K(2) True sage: K.<a> = GF(17^2) sage: K(5) is K(5) True
I see absolutely no reason why all 17^2
elements should be cached.
Fortunately, we have no caching for larger finite fields:
sage: K.<a> = GF(17^10) sage: K(5) is K(5) False
comment:21 Changed 9 years ago by
- Status changed from needs_review to needs_work
In the following example, there is no memory leak that would be caused by the sage.categories.homset
cache:
sage: len(sage.categories.homset._cache.keys()) 100 sage: for p in prime_range(10^5): ....: K = GF(p) ....: sage: len(sage.categories.homset._cache.keys()) 100
However, when you do a conversion K(...)
then a convert map is created, and apparently is cached:
sage: for p in prime_range(10^5): ....: K = GF(p) ....: a = K(0) ....: sage: len(sage.categories.homset._cache.keys()) 9692
The homset cache does use weak references. Hence, it is surprising that the unused stuff can not be garbage collected. Apparently there is some direct reference involved at some point.
I am very stronglyagainst removing the cache of sage.categories.homset
. Namely, elliptic curve code uses finite fields and maps involving finite fields a lot, and killing the cache is likely to cause a massive regression.
However, since we actually have coercion maps (not just any odd map), I expect that the direct reference comes from the coercion model. I suggest to look into the coercion code and use weak references there.
By the way, I don't know why the status is "needs review". I think it clearly is "needs work".
comment:22 in reply to: ↑ 8 Changed 9 years ago by
Replying to jpflori:
So the culprit is "_cache" in sage.categories.homset which has a direct reference to the finite fields in its keys.
Oops, that could indeed be the problem! Namely, the homset cache uses weak references to its values, but uses direct references to its keys! Perhaps using weak references as keys would work?
comment:23 Changed 9 years ago by
it seems the complete caching of field elements only occurs for p < 500:
sage: K=GF(499) sage: K(5) is K(5) True sage: K=GF(503) sage: K(5) is K(5) False
A workaround to this memory leak is to free the cache from time to time (thanks Simon):
sage: sage.categories.homset._cache.clear()
Paul
comment:24 Changed 9 years ago by
On the other hand, it could be that using weak keys in the homset cache will not work: The keys are triples: domain, codomain and category.
What we want is: If either the domain or the codomain or the category have no strong reference, then the homset can be garbage collected.
Hence: Why don't we use a dictionary of dictionaries of dictionaries?
What I mean is:
- The keys of sage.categories.homset._cache should be weak references to the domain
- The values of sage.categories.homset._cache should be dictionaries whose keys are weak references to the codomain.
- The keys of these dictionaries should be weak references to the category, and the value a weak reference to the homset.
Hence, if there is no strong reference to either domain or codomain or category, then the homset can be deallocated.
comment:25 Changed 9 years ago by
The idea sketched in the previous comment seems to work!!!
With it, after running
sage: for p in prime_range(10^5): ....: K = GF(p) ....: a = K(0) ....: print get_memory_usage()
ends with printing 825.45703125
Without it, it ends with printing 902.8125
I don't know if we should ban caching of field elements?
How could fixing that memory leak be demonstrated by a doc test?
Anyway, I will post a preliminary patch in a few minutes (so that you can see if it fixes at least part of the problem for you), while I am running sage -tp 2 devel/sage
.
comment:26 Changed 9 years ago by
Patch's up!
comment:27 Changed 9 years ago by
Hm. There seems to be a problem.
sage -t devel/sage/doc/en/constructions/linear_codes.rst The doctested process was killed by signal 11
What is signal 11?
comment:28 Changed 9 years ago by
signal 11 is Segmentation Fault
Paul
comment:29 Changed 9 years ago by
Indeed it is a segfault. And it is triggered by
sage: w = vector([1,1,-4])
comment:30 Changed 9 years ago by
Monique van Beek just pointed me to the fact that the error occurs even earlier:
sage: is_Ring(None) <BOOOOOM>
comment:31 Changed 9 years ago by
Moreover,
sage: None in Rings() <BOOOOOOM>
comment:32 Changed 9 years ago by
That said: I am not working on top of vanilla sage, but I use some patches. In particular, I use #11900, which introduces so called Category_singleton
, which has a specialised and very fast containment test.
