I have create https://trac.sagemath.org/ticket/30427 for the memory leak in
divisors of integers.
jonatha...@googlemail.com schrieb am Freitag, 21. August 2020 um 09:08:44
UTC+2:
> I can confirm the rings/integer.pyx failure from running it in the shell.
>
> sage: n = prod(primes_first_n(25))
> sage: _ = n.divisors()
>
> If I cancel the second line many time (after a few seconds each), I see an
> increase in memory usage.
> There doesn't seem to be a limit to it.
>
> I can immitate the problem by the following (this is what divisors does
> along the way):
>
> sage: cython('''
> ....: from sage.rings.integer cimport Integer
> ....: from sage.ext.stdsage cimport PY_NEW
> ....: from cysignals.signals cimport sig_check
> ....: def foo():
> ....: cdef list sorted = []
> ....: cdef Integer apn
> ....: cdef Py_ssize_t i
> ....: for i in range(100000000):
> ....: apn = <Integer>PY_NEW(Integer)
> ....: sorted.append(apn)
> ....: sig_check()
> ....: ''')
>
> If I cancel the function foo after a few seconds, it leaks.
>
> Looks to me like this list isn't garbage collected at interrupt.
>
> Btw, note that alarm might be triggered much later than expected:
>
> sage: def test_alarm():
> ....: n = prod(primes_first_n(25))
> ....: try:
> ....: alarm(RDF.random_element(1e-3,0.5))
> ....: _ = n.divisors()
> ....: sleep(20)
> ....: except AlarmInterrupt:
> ....: pass
> ....:
>
>
>
> sage: %time
> test_alarm()
>
>
>
> CPU times: user 127 ms, sys: 24 ms, total: 151 ms
> Wall time: 150 ms
> sage: %time
> test_alarm()
>
>
>
> CPU times: user 1.22 s, sys: 88.1 ms, total: 1.31 s
> Wall time: 1.31 s
> Steven Trogdon schrieb am Freitag, 21. August 2020 um 00:22:32 UTC+2:
>
>> I've seen the following failures when doctesting Sage-on-Gentoo but I'm
>> now seeing them when doctesting vanilla Sage:
>>
>> sage -t --long --warn-long 165.2 --random-seed=0
>> src/sage/rings/integer.pyx
>> **********************************************************************
>> File "src/sage/rings/integer.pyx", line 3100, in
>> sage.rings.integer.Integer.divisors
>> Failed example:
>> for i in range(20): # long time
>> try:
>> alarm(RDF.random_element(1e-3, 0.5))
>> _ = n.divisors()
>> cancel_alarm() # we never get here
>> except AlarmInterrupt:
>> pass
>> Exception raised:
>> Traceback (most recent call last):
>> File
>> "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>
>> line 715, in _run
>> self.compile_and_execute(example, compiler, test.globs)
>> File
>> "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>
>> line 1139, in compile_and_execute
>> exec(compiled, globs)
>> File "<doctest sage.rings.integer.Integer.divisors[20]>", line 4,
>> in <module>
>> _ = n.divisors()
>> File "sage/rings/integer.pyx", line 3170, in
>> sage.rings.integer.Integer.divisors
>> (build/cythonized/sage/rings/integer.c:20840)
>> ptr = <unsigned long*>check_allocarray(divisor_count, 3 *
>> sizeof(unsigned long))
>> File "memory.pxd", line 87, in cysignals.memory.check_allocarray
>> (build/cythonized/sage/rings/integer.c:47465)
>> MemoryError: failed to allocate 33554432 * 24 bytes
>> **********************************************************************
>> File "src/sage/rings/integer.pyx", line 3912, in
>> sage.rings.integer.Integer.?
>> Failed example:
>> n.factor(proof=True)
>> Exception raised:
>> Traceback (most recent call last):
>> File
>> "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>
>> line 715, in _run
>> self.compile_and_execute(example, compiler, test.globs)
>> File
>> "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>
>> line 1139, in compile_and_execute
>> exec(compiled, globs)
>> File "<doctest sage.rings.integer.Integer.?[9]>", line 1, in
>> <module>
>> n.factor(proof=True)
>> File "sage/rings/integer.pyx", line 3994, in
>> sage.rings.integer.Integer.factor
>> (build/cythonized/sage/rings/integer.c:25893)
>> F = factor_using_pari(n, int_=int_, debug_level=verbose,
>> proof=proof)
>> File "sage/rings/factorint.pyx", line 345, in
>> sage.rings.factorint.factor_using_pari
>> (build/cythonized/sage/rings/factorint.c:6481)
>> p, e = n.__pari__().factor(proof=proof)
>> File "cypari2/gen.pyx", line 4311, in cypari2.gen.Gen.factor
>> cysignals.signals.AlarmInterrupt
>> **********************************************************************
>>
>> and
>>
>> sage -t --long --warn-long 165.2 --random-seed=0 src/sage/doctest/test.py
>> **********************************************************************
>> File "src/sage/doctest/test.py", line 521, in sage.doctest.test
>> Failed example:
>> if system() == "Linux":
>> P = subprocess.Popen(["sage", "-t", "--warn-long", "0",
>> "--random-seed=0", "--memlimit=2000", "memlimit.rst"],
>> stdout=subprocess.PIPE, **kwds)
>> out, err = P.communicate()
>> ok = ("MemoryError: failed to allocate" in bytes_to_str(out))
