Opened 5 months ago
Last modified 21 hours ago
#31245 positive_review enhancement
Implement parallel fvector for polytopes
Reported by:  ghkliem  Owned by:  

Priority:  major  Milestone:  sage9.4 
Component:  geometry  Keywords:  parallel fvector 
Cc:  jipilab, ghLaisRast, stumpc5, tscrim  Merged in:  
Authors:  Jonathan Kliem  Reviewers:  Travis Scrimshaw 
Report Upstream:  N/A  Work issues:  
Branch:  u/ghkliem/first_parallel_version_of_face_iterator_reb3 (Commits, GitHub, GitLab)  Commit:  4c0a4ae74c28680e48080c39c5e3b171a79a9ad3 
Dependencies:  Stopgaps: 
Description (last modified by )
This ticket parallelizes the fvector for polytopes.
Each thread has its private structure with which it does partial jobs. Depending on the parallelization depth, there is one job per face of fixed codimension (usually 1,2 or 3). After everything has finished, the partial fvectors will be added.
Actually, every face is visited and thus the code could be modified in the future, to explore other properties of faces then just the dimension. The parallelization seems to work well with at least 40 threads (for computations taking long enough such that this pays off, see https://arxiv.org/pdf/1905.01945.pdf).
Also the algorithm does work in other situations (simplicial complex, lattice of flats of a matroid) and this parallel structure could be used for this as well.
On the downside, sig_on()/sig_off()
doesn't work with with multiple threads and has to be replaced by a simple sig_check()
. Also raising errors in parallel code results in terrible slow down. Hence the errors are replaced by returning the exception value. In case of a bug there won't be any traceback anymore, but at least also no segmenation fault.
Before:
sage: P = P.base_extend(QQ) sage: P = P.base_extend(QQ) sage: Q = P.join(P.polar(in_affine_span=True)) sage: C = CombinatorialPolyhedron(Q) sage: %time C.f_vector() CPU times: user 111 ms, sys: 186 µs, total: 111 ms Wall time: 111 ms (1, 150, 3990, 25590, 69450, 95402, 69450, 25590, 3990, 150, 1) sage: P = polytopes.Birkhoff_polytope(5) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector() CPU times: user 584 ms, sys: 25 µs, total: 584 ms Wall time: 583 ms (1, 120, 5040, 50250, 233400, 631700, 1113700, 1367040, 1220550, 817150, 419225, 167200, 52120, 12600, 2300, 300, 25, 1) # Using the <simple> version of the algorithm. sage: P = polytopes.associahedron(['A', 11], backend='normaliz') sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector() CPU times: user 37.9 s, sys: 17.2 ms, total: 37.9 s Wall time: 37.9 s (1, 208012, 1144066, 2735810, 3730650, 3197700, 1790712, 659736, 157080, 23100, 1925, 77, 1)
After (machine has 4 cores):
sage: P = polytopes.permutahedron(5) sage: P = P.base_extend(QQ) sage: Q = P.join(P.polar(in_affine_span=True)) sage: C = CombinatorialPolyhedron(Q) sage: %time C.f_vector(num_threads=1) CPU times: user 107 ms, sys: 0 ns, total: 107 ms Wall time: 107 ms (1, 150, 3990, 25590, 69450, 95402, 69450, 25590, 3990, 150, 1) sage: C = CombinatorialPolyhedron(Q) sage: %time C.f_vector(num_threads=2) CPU times: user 108 ms, sys: 0 ns, total: 108 ms Wall time: 55.6 ms (1, 150, 3990, 25590, 69450, 95402, 69450, 25590, 3990, 150, 1) sage: C = CombinatorialPolyhedron(Q) sage: %time C.f_vector(num_threads=4) CPU times: user 147 ms, sys: 52 µs, total: 147 ms Wall time: 38.6 ms (1, 150, 3990, 25590, 69450, 95402, 69450, 25590, 3990, 150, 1) sage: C = CombinatorialPolyhedron(Q) sage: %time C.f_vector(num_threads=8) CPU times: user 236 ms, sys: 0 ns, total: 236 ms Wall time: 31.2 ms (1, 150, 3990, 25590, 69450, 95402, 69450, 25590, 3990, 150, 1) sage: P = polytopes.Birkhoff_polytope(5) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=1) CPU times: user 354 ms, sys: 0 ns, total: 354 ms Wall time: 354 ms (1, 120, 5040, 50250, 233400, 631700, 1113700, 1367040, 1220550, 817150, 419225, 167200, 52120, 12600, 2300, 300, 25, 1) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=2) CPU times: user 363 ms, sys: 0 ns, total: 363 ms Wall time: 181 ms (1, 120, 5040, 50250, 233400, 631700, 1113700, 1367040, 1220550, 817150, 419225, 167200, 52120, 12600, 2300, 300, 25, 1) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=4) CPU times: user 459 ms, sys: 0 ns, total: 459 ms Wall time: 117 ms (1, 120, 5040, 50250, 233400, 631700, 1113700, 1367040, 1220550, 817150, 419225, 167200, 52120, 12600, 2300, 300, 25, 1) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=8) CPU times: user 776 ms, sys: 154 µs, total: 776 ms Wall time: 103 ms (1, 120, 5040, 50250, 233400, 631700, 1113700, 1367040, 1220550, 817150, 419225, 167200, 52120, 12600, 2300, 300, 25, 1) # Using the <simple> version of the algorithm. sage: P = polytopes.associahedron(['A', 11], backend='normaliz') sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=1) CPU times: user 33.5 s, sys: 0 ns, total: 33.5 s Wall time: 33.5 s (1, 208012, 1144066, 2735810, 3730650, 3197700, 1790712, 659736, 157080, 23100, 1925, 77, 1) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=2) CPU times: user 34.4 s, sys: 3.49 ms, total: 34.4 s Wall time: 17.2 s (1, 208012, 1144066, 2735810, 3730650, 3197700, 1790712, 659736, 157080, 23100, 1925, 77, 1) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=4) CPU times: user 35.9 s, sys: 15.5 ms, total: 35.9 s Wall time: 9 s (1, 208012, 1144066, 2735810, 3730650, 3197700, 1790712, 659736, 157080, 23100, 1925, 77, 1) sage: C = CombinatorialPolyhedron(P) sage: %time C.f_vector(num_threads=8) CPU times: user 1min 6s, sys: 31.3 ms, total: 1min 6s Wall time: 8.44 s (1, 208012, 1144066, 2735810, 3730650, 3197700, 1790712, 659736, 157080, 23100, 1925, 77, 1)
Change History (48)
comment:1 Changed 5 months ago by
 Status changed from new to needs_review
comment:2 Changed 5 months ago by
 Description modified (diff)
comment:3 followup: ↓ 7 Changed 5 months ago by
 Reviewers set to Travis Scrimshaw
comment:4 Changed 5 months ago by
 Commit changed from d051f283c08d117bd51d2167fb3d0ccf641dd620 to 0dae7a061df9a2f05f9ef2d43602cc04fb351fb0
Branch pushed to git repo; I updated commit sha1. New commits:
0dae7a0  remove redundant sig_checks