I would not like to change #11900, but prefer to change my patch from here so that it works on top of #11900.
comment:33 Changed 9 years ago by
It turns out that indeed the bug is in #11900. So, I have to fix it there.
comment:34 follow-up: ↓ 41 Changed 9 years ago by
Cc to Nicolas, since it concerns categories:
Do we want that Hom(1,1)
is still supported?
I think it does not make sense at all to talk about the homomorphisms of the number 1 to the number 1. The problem (for my patch as it is posted here) is the fact that one can't create a weak reference to the number 1.
comment:35 Changed 9 years ago by
- Cc nthiery added
Sorry, I forgot to update the Cc field.
Nicolas, please read my previous comment.
comment:36 Changed 9 years ago by
With my patch, applied on top of #11900, I get
sage -t devel/sage-main/sage/structure/parent.pyx # 2 doctests failed sage -t devel/sage-main/sage/structure/category_object.pyx # 2 doctests failed sage -t devel/sage-main/sage/rings/polynomial/polynomial_singular_interface.py # 1 doctests failed sage -t devel/sage-main/sage/rings/polynomial/multi_polynomial_ring.py # 36 doctests failed sage -t devel/sage-main/sage/structure/parent_base.pyx # 2 doctests failed
At least some of the errors are like
sage: n = 5; Hom(n,7) Exception raised: Traceback (most recent call last): File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_3[4]>", line 1, in <module> n = Integer(5); Hom(n,Integer(7))###line 108: sage: n = 5; Hom(n,7) File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python/site-packages/sage/categories/homset.py", line 159, in Hom cache2 = _cache[X] File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python2.6/weakref.py", line 243, in __getitem__ return self.data[ref(key)] TypeError: cannot create weak reference to 'sage.rings.integer.Integer' object
and I really don't see why this should be considered a bug.
comment:37 Changed 9 years ago by
- Status changed from needs_work to needs_info
At least one of the errors in polynomial rings is due to a wrong order of initialising things: There is some information missing, and by consequence a weak reference can't be created.
I fixed this problem in the new patch version.
I put it as "needs info", because of my question on whether or not we want to consider an integer as object in a category.
comment:38 Changed 9 years ago by
I was told by Mike Hansen why weak references to integers and rationals do not work.
I see three options:
#. Drop the support for
Hom(1,1)
(which I'd prefer) #. Add a cdef'd attribute__weakref__
tosage.structure.element.Element
, which would create an overhead for garbage collection for elements, and also a memory overhead. #. Use two category.homset caches in parallel: One (the default) that uses weak references, and another one that uses "normal" references if weak references fail.
comment:39 Changed 9 years ago by
FWIW:
With the latest patch, the tests in polynomial_singular_interface and in multi_polynomial_ring pass.