>> Expected nothing
>> Got:
>> Process DocTestWorker-1:
>> Traceback (most recent call last):
>> File
>> "/local/sage-git/sage/local/lib/python3.7/multiprocessing/process.py", line
>> 297, in _bootstrap
>> self.run()
>> File
>> "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>
>> line 2185, in run
>> task(self.options, self.outtmpfile, msgpipe, self.result_queue)
>> File
>> "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>
>> line 2535, in __call__
>> result_queue.put(result, False)
>> File
>> "/local/sage-git/sage/local/lib/python3.7/multiprocessing/queues.py", line
>> 87, in put
>> self._start_thread()
>> File
>> "/local/sage-git/sage/local/lib/python3.7/multiprocessing/queues.py", line
>> 170, in _start_thread
>> self._thread.start()
>> File "/local/sage-git/sage/local/lib/python3.7/threading.py", line
>> 847, in start
>> _start_new_thread(self._bootstrap, ())
>> RuntimeError: can't start new thread
>>
>>
>> On Tuesday, August 18, 2020 at 5:01:42 PM UTC-6, Volker Braun wrote:
>>
>>> As always, you can get the latest beta version from the "develop" git
>>> branch. Alternatively, the self-contained source tarball is at
>>> http://www.sagemath.org/download-latest.html
>>>
>>>
>>> 548666e9f2 (tag: 9.2.beta9, trac/develop) Updated SageMath version to
>>> 9.2.beta9
>>> 842a6866f1 Trac #29974: Make combinat doctests ready for random seeds
>>> 1de1d457b4 Trac #29971: Make categories doctests ready for random seeds
>>> 6864757e11 Trac #29968: Make algebras doctests ready for random seeds
>>> b526019731 Trac #29963: Make geometry doctests ready for random seeds
>>> 719f9af12c Trac #29509: rational_points fails for some hyperelliptic
>>> curves
>>> 4d5ab773b5 Trac #29257: use solve_left for division operation of matrices
>>> e18e84219d Trac #30365: Disable LTO in matplotlib build
>>> 01f536726d Trac #29989: fix random test failures in PSage interface
>>> f531b354f7 Trac #30345: build/make/Makefile.in: Filter out "-j" from
>>> sub-make invocations to avoid excessive parallel load
>>> 8417e64af6 Trac #29511: Broken coercion between cyclotomic fields
>>> b4a8c5745b Trac #29325: Set up permutahedron with both Vrep and Hrep (if
>>> backend supports it)
>>> 9b14ca3e86 Trac #29248: Index notation for tensors should allow for
>>> unicode characters
>>> a331d47ef3 Trac #28966: Provide unicode aliases for some globals in
>>> Python 3
>>> 95d0cd5b9e Trac #28951: Fixing a bug in
>>> sage.schemes.cyclic_covers.charpoly_frobenius
>>> 4986d5ea7f Trac #28816: database_stein_watkins Python 3 issues
>>> 193e14365a Trac #30127: cygwin-minimal: pip-20.1.1 fails to install
>>> a92871805f Trac #26919: Upgrade Jupyter notebook to latest (6.1.1) and
>>> its dependencies to latest
>>> 66472811de Trac #30251: ExtPowerFreeModule, ExtPowerDualFreeModule:
>>> Simplify _repr_
>>> 7030fa15a7 Trac #30175: Remove outdated spkg-src script for ecl
>>> 11bb005e98 Trac #30165: normalize_coordinates broken for p-adic fields
>>> 82568e3cbd Trac #30044: tox.ini: Test on voidlinux
>>> 294931e00b Trac #30339: tox.ini: Update for latest ubuntu, fedora
>>> versions
>>> ea615c4ce6 Trac #30331: Issue with toric_substitute for Laurent
>>> polynomials
>>> df3cf63875 Trac #30327: affine group element * a polytope raises KeyError
>>> 9cfaefb544 Trac #30303: Graphs: two families of distance-regular graphs
>>> 81a7e50cd2 Trac #30301: Italian translation of FAQ
>>> 48fb9141da Trac #30286: Graph: last sporadic distance-regular graphs
>>> 6f2561fdca Trac #30260: Graphs: more distance-regular graphs
>>> 29098c6af9 Trac #30240: Graphs: a few distance-regular graphs
>>> 1b8dff7172 Trac #30178: Manifolds: add orientability
>>> 24eb3aa28d Trac #29911: sage.rings.integer, integer_ring: Remove
>>> dependencies on sage.libs.ntl
>>> 8b9743d0af Trac #29654: Improve face generator of polyhedra by exposing
>>> `FaceIterator` class
>>> c0b61fd5cf Trac #28904: Move reversed graph from backend to CGraph for
>>> sparse graphs
>>> 04c64492a6 Trac #30335: openblas: clear out .pc symlinks before
>>> installation
>>> ef6132b817 Trac #25363: Add '--simple-prompt' argument for sage
>>> 3682402983 Trac #30277: Remove src/module_list.py
>>> 0cc658a1f9 Trac #30257: Fusion Ring - Rmatrix
>>> 6ffe4c9e55 Trac #30209: Action for Bundle Connections
>>> eaa2f0a361 Trac #29950: Build sagelib from build/pkgs/sagelib/src, fix
>>> `setup.py sdist`, add spkg-src and tox.ini
>>> e002ee071c Trac #29539: Bug in saturation of elliptic curves over number
>>> fields
>>> a4b8705ae5 Trac #30330: `cdd` backend fails to initialize empty
>>> polyhedron from double description
>>> c3e5ce6ea1 Trac #30292: is_pyramid returns a wrong certificate
>>> 3d594b5cc6 Trac #30262: Update e-antic to 0.1.8
>>> 415221a9a8 (tag: 9.2.beta8) Updated SageMath version to 9.2.beta8
>>>
>>>
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