comment:5 Changed 5 months ago by
 Commit changed from 0dae7a061df9a2f05f9ef2d43602cc04fb351fb0 to e3bdc617538af4ab8cdcf147fd74f4e62da5ff2a
comment:6 Changed 5 months ago by
 Dependencies set to #31226
comment:7 in reply to: ↑ 3 Changed 5 months ago by
Replying to tscrim:
The
sig_check()
outside the loop is unnecessary:cdef size_t j + sig_check() for j in range(n_faces): + sig_check() if (is_not_maximal_fused(new_faces, j, algorithm) or # Step 2 is_contained_in_one_fused(new_faces.faces[j], visited_all, algorithm)): # Step 3 is_not_new_face[j] = TrueLikewise here:
face_list_t visited_all) nogil except 1: cdef size_t output  sig_on() + sig_check() if faces.polyhedron_is_simple: output = get_next_level_fused(faces, new_faces, visited_all, <simple> 0) else: output = get_next_level_fused(faces, new_faces, visited_all, <standard> 0)  sig_off() return output cdef inline size_t bit_rep_to_coatom_rep(face_t face, face_list_t coatoms, size_t *output):Here you either need the
sig_on/sig_off
or some more targeted checking. I don't see the point in performing a single check here.Otherwise LGTM.
I removed the redundant sig_checks.
As mentioned, sig_on, sig_off doesn't work well with parallelization. It crashes hard because sig_on, sig_off doesn't appear in correct order anymore.
Wrapping prange
in sig_on/sig_off has a large performance penalty (8.45 s > 9 s).
Currently there is one sig_check
before checking that a face is inclusion maximal. One can add more sig checks, which wouldn't affect performance much for large examples, but for the small examples there is a penalty of about 50 percent.
I think the current solution should be fine: The largest thing I ever computed with this algorithm, which took about a month on 40 cores, had 11,665,781 vertices and 162 facets. In this case between the sig_checks A &~ B == 0
is performed for about 2 billion bits. Currently, without intrinsics, I get:
sage: B = Bitset((randint(0,2**20) for _ in range(2**19))) sage: %timeit B.issubset(B) 6.18 µs ± 9.8 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each) sage: %timeit B.intersection_update(B) 6.02 µs ± 2.72 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)
On this rate performing this for 2 billion bits should take about 12 ms. And even if the example has many more coatoms, in the worst case (completely unrealistic, because the dimension is not 1 and more memory is needed for other dimensions and probably for other threads), there are bitwise operations performed twice for the entire RAM. Say, we have 1 TB RAM, this would then take 96 seconds. Okay, that is long, but in any realistic sceanrio it would only take about a second, even with 1 TB RAM.
To sum up, I think the current amount of sig_checks
suffices for the next years until more than 1 TB RAM is common (and even then, it doubt that there is an application for such a large example, as it would take forever to compute).
comment:8 Changed 5 months ago by
 Branch changed from u/ghkliem/first_parallel_version_of_face_iterator to u/ghkliem/first_parallel_version_of_face_iterator_reb
 Commit changed from e3bdc617538af4ab8cdcf147fd74f4e62da5ff2a to 928ea608dc56698cd8df3d71b8266e75c28670eb
Rebased.
I didn't have this ticket here ready when writing #30445.
Eventually, one could also store edges/ridges or any sort of face in parallel. This would also help with applications for simplicial complexes and lattice of flats of manifolds.
But that should be left for another time.
New commits:
6a2a9b4  fix merge conflict with develop in particual #30445