There remain the following problems:
sage -t "devel/sage-main/sage/structure/parent.pyx" ********************************************************************** File "/home/simon/SAGE/sage-4.8.alpha3/devel/sage-main/sage/structure/parent.pyx", line 1410: sage: n = 5; Hom(n,7) Exception raised: Traceback (most recent call last): File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_33[4]>", line 1, in <module> n = Integer(5); Hom(n,Integer(7))###line 1410: sage: n = 5; Hom(n,7) File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python/site-packages/sage/categories/homset.py", line 159, in Hom cache2 = _cache[X] File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python2.6/weakref.py", line 243, in __getitem__ return self.data[ref(key)] TypeError: cannot create weak reference to 'sage.rings.integer.Integer' object ********************************************************************** File "/home/simon/SAGE/sage-4.8.alpha3/devel/sage-main/sage/structure/parent.pyx", line 1412: sage: z=(2/3); Hom(z,8/1) Exception raised: Traceback (most recent call last): File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_33[5]>", line 1, in <module> z=(Integer(2)/Integer(3)); Hom(z,Integer(8)/Integer(1))###line 1412: sage: z=(2/3); Hom(z,8/1) File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python/site-packages/sage/categories/homset.py", line 159, in Hom cache2 = _cache[X] File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python2.6/weakref.py", line 243, in __getitem__ return self.data[ref(key)] TypeError: cannot create weak reference to 'sage.rings.rational.Rational' object ********************************************************************** 1 items had failures: 2 of 8 in __main__.example_33 ***Test Failed*** 2 failures. For whitespace errors, see the file /home/simon/.sage//tmp/parent_2986.py [11.6 s]
and
sage -t "devel/sage-main/sage/structure/category_object.pyx" ********************************************************************** File "/home/simon/SAGE/sage-4.8.alpha3/devel/sage-main/sage/structure/category_object.pyx", line 590: sage: n = 5; Hom(n,7) Exception raised: Traceback (most recent call last): File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_17[4]>", line 1, in <module> n = Integer(5); Hom(n,Integer(7))###line 590: sage: n = 5; Hom(n,7) File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python/site-packages/sage/categories/homset.py", line 159, in Hom cache2 = _cache[X] File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python2.6/weakref.py", line 243, in __getitem__ return self.data[ref(key)] TypeError: cannot create weak reference to 'sage.rings.integer.Integer' object ********************************************************************** File "/home/simon/SAGE/sage-4.8.alpha3/devel/sage-main/sage/structure/category_object.pyx", line 592: sage: z=(2/3); Hom(z,8/1) Exception raised: Traceback (most recent call last): File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_17[5]>", line 1, in <module> z=(Integer(2)/Integer(3)); Hom(z,Integer(8)/Integer(1))###line 592: sage: z=(2/3); Hom(z,8/1) File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python/site-packages/sage/categories/homset.py", line 159, in Hom cache2 = _cache[X] File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python2.6/weakref.py", line 243, in __getitem__ return self.data[ref(key)] TypeError: cannot create weak reference to 'sage.rings.rational.Rational' object ********************************************************************** 1 items had failures: 2 of 8 in __main__.example_17 ***Test Failed*** 2 failures. For whitespace errors, see the file /home/simon/.sage//tmp/category_object_3050.py [2.7 s]
and
sage -t "devel/sage-main/sage/structure/parent_base.pyx" ********************************************************************** File "/home/simon/SAGE/sage-4.8.alpha3/devel/sage-main/sage/structure/parent_base.pyx", line 108: sage: n = 5; Hom(n,7) Exception raised: Traceback (most recent call last): File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_3[4]>", line 1, in <module> n = Integer(5); Hom(n,Integer(7))###line 108: sage: n = 5; Hom(n,7) File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python/site-packages/sage/categories/homset.py", line 159, in Hom cache2 = _cache[X] File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python2.6/weakref.py", line 243, in __getitem__ return self.data[ref(key)] TypeError: cannot create weak reference to 'sage.rings.integer.Integer' object ********************************************************************** File "/home/simon/SAGE/sage-4.8.alpha3/devel/sage-main/sage/structure/parent_base.pyx", line 110: sage: z=(2/3); Hom(z,8/1) Exception raised: Traceback (most recent call last): File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/simon/SAGE/sage-4.8.alpha3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_3[5]>", line 1, in <module> z=(Integer(2)/Integer(3)); Hom(z,Integer(8)/Integer(1))###line 110: sage: z=(2/3); Hom(z,8/1) File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python/site-packages/sage/categories/homset.py", line 159, in Hom cache2 = _cache[X] File "/home/simon/SAGE/sage-4.8.alpha3/local/lib/python2.6/weakref.py", line 243, in __getitem__ return self.data[ref(key)] TypeError: cannot create weak reference to 'sage.rings.rational.Rational' object ********************************************************************** 1 items had failures: 2 of 8 in __main__.example_3 ***Test Failed*** 2 failures. For whitespace errors, see the file /home/simon/.sage//tmp/parent_base_3078.py [2.6 s]
So, essentially this is just a single test that comes in two versions and is repeated three times - and I would actually say that not raising an error was a bug.
