Implement parallel f-vector for polytopes

[gh-kliem]

This ticket parallelizes the f-vector 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 f-vectors 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)

[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] = True

Likewise 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.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​0dae7a0

remove redundant sig_checks

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​609bd92	do not delete all duplicates
​5c6ccee	fix index
​e3bdc61	pull in 31226 and fix merge conflict

[gh-kliem]

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] = True

Likewise 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).

[gh-kliem]

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

[tscrim]

Thank you. This is quite a nice improvement.

[gh-kliem]

Thank you.

[vbraun]

On the kucalc buildbot:

[sagelib-9.3.beta6] [1/1] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -march=native -fPIC -I/var/lib/buildbot/slave/sage_git/build/local/lib/python3.9/site-packages/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/site-packages/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.linux-x86_64-3.9/build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -fopenmp -std=c99
[sagelib-9.3.beta6] In file included from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:660:0:
[sagelib-9.3.beta6] /var/lib/buildbot/slave/sage_git/build/local/lib/python3.9/site-packages/cysignals/struct_signals.h:45:1: sorry, unimplemented: ‘_Atomic’ with OpenMP
[sagelib-9.3.beta6]  typedef volatile _Atomic int cy_atomic_int;
[sagelib-9.3.beta6]  ^
[sagelib-9.3.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’:
[sagelib-9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9035:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta6]    __pyx_t_2 = ((__pyx_v_structure->current_dimension == (__pyx_v_structure->dimension - __pyx_v_parallelization_depth)) != 0);
[sagelib-9.3.beta6]                                                       ^
[sagelib-9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9322:84: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta6]      __pyx_t_1 = (((__pyx_v_parallel_struct->current_job_id[__pyx_v_current_depth]) == -1L) != 0);
[sagelib-9.3.beta6]                                                                                     ^
[sagelib-9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9673:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta6]    __pyx_t_1 = ((__pyx_v_structure->current_dimension != ((__pyx_v_structure->dimension - __pyx_v_parallelization_depth) - 1)) != 0);
[sagelib-9.3.beta6]                                                       ^
[sagelib-9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__Pyx_InitGlobals’:
[sagelib-9.3.beta6] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:23283:1: warning: ‘PyEval_InitThreads’ is deprecated [-Wdeprecated-declarations]
[sagelib-9.3.beta6]  PyEval_InitThreads();
[sagelib-9.3.beta6]  ^
[sagelib-9.3.beta6] In file included from /var/lib/buildbot/slave/sage_git/build/local/include/python3.9/Python.h:145:0,
[sagelib-9.3.beta6]                  from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:52:
[sagelib-9.3.beta6] /var/lib/buildbot/slave/sage_git/build/local/include/python3.9/ceval.h:130:37: note: declared here
[sagelib-9.3.beta6]  Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
[sagelib-9.3.beta6]                                      ^
[sagelib-9.3.beta6] error: command '/usr/bin/gcc' failed with exit code 1

[gh-kliem]

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).

[gh-kliem]

Actually, that is a problem with cysignals that should be fixed there.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​baf80de

try disabling CYSIGNALS_C_ATOMIC

[gh-kliem]

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.

[tscrim]

Back off to the builbots.

[vbraun]

Build fails on various buildbots:

[sagelib-9.3.beta7] [1/1] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -march=native -O2 -g -march=native -fPIC -UCYSIGNALS_C_ATOMIC -I/home/buildbot/slave/sage_git/build/local/lib/python3.9/site-packages/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/site-packages/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.linux-x86_64-3.9/build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -fopenmp -std=c99
[sagelib-9.3.beta7] In file included from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:662:0:
[sagelib-9.3.beta7] /home/buildbot/slave/sage_git/build/local/lib/python3.9/site-packages/cysignals/struct_signals.h:45:1: sorry, unimplemented: ‘_Atomic’ with OpenMP
[sagelib-9.3.beta7]  typedef volatile _Atomic int cy_atomic_int;
[sagelib-9.3.beta7]  ^~~~~~~
[sagelib-9.3.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’:
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9037:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta7]    __pyx_t_2 = ((__pyx_v_structure->current_dimension == (__pyx_v_structure->dimension - __pyx_v_parallelization_depth)) != 0);
[sagelib-9.3.beta7]                                                       ^~
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9324:84: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta7]      __pyx_t_1 = (((__pyx_v_parallel_struct->current_job_id[__pyx_v_current_depth]) == -1L) != 0);
[sagelib-9.3.beta7]                                                                                     ^~
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9675:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta7]    __pyx_t_1 = ((__pyx_v_structure->current_dimension != ((__pyx_v_structure->dimension - __pyx_v_parallelization_depth) - 1)) != 0);
[sagelib-9.3.beta7]                                                       ^~
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__Pyx_InitGlobals’:
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:23285:1: warning: ‘PyEval_InitThreads’ is deprecated [-Wdeprecated-declarations]
[sagelib-9.3.beta7]  PyEval_InitThreads();
[sagelib-9.3.beta7]  ^~~~~~~~~~~~~~~~~~
[sagelib-9.3.beta7] In file included from /home/buildbot/slave/sage_git/build/local/include/python3.9/Python.h:145:0,
[sagelib-9.3.beta7]                  from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:54:
[sagelib-9.3.beta7] /home/buildbot/slave/sage_git/build/local/include/python3.9/ceval.h:130:37: note: declared here
[sagelib-9.3.beta7]  Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
[sagelib-9.3.beta7]                                      ^~~~~~~~~~~~~~~~~~
[sagelib-9.3.beta7] error: command '/usr/bin/gcc' failed with exit code 1
[sagelib-9.3.beta7] 
[sagelib-9.3.beta7] real	0m3.325s
[sagelib-9.3.beta7] user	0m2.798s
[sagelib-9.3.beta7] sys	0m0.563s
Makefile:2233: recipe for target 'sagelib-no-deps' failed

[git]

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"

[gh-kliem]

I don't think this is going to happen with 9.3 anymore, if this is waiting on a cysignals patch/update.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​405ef3e

Merge branch 'u/gh-kliem/first_parallel_version_of_face_iterator_reb' of git://trac.sagemath.org/sage into u/gh-kliem/first_parallel_version_of_face_iterator_reb2

[gh-kliem]

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:

[sagelib-9.3.beta7] [1/1] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -march=native -O2 -g -march=native -fPIC -UCYSIGNALS_C_ATOMIC -I/home/buildbot/slave/sage_git/build/local/lib/python3.9/site-packages/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/site-packages/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.linux-x86_64-3.9/build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -fopenmp -std=c99
[sagelib-9.3.beta7] In file included from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:662:0:
[sagelib-9.3.beta7] /home/buildbot/slave/sage_git/build/local/lib/python3.9/site-packages/cysignals/struct_signals.h:45:1: sorry, unimplemented: ‘_Atomic’ with OpenMP
[sagelib-9.3.beta7]  typedef volatile _Atomic int cy_atomic_int;
[sagelib-9.3.beta7]  ^~~~~~~
[sagelib-9.3.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’:
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9037:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta7]    __pyx_t_2 = ((__pyx_v_structure->current_dimension == (__pyx_v_structure->dimension - __pyx_v_parallelization_depth)) != 0);
[sagelib-9.3.beta7]                                                       ^~
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9324:84: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta7]      __pyx_t_1 = (((__pyx_v_parallel_struct->current_job_id[__pyx_v_current_depth]) == -1L) != 0);
[sagelib-9.3.beta7]                                                                                     ^~
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:9675:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[sagelib-9.3.beta7]    __pyx_t_1 = ((__pyx_v_structure->current_dimension != ((__pyx_v_structure->dimension - __pyx_v_parallelization_depth) - 1)) != 0);
[sagelib-9.3.beta7]                                                       ^~
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c: In function ‘__Pyx_InitGlobals’:
[sagelib-9.3.beta7] build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:23285:1: warning: ‘PyEval_InitThreads’ is deprecated [-Wdeprecated-declarations]
[sagelib-9.3.beta7]  PyEval_InitThreads();
[sagelib-9.3.beta7]  ^~~~~~~~~~~~~~~~~~
[sagelib-9.3.beta7] In file included from /home/buildbot/slave/sage_git/build/local/include/python3.9/Python.h:145:0,
[sagelib-9.3.beta7]                  from build/cythonized/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.c:54:
[sagelib-9.3.beta7] /home/buildbot/slave/sage_git/build/local/include/python3.9/ceval.h:130:37: note: declared here
[sagelib-9.3.beta7]  Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
[sagelib-9.3.beta7]                                      ^~~~~~~~~~~~~~~~~~
[sagelib-9.3.beta7] error: command '/usr/bin/gcc' failed with exit code 1
[sagelib-9.3.beta7] 
[sagelib-9.3.beta7] real	0m3.325s
[sagelib-9.3.beta7] user	0m2.798s
[sagelib-9.3.beta7] sys	0m0.563s
Makefile:2233: recipe for target 'sagelib-no-deps' failed