928ea60  remove redundant allocation

comment:9 Changed 5 months ago by
 Status changed from needs_review to positive_review
Thank you. This is quite a nice improvement.
comment:10 Changed 5 months ago by
Thank you.
comment:11 Changed 5 months ago by
On the kucalc buildbot:
[sagelib9.3.beta6] [1/1] gcc Wnounusedresult Wsigncompare DNDEBUG g fwrapv O3 Wall Wnounused O2 g march=native fPIC I/var/lib/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/cysignals I./sage/data_structures I./sage/cpython Isage/cpython Isage/data_structures I/var/lib/buildbot/slave/sage_git/build/build/pkgs/sagelib/src I/var/lib/buildbot/slave/sage_git/build/local/include/python3.9 I/var/lib/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/numpy/core/include Ibuild/cythonized I/var/lib/buildbot/slave/sage_git/build/local/include/python3.9 c build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c o build/temp.linuxx86_643.9/build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.o fnostrictaliasing DCYTHON_CLINE_IN_TRACEBACK=1 fopenmp std=c99 [sagelib9.3.beta6] In file included from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:660:0: [sagelib9.3.beta6] /var/lib/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/cysignals/struct_signals.h:45:1: sorry, unimplemented: ‘_Atomic’ with OpenMP [sagelib9.3.beta6] typedef volatile _Atomic int cy_atomic_int; [sagelib9.3.beta6] ^ [sagelib9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__pyx_f_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_13face_iterator_prepare_face_iterator_for_partial_job’: [sagelib9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9035:54: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta6] __pyx_t_2 = ((__pyx_v_structure>current_dimension == (__pyx_v_structure>dimension  __pyx_v_parallelization_depth)) != 0); [sagelib9.3.beta6] ^ [sagelib9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9322:84: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta6] __pyx_t_1 = (((__pyx_v_parallel_struct>current_job_id[__pyx_v_current_depth]) == 1L) != 0); [sagelib9.3.beta6] ^ [sagelib9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9673:54: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta6] __pyx_t_1 = ((__pyx_v_structure>current_dimension != ((__pyx_v_structure>dimension  __pyx_v_parallelization_depth)  1)) != 0); [sagelib9.3.beta6] ^ [sagelib9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__Pyx_InitGlobals’: [sagelib9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:23283:1: warning: ‘PyEval_InitThreads’ is deprecated [Wdeprecateddeclarations] [sagelib9.3.beta6] PyEval_InitThreads(); [sagelib9.3.beta6] ^ [sagelib9.3.beta6] In file included from /var/lib/buildbot/slave/sage_git/build/local/include/python3.9/Python.h:145:0, [sagelib9.3.beta6] from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:52: [sagelib9.3.beta6] /var/lib/buildbot/slave/sage_git/build/local/include/python3.9/ceval.h:130:37: note: declared here [sagelib9.3.beta6] Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); [sagelib9.3.beta6] ^ [sagelib9.3.beta6] error: command '/usr/bin/gcc' failed with exit code 1
comment:12 Changed 5 months ago by
 Status changed from positive_review to needs_work
comment:13 Changed 5 months ago by
This appears to be an issue with python 3.5 to 3.7 according to https://bugs.python.org/issue25150
From this I get that this can be "fixed" by doing this specific module as a C++ extension (or by requiring system python >= 3.8, but that isn't an option for the moment).
I'll check if I can reproduce this with system python 3.7 (need to rebuild first).
comment:14 Changed 5 months ago by
Actually, that is a problem with cysignals that should be fixed there.
comment:15 Changed 5 months ago by
 Commit changed from 928ea608dc56698cd8df3d71b8266e75c28670eb to baf80deaca74b037c11e5eee914009e216f3beed
Branch pushed to git repo; I updated commit sha1. New commits:
baf80de  try disabling CYSIGNALS_C_ATOMIC