It seems that Hom(1/2,2/3)
and similar nonsense is not used in Sage. Hence, I think these tests should be removed. I'll ask sage-devel.
comment:40 Changed 9 years ago by
Without the patch:
sage: def test(): ....: for p in prime_range(10^5): ....: K = GF(p) ....: a = K(0) ....: sage: m0 = get_memory_usage() sage: %time test() CPU times: user 7.75 s, sys: 0.08 s, total: 7.83 s Wall time: 7.84 s sage: get_memory_usage() - m0 80.234375
With the patch:
sage: def test(): ....: for p in prime_range(10^5): ....: K = GF(p) ....: a = K(0) ....: sage: m0 = get_memory_usage() sage: %time test() CPU times: user 7.59 s, sys: 0.01 s, total: 7.60 s Wall time: 7.61 s sage: get_memory_usage() - m0 8.53515625
So, the memory does mildly increase, but it seems that most of the leak is fixed.
I think that a test of the kind
sage: get_memory_usage() - -m0 < 10 True
might be used as a doc test.
comment:41 in reply to: ↑ 34 Changed 9 years ago by
Replying to SimonKing:
Cc to Nicolas, since it concerns categories:
Do we want that
Hom(1,1)
is still supported?I think it does not make sense at all to talk about the homomorphisms of the number 1 to the number 1. The problem (for my patch as it is posted here) is the fact that one can't create a weak reference to the number 1.
I don't see much point either. We had a similar discussion a while ago about whether elements should be objects in a category, and as far as I remember, the answer was no by default (Element does not inherit from CategoryObject?). So +1 on my side to kill this dubious feature. You might want to double check on sage-algebra just to make sure.
comment:42 follow-up: ↓ 43 Changed 9 years ago by
Simon, you can also use the test suggested by Jean-Pierre Flori (see comment 18 for an example).
Paul
comment:43 in reply to: ↑ 42 Changed 9 years ago by
Hi Paul,
Replying to zimmerma:
Simon, you can also use the test suggested by Jean-Pierre Flori (see comment 18 for an example).
Yes, that looks good. With my patch, the test would be like
sage: for p in prime_range(10^5): ....: K = GF(p) ....: a = K(0) ....: sage: import gc sage: gc.collect() 1881 sage: from sage.rings.finite_rings.finite_field_prime_modn import FiniteField_prime_modn as FF sage: L = [x for x in gc.get_objects() if isinstance(x, FF)] sage: len(L), L[0], L[len(L)-1] (2, Finite Field of size 2, Finite Field of size 99991)
The people at sage-devel somehow seem to agree that objects of a category should be instances of CategoryObject
(which elements aren't!), and that we should thus drop the Hom(2/3,8/1)
test.
In addition to that, I suggest to provide a better error message, something like
sage: Hom(2/3, 8/1) Traceback (most recent call last): ... TypeError: Objects of categories must be instances of <type 'sage.structure.category_object.CategoryObject'>, but 2/3 isn't.
Cheers,
Simon
comment:44 Changed 9 years ago by
- Keywords sd35 added
comment:45 Changed 9 years ago by
- Dependencies set to #11900
- Status changed from needs_info to needs_review
comment:46 Changed 9 years ago by
- Status changed from needs_review to needs_work
I did try the new doctests in sage/categories/homset.py. However, with other patches applied, the number returned by gc.collect()
changes.
So, for stability, I suggest to simplify the test, so that only the number of finite fields remaining in the cache is tested.
comment:47 Changed 9 years ago by
- Status changed from needs_work to needs_review
I updated the patch.
Difference to the previous patch: The number of objects collect by gc is marked as random (indeed, it will change with #11115 applied). What we are really interested in is the number of finite fields that remains in the cache after garbage collection. This number is two and is not random. Thus, that test is preserved.
comment:48 Changed 9 years ago by
- Status changed from needs_review to needs_work
I think I need help with debugging.
When I have sage-4.8.alpha3 with #9138, #11900, #715 and #11115, then all doctests pass.