[gh-kliem]

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.

[git]

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/gh-kliem/check_openmp_at_configuration' of git://trac.sagemath.org/sage into u/gh-kliem/first_parallel_version_of_face_iterator_reb
​27baa07	use OPENMP_CFLAGS

[gh-kliem]

Tests are running here:

​https://github.com/kliem/sage/pull/40/checks

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​a9d3dfe	split to account for multiple arguments
​ae482a4	Merge branch 'u/gh-kliem/check_openmp_at_configuration' of git://trac.sagemath.org/sage into u/gh-kliem/first_parallel_version_of_face_iterator_reb

[gh-kliem]

Thanks again.

[vbraun]

Merge conflict

[gh-kliem]

New commits:

​2474ccc

Merge branch 'u/gh-kliem/first_parallel_version_of_face_iterator_reb' of git://trac.sagemath.org/sage into u/gh-kliem/first_parallel_version_of_face_iterator_reb2

[git]

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/gh-kliem/check_openmp_at_configuration' of git://trac.sagemath.org/sage into u/gh-kliem/first_parallel_version_of_face_iterator_reb2
​fdbe95f	use cython.parallel.threadid instead of omp_get_thread_num

[gh-kliem]

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.

[tscrim]

Works for me. Let's try this again...

[vbraun]

Merge conflict

[mkoeppe]

New commits:

​4ae6966

Merge tag '9.4.beta0' into t/31245/first_parallel_version_of_face_iterator_reb2

[vbraun]

Segfaults reliably on OSX

sage -t --long --random-seed=0 src/sage/geometry/polyhedron/combinatorial_polyhedron/base.pyx  # Killed due to segmentation fault
sage -t --long --random-seed=0 src/sage/geometry/polyhedron/base.py  # Killed due to segmentation fault

Debugger:

$ sage -sh
(sage-sh) sudo lldb ./local/bin/python3
(lldb) target create "./local/bin/python3"
Current executable set to '/Users/buildbot-sage/slave/sage_git/build/local/bin/python3' (x86_64).
(lldb) rfrom
error: 'rfrom' is not a valid command.
(lldb) r
Process 81901 launched: '/Users/buildbot-sage/slave/sage_git/build/local/bin/python3' (x86_64)
Python 3.9.5 (default, Jun  8 2021, 19:13:24) 
[Clang 12.0.5 (clang-1205.0.22.9)] 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.cpython-39-darwin.so was compiled with optimization - stepping may behave oddly; variables may not be available.
Process 81901 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
    frame #0: 0x00000001142ae934 base.cpython-39-darwin.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.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
  * frame #0: 0x00000001142ae934 base.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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.cpython-39-darwin.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

[gh-kliem]

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.

[gh-kliem]

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

[gh-kliem]

I really don't understand why this pops out just now and not earlier.

[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 previously-used 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)

[gh-kliem]

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 previously-used 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.

[tscrim]

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.