comment:16 Changed 5 months ago by
According to
https://github.com/sagemath/cysignals/blob/master/src/cysignals/struct_signals.h
and
https://github.com/sagemath/cysignals/blob/master/src/cysignals/cysignals_config.h.in
just undefininig CYSIGNALS_C_ATOMIC
should fix this.
comment:17 Changed 5 months ago by
 Status changed from needs_work to needs_review
comment:18 Changed 5 months ago by
 Status changed from needs_review to positive_review
Back off to the builbots.
comment:19 followup: ↓ 24 Changed 4 months ago by
Build fails on various buildbots:
[sagelib9.3.beta7] [1/1] gcc Wnounusedresult Wsigncompare DNDEBUG g fwrapv O3 Wall Wnounused O2 g march=native O2 g march=native fPIC UCYSIGNALS_C_ATOMIC I/home/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/cysignals I./sage/data_structures I./sage/cpython Isage/cpython I/home/buildbot/slave/sage_git/build/build/pkgs/sagelib/src I/home/buildbot/slave/sage_git/build/local/include/python3.9 I/home/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/numpy/core/include Ibuild/cythonized I/home/buildbot/slave/sage_git/build/local/include/python3.9 c build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c o build/temp.linuxx86_643.9/build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.o fnostrictaliasing DCYTHON_CLINE_IN_TRACEBACK=1 fopenmp std=c99 [sagelib9.3.beta7] In file included from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:662:0: [sagelib9.3.beta7] /home/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/cysignals/struct_signals.h:45:1: sorry, unimplemented: ‘_Atomic’ with OpenMP [sagelib9.3.beta7] typedef volatile _Atomic int cy_atomic_int; [sagelib9.3.beta7] ^~~~~~~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__pyx_f_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_13face_iterator_prepare_face_iterator_for_partial_job’: [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9037:54: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta7] __pyx_t_2 = ((__pyx_v_structure>current_dimension == (__pyx_v_structure>dimension  __pyx_v_parallelization_depth)) != 0); [sagelib9.3.beta7] ^~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9324:84: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta7] __pyx_t_1 = (((__pyx_v_parallel_struct>current_job_id[__pyx_v_current_depth]) == 1L) != 0); [sagelib9.3.beta7] ^~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9675:54: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta7] __pyx_t_1 = ((__pyx_v_structure>current_dimension != ((__pyx_v_structure>dimension  __pyx_v_parallelization_depth)  1)) != 0); [sagelib9.3.beta7] ^~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__Pyx_InitGlobals’: [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:23285:1: warning: ‘PyEval_InitThreads’ is deprecated [Wdeprecateddeclarations] [sagelib9.3.beta7] PyEval_InitThreads(); [sagelib9.3.beta7] ^~~~~~~~~~~~~~~~~~ [sagelib9.3.beta7] In file included from /home/buildbot/slave/sage_git/build/local/include/python3.9/Python.h:145:0, [sagelib9.3.beta7] from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:54: [sagelib9.3.beta7] /home/buildbot/slave/sage_git/build/local/include/python3.9/ceval.h:130:37: note: declared here [sagelib9.3.beta7] Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); [sagelib9.3.beta7] ^~~~~~~~~~~~~~~~~~ [sagelib9.3.beta7] error: command '/usr/bin/gcc' failed with exit code 1 [sagelib9.3.beta7] [sagelib9.3.beta7] real 0m3.325s [sagelib9.3.beta7] user 0m2.798s [sagelib9.3.beta7] sys 0m0.563s Makefile:2233: recipe for target 'sagelibnodeps' failed
comment:20 Changed 4 months ago by
 Commit changed from baf80deaca74b037c11e5eee914009e216f3beed to da65d28f81ddb7a865d0af830d14bb4132c3c1cb
 Status changed from positive_review to needs_review
Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:
da65d28  Revert "try disabling CYSIGNALS_C_ATOMIC"

comment:21 Changed 4 months ago by
 Dependencies changed from #31226 to #31226, #31455
comment:22 Changed 4 months ago by
 Milestone changed from sage9.3 to sage9.4
I don't think this is going to happen with 9.3 anymore, if this is waiting on a cysignals patch/update.
comment:23 Changed 3 months ago by
 Commit changed from da65d28f81ddb7a865d0af830d14bb4132c3c1cb to 405ef3e3bb65ac1c610727c590daf75c19048c45
Branch pushed to git repo; I updated commit sha1. New commits:
405ef3e  Merge branch 'u/ghkliem/first_parallel_version_of_face_iterator_reb' of git://trac.sagemath.org/sage into u/ghkliem/first_parallel_version_of_face_iterator_reb2

comment:24 in reply to: ↑ 19 Changed 3 months ago by
This bug isn't too hard to reproduce actually:
https://github.com/kliem/sage/runs/2064520070?check_suite_focus=true
Seems to be connected to older GCC.
Replying to vbraun:
Build fails on various buildbots:
[sagelib9.3.beta7] [1/1] gcc Wnounusedresult Wsigncompare DNDEBUG g fwrapv O3 Wall Wnounused O2 g march=native O2 g march=native fPIC UCYSIGNALS_C_ATOMIC I/home/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/cysignals I./sage/data_structures I./sage/cpython Isage/cpython I/home/buildbot/slave/sage_git/build/build/pkgs/sagelib/src I/home/buildbot/slave/sage_git/build/local/include/python3.9 I/home/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/numpy/core/include Ibuild/cythonized I/home/buildbot/slave/sage_git/build/local/include/python3.9 c build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c o build/temp.linuxx86_643.9/build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.o fnostrictaliasing DCYTHON_CLINE_IN_TRACEBACK=1 fopenmp std=c99 [sagelib9.3.beta7] In file included from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:662:0: [sagelib9.3.beta7] /home/buildbot/slave/sage_git/build/local/lib/python3.9/sitepackages/cysignals/struct_signals.h:45:1: sorry, unimplemented: ‘_Atomic’ with OpenMP [sagelib9.3.beta7] typedef volatile _Atomic int cy_atomic_int; [sagelib9.3.beta7] ^~~~~~~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__pyx_f_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_13face_iterator_prepare_face_iterator_for_partial_job’: [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9037:54: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta7] __pyx_t_2 = ((__pyx_v_structure>current_dimension == (__pyx_v_structure>dimension  __pyx_v_parallelization_depth)) != 0); [sagelib9.3.beta7] ^~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9324:84: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta7] __pyx_t_1 = (((__pyx_v_parallel_struct>current_job_id[__pyx_v_current_depth]) == 1L) != 0); [sagelib9.3.beta7] ^~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9675:54: warning: comparison between signed and unsigned integer expressions [Wsigncompare] [sagelib9.3.beta7] __pyx_t_1 = ((__pyx_v_structure>current_dimension != ((__pyx_v_structure>dimension  __pyx_v_parallelization_depth)  1)) != 0); [sagelib9.3.beta7] ^~ [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__Pyx_InitGlobals’: [sagelib9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:23285:1: warning: ‘PyEval_InitThreads’ is deprecated [Wdeprecateddeclarations] [sagelib9.3.beta7] PyEval_InitThreads(); [sagelib9.3.beta7] ^~~~~~~~~~~~~~~~~~ [sagelib9.3.beta7] In file included from /home/buildbot/slave/sage_git/build/local/include/python3.9/Python.h:145:0, [sagelib9.3.beta7] from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:54: [sagelib9.3.beta7] /home/buildbot/slave/sage_git/build/local/include/python3.9/ceval.h:130:37: note: declared here [sagelib9.3.beta7] Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); [sagelib9.3.beta7] ^~~~~~~~~~~~~~~~~~ [sagelib9.3.beta7] error: command '/usr/bin/gcc' failed with exit code 1 [sagelib9.3.beta7] [sagelib9.3.beta7] real 0m3.325s [sagelib9.3.beta7] user 0m2.798s [sagelib9.3.beta7] sys 0m0.563s Makefile:2233: recipe for target 'sagelibnodeps' failed
comment:25 Changed 3 months ago by
 Dependencies changed from #31226, #31455 to #31474
comment:26 Changed 3 months ago by
 Status changed from needs_review to needs_work
This might need more work, as the flag fopenmp
isn't understood everywhere: https://github.com/kliem/sage/pull/40/checks?check_run_id=2076988665
So we should probably check out at configure time, whether our compiler supports this, similar to https://trac.sagemath.org/ticket/27122.
comment:27 Changed 3 months ago by
 Dependencies changed from #31474 to #31474, #31499
comment:28 Changed 3 months ago by
 Commit changed from 405ef3e3bb65ac1c610727c590daf75c19048c45 to 27baa071a64d5f93ca49d5ca4c18ae8ca7fa892a
Branch pushed to git repo; I updated commit sha1. New commits:
55a4634  merge with current develop

6edd48b  define cython aliases OPENMP_CFLAGS and OPENMP_CXXFLAGS

71f8950  fixes to get the aliases to work

b76dc3c  add doctest that shows how use cython.parallel.prange

07cb470  Merge branch 'u/ghkliem/check_openmp_at_configuration' of git://trac.sagemath.org/sage into u/ghkliem/first_parallel_version_of_face_iterator_reb

27baa07  use OPENMP_CFLAGS

comment:29 Changed 3 months ago by
 Status changed from needs_work to needs_review
comment:30 Changed 3 months ago by
Tests are running here:
comment:31 Changed 3 months ago by
 Commit changed from 27baa071a64d5f93ca49d5ca4c18ae8ca7fa892a to ae482a4d07ebc5f68fe78b37a32919c85b94aef5
comment:32 Changed 2 months ago by
 Status changed from needs_review to positive_review
comment:33 Changed 2 months ago by
Thanks again.
comment:35 Changed 5 weeks ago by
 Branch changed from u/ghkliem/first_parallel_version_of_face_iterator_reb to u/ghkliem/first_parallel_version_of_face_iterator_reb2
 Commit changed from ae482a4d07ebc5f68fe78b37a32919c85b94aef5 to 2474ccc2d1b7fcbead0a5f9eb27470c9ee365e00
New commits:
2474ccc  Merge branch 'u/ghkliem/first_parallel_version_of_face_iterator_reb' of git://trac.sagemath.org/sage into u/ghkliem/first_parallel_version_of_face_iterator_reb2

comment:36 Changed 5 weeks ago by
 Commit changed from 2474ccc2d1b7fcbead0a5f9eb27470c9ee365e00 to fdbe95f9cf2b4787a59a459231074a7c528397f3
Branch pushed to git repo; I updated commit sha1. Last 10 new commits:
499af5d  remove SAGE_HAVE_OPENMP

7b3da21  move to sage_conf.py.in

927291f  simplifications

d71c54a  set default

7d3f230  more solid check

4f42440  sage.env.cython_aliases: Do not fail if one of the listed libraries is not known to pkgconfig

3cb8f90  sage.env.cython_aliases: Make module lapack optional; generalize the interface

c3cc31e  merge in 31384

70a8791  Merge branch 'u/ghkliem/check_openmp_at_configuration' of git://trac.sagemath.org/sage into u/ghkliem/first_parallel_version_of_face_iterator_reb2

fdbe95f  use cython.parallel.threadid instead of omp_get_thread_num

comment:37 Changed 5 weeks ago by
 Status changed from needs_work to needs_review
I'm not sure this was actually a merge conflict.
But even on my laptop with OPENMP support I got missing symbols. Don't exactly understand this.
However, we can't use openmp.omp_get_num_threads
for obvious reasons, because it doesn't have to be defined. Instead we should use cython.parallel.threadid
, which takes care of this. It is supposed to work, just like prange.
comment:38 Changed 5 weeks ago by
 Status changed from needs_review to positive_review
Works for me. Let's try this again...
comment:40 Changed 4 weeks ago by
 Branch changed from u/ghkliem/first_parallel_version_of_face_iterator_reb2 to u/mkoeppe/first_parallel_version_of_face_iterator_reb2
comment:41 Changed 4 weeks ago by
 Commit changed from fdbe95f9cf2b4787a59a459231074a7c528397f3 to 4ae6966e49618739268625fbe5b9767ca6175200
 Dependencies changed from #31474, #31499 to #31499
 Status changed from needs_work to positive_review
New commits:
4ae6966  Merge tag '9.4.beta0' into t/31245/first_parallel_version_of_face_iterator_reb2

comment:42 Changed 2 days ago by
 Status changed from positive_review to needs_work
Segfaults reliably on OSX
sage t long randomseed=0 src/sage/geometry/polyhedron/combinatorial_polyhedron/base.pyx # Killed due to segmentation fault sage t long randomseed=0 src/sage/geometry/polyhedron/base.py # Killed due to segmentation fault
Debugger:
$ sage sh (sagesh) sudo lldb ./local/bin/python3 (lldb) target create "./local/bin/python3" Current executable set to '/Users/buildbotsage/slave/sage_git/build/local/bin/python3' (x86_64). (lldb) rfrom error: 'rfrom' is not a valid command. (lldb) r Process 81901 launched: '/Users/buildbotsage/slave/sage_git/build/local/bin/python3' (x86_64) Python 3.9.5 (default, Jun 8 2021, 19:13:24) [Clang 12.0.5 (clang1205.0.22.9)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from sage.all import * >>> line = Polyhedron(lines=[[0,1]]) >>> line.vertex_graph() ## line 7185 ## base.cpython39darwin.so was compiled with optimization  stepping may behave oddly; variables may not be available. Process 81901 stopped * thread #1, queue = 'com.apple.mainthread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0) frame #0: 0x00000001142ae934 base.cpython39darwin.so`__pyx_gb_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_24_compute_edges_or_ridges_5generator29(__pyx_generator=0x0000000114562160, __pyx_tstate=0x0000000100508140, __pyx_sent_value=0x00000001003a8580) at base.c:28817:74 [opt] 28814 __pyx_t_2 = __pyx_t_1; 28815 for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 28816 __pyx_cur_scope>__pyx_v_i = __pyx_t_3; > 28817 __pyx_t_4 = ((PyObject *)__pyx_f_4sage_5rings_7integer_smallInteger((__pyx_cur_scope>__pyx_outer_scope>__pyx_v_f_vector[__pyx_cur_scope>__pyx_v_i]))); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 3071, __pyx_L1_error) 28818 __Pyx_GOTREF(__pyx_t_4); 28819 __pyx_r = __pyx_t_4; 28820 __pyx_t_4 = 0; Target 0: (python3) stopped. (lldb) error: No auto repeat. (lldb) bt * thread #1, queue = 'com.apple.mainthread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0) * frame #0: 0x00000001142ae934 base.cpython39darwin.so`__pyx_gb_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_24_compute_edges_or_ridges_5generator29(__pyx_generator=0x0000000114562160, __pyx_tstate=0x0000000100508140, __pyx_sent_value=0x00000001003a8580) at base.c:28817:74 [opt] frame #1: 0x00000001033bc4fa cachefunc.cpython39darwin.so`__Pyx_Coroutine_SendEx(self=0x0000000114562160, value=0x00000001003a8580, closing=<unavailable>) at cachefunc.c:28545:14 [opt] frame #2: 0x00000001001573c0 libpython3.9.dylib`PySequence_Tuple + 144 frame #3: 0x00000001142abde3 base.cpython39darwin.so`__pyx_f_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron__compute_edges_or_ridges(__pyx_v_self=<unavailable>, __pyx_v_dual=<unavailable>, __pyx_v_do_edges=<unavailable>) at base.c:29447:19 [opt] frame #4: 0x00000001142b7aa7 base.cpython39darwin.so`__pyx_pw_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_23edges [inlined] __pyx_f_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron__compute_edges(__pyx_v_self=<unavailable>, __pyx_v_dual=<unavailable>) at base.c:43309:15 [opt] frame #5: 0x00000001142b7a9b base.cpython39darwin.so`__pyx_pw_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_23edges [inlined] __pyx_pf_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_22edges(__pyx_v_self=0x0000000114235ca0, __pyx_v_names=0x0000000000000000) at base.c:14187 [opt] frame #6: 0x00000001142b742a base.cpython39darwin.so`__pyx_pw_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_23edges(__pyx_v_self=0x0000000114235ca0, __pyx_args=<unavailable>, __pyx_kwds=<unavailable>) at base.c:13668 [opt] frame #7: 0x00000001001ab7c5 libpython3.9.dylib`cfunction_call + 69 frame #8: 0x00000001142ca4d7 base.cpython39darwin.so`__pyx_gb_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_12vertex_graph_2generator13 [inlined] __Pyx_PyObject_Call(func=0x0000000114569860, arg=<unavailable>, kw=0x0000000100722e80) at base.c:52465:14 [opt] frame #9: 0x00000001142ca49a base.cpython39darwin.so`__pyx_gb_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_12vertex_graph_2generator13(__pyx_generator=0x0000000112ae5b80, __pyx_tstate=<unavailable>, __pyx_sent_value=<unavailable>) at base.c:14600 [opt] frame #10: 0x00000001033bc4fa cachefunc.cpython39darwin.so`__Pyx_Coroutine_SendEx(self=0x0000000112ae5b80, value=0x00000001003a8580, closing=<unavailable>) at cachefunc.c:28545:14 [opt] frame #11: 0x00000001001573c0 libpython3.9.dylib`PySequence_Tuple + 144 frame #12: 0x00000001142b86c8 base.cpython39darwin.so`__pyx_pw_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_25vertex_graph [inlined] __pyx_pf_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_24vertex_graph(__pyx_v_self=<unavailable>, __pyx_v_names=0x0000000000000000) at base.c:14808:15 [opt] frame #13: 0x00000001142b85bb base.cpython39darwin.so`__pyx_pw_4sage_8geometry_10polyhedron_24combinatorial_polyhedron_4base_23CombinatorialPolyhedron_25vertex_graph(__pyx_v_self=<unavailable>, __pyx_args=<unavailable>, __pyx_kwds=<unavailable>) at base.c:14515 [opt] frame #14: 0x00000001001759c3 libpython3.9.dylib`method_vectorcall_VARARGS_KEYWORDS + 275 frame #15: 0x000000010024bc1b libpython3.9.dylib`call_function + 411 frame #16: 0x0000000100248c0b libpython3.9.dylib`_PyEval_EvalFrameDefault + 27147 frame #17: 0x000000010016d5b5 libpython3.9.dylib`function_code_fastcall + 229 frame #18: 0x000000010016f89c libpython3.9.dylib`method_vectorcall + 204 frame #19: 0x000000010024bc1b libpython3.9.dylib`call_function + 411 frame #20: 0x0000000100248c2e libpython3.9.dylib`_PyEval_EvalFrameDefault + 27182 frame #21: 0x000000010024c9d4 libpython3.9.dylib`_PyEval_EvalCode + 2580 frame #22: 0x0000000100242107 libpython3.9.dylib`PyEval_EvalCode + 87 frame #23: 0x000000010028c45f libpython3.9.dylib`PyRun_InteractiveOneObjectEx + 847 frame #24: 0x000000010028ba59 libpython3.9.dylib`PyRun_InteractiveLoopFlags + 169 frame #25: 0x000000010028b97c libpython3.9.dylib`PyRun_AnyFileExFlags + 60 frame #26: 0x00000001002a84ea libpython3.9.dylib`Py_RunMain + 2362 frame #27: 0x00000001002a87ec libpython3.9.dylib`pymain_main + 348 frame #28: 0x00000001002a883b libpython3.9.dylib`Py_BytesMain + 43 frame #29: 0x00007fff20394621 libdyld.dylib`start + 1 frame #30: 0x00007fff20394621 libdyld.dylib`start + 1
comment:43 Changed 2 days ago by
Thanks Volker for the precise log.
Unfortunately, I neither understand the problem nor can reproduce it. I could just disable OpenMP with clang by default and hope this solves the problem.
comment:44 Changed 2 days ago by
 Branch changed from u/mkoeppe/first_parallel_version_of_face_iterator_reb2 to u/ghkliem/first_parallel_version_of_face_iterator_reb3
 Commit changed from 4ae6966e49618739268625fbe5b9767ca6175200 to 4c0a4ae74c28680e48080c39c5e3b171a79a9ad3
 Dependencies #31499 deleted
 Status changed from needs_work to needs_review
I think I tracked it down. I assumed that
cdef bint do_f_vector
is initialized to zero, which apparently isn't always the case.
Then Volkers report also makes sense.
New commits:
bfb4efb  Merge branch 'u/mkoeppe/first_parallel_version_of_face_iterator_reb2' of git://trac.sagemath.org/sage into u/mkoeppe/first_parallel_version_of_face_iterator_reb3

4c0a4ae  initialize do_f_vector

comment:45 Changed 2 days ago by
I really don't understand why this pops out just now and not earlier.
comment:46 followup: ↓ 47 Changed 2 days ago by
Uninitialized variables are whatever the RAM content is when they enter scope. However, any RAM region that you get from the OS is zeroed out (so you can't read content from older processes). So uninitialized variables tend to be zero initially, but the longer the program runs the more likely it becomes that the variable occupies a previouslyused memory location.
More precisely, only global and static C variables are guaranteed to be initialized to zero, local variables are not.
Valgrind can detect these things for you (i.e. when you read uninitialized memory)
comment:47 in reply to: ↑ 46 Changed 2 days ago by
Replying to vbraun:
Uninitialized variables are whatever the RAM content is when they enter scope. However, any RAM region that you get from the OS is zeroed out (so you can't read content from older processes). So uninitialized variables tend to be zero initially, but the longer the program runs the more likely it becomes that the variable occupies a previouslyused memory location.
More precisely, only global and static C variables are guaranteed to be initialized to zero, local variables are not.
Valgrind can detect these things for you (i.e. when you read uninitialized memory)
Thank you for the explanation.
Once I found out where the problem lies, I wasn't that confused anymore. I originally thought it had something to do with the current ticket, but it doesn't, it just appears now, probably because it now gets stabely compiled in a slightly different way.
In this case it is actually a mistake I made (which I in theory knew about, when I made it). I never meant to assume anything on an unitialized bint
: There where two cases and depending on the case I would set it to True
and False
and then I added special handling for corner cases and forgot to initialize the bint
.
I didn't know that RAM is zeroed out before the process, but once you mention it, of course this is how it ought to be.
comment:48 Changed 21 hours ago by
 Status changed from needs_review to positive_review
Hopefully this will be the last iteration of this. Sorry for having to redo this a bunch of times Volker; I just haven't been able to locally recreate any of the issues.
The
sig_check()
outside the loop is unnecessary:Likewise here:
Here you either need the
sig_on/sig_off
or some more targeted checking. I don't see the point in performing a single check here.Otherwise LGTM.