When I also have #11521, then the test sage/rings/number_field/number_field_rel.py segfaults. When I run the tests in verbose mode, then all tests seem to pass, but in the very end it says
4 items had no tests: __main__ __main__.change_warning_output __main__.check_with_tolerance __main__.warning_function 69 items passed all tests: ... 660 tests in 73 items. 660 passed and 0 failed. Test passed. The doctested process was killed by signal 11 [15.0 s]
So, could it be that not one of the tests was killed, but the test process itself?
What is even more confusing: When I run the tests with the option -randorder, then most of the time the tests pass without a problem.
Can you give me any pointer on how those things could possibly be debugged?
comment:49 Changed 9 years ago by
It sometimes happen that the sage session itself crash on exit. This is probably one of these. Last time I got one it was related to singular I think. It is quite difficult to corner these with gdb. The best you can hope is start a sage session with gdb and then try the last doctest sequence and quit sage, it may lead to the crash in which case you may have some luck with gdb. But this is one of these case where gdb itself may be interfering. I don't think I have time to look into this right now but I'll put it into my "To do" list in case it isn't solved when i have time to spare.
Changed 9 years ago by
Use weak references for the keys of the homset cache. If weak references are not supported, then raise an error, pointing out that category objects should be CategoryObject
s.
comment:50 Changed 9 years ago by
- Work issues set to Understand why a weak key dictionary is not enough
I have attached a new patch version. It fixes the segfault I mentioned. However, it also does not fix the memory leak.
The difference between the two versions is: The new patch still uses weak references to the key of the cache, but a strong reference to the value (i.e., the homset).
The homset has a reference to domain and codomain, which constitute the cache key. Thus, I expected that it does not make any difference whether one has a strong or a weak reference to the homset. But I stand corrected. That needs to be investigated more deeply.
comment:51 follow-up: ↓ 52 Changed 9 years ago by
Dear Simon,
Thanks a lot for taking care of all of this !
I'm just back from vacation and will have a look at all your patches in the following days.
I must point out that even if the memory leak was small, it did still mater because I used a LOT of them and after several hours of computations it ate all the available memory the piece of code in the ticket description is just a minimal example, in my actual code I used different curves and similar simple computations on them)...
And to make things clear, I must say I put that ticket as need review in order to get it closed as wont fix/duplicate because I thought it could be seen as a concrete example of ticket 715 and all the work could be done there.
Of course youre the one currently doing all the wok, so do as you want :)
Cheers,
JP
comment:52 in reply to: ↑ 51 Changed 9 years ago by
Hi Jean-Pierre,
Replying to jpflori:
I must point out that even if the memory leak was small,
It isn't small.
And to make things clear, I must say I put that ticket as need review in order to get it closed as wont fix/duplicate because I thought it could be seen as a concrete example of ticket 715 and all the work could be done there.
I am not sure whether it would be good to do everything on one ticket, as the topics are related, but clearly disting: #715 is about weak "TripleDict
" for coercion, #12215 is about a weak version of cached_function, and the ticket here is about the cache of homsets.
On the other hand: I am about to post a new patch here, with #715 as a dependency. It will use the new version of TripleDict
from #715. So, one could argue that there is a common tool for both tickets, and they belong together.
Anyway. The new patch will fix the leak, but it will not suffer from the segfaults.
Cheers,
Simon
comment:53 Changed 9 years ago by
- Dependencies changed from #11900 to #11900 #715
- Description modified (diff)
- Status changed from needs_work to needs_review
- Work issues Understand why a weak key dictionary is not enough deleted
I have attached another patch under a new name, using a new approach: The weak TripleDict
, that I introduce at #715, is an appropriate tool for the cache of homsets. The key is the triple (domain, codomain, category)
, and the value is a weak reference to the corresponding homset.
There is a new test (the same as in the other patch), showing that the leak is fixed. And all tests in sage/schemes, sage/rings, sage/categories and sage/structure pass.
Hence: Needs review!
Apply trac11521_triple_homset.patch
After looking at #10548, I might have a better idea of the culprit: