On Thu, Jun 20, 2019 at 4:56 PM Sébastien Labbé <[email protected]> wrote: > > My current sage-8.8.rc1 has normaliz installed: > > slabbe@miami ~ $ sage -optional | grep normaliz > normaliz................................3.7.2 (3.7.2) > pynormaliz..............................2.7 (2.7) > > and my current sage-8.7 has no optional packages installed: > > slabbe@miami ~ $ GitBox/sage-8.7/sage -optional | grep normaliz > normaliz................................3.6.3 (not_installed) > pynormaliz..............................1.19 (not_installed) > > If I do %prun on the first command which takes much longer (90s instead of > 5s), I get on both systems, the following: > > > ┌────────────────────────────────────────────────────────────────────┐ > │ SageMath version 8.7, Release Date: 2019-03-23 │ > │ Using Python 2.7.15. Type "help()" for help. │ > └────────────────────────────────────────────────────────────────────┘ > sage: from slabbe import PolyhedronPartition > sage: from slabbe import PolyhedronExchangeTransformation as PET > sage: from slabbe import Substitution2d > sage: z = polygen(QQ, 'z') > sage: K = NumberField(z**2-z-1, 'phi', embedding=RR(1.6)) > sage: phi = K.gen() > sage: P0 = PolyhedronPartition.jeandel_rao_tilings_partition() > sage: Gamma0 = matrix.column([(phi,0), (1,phi+3)]) > sage: fundamental_domain = polytopes.parallelotope([(phi,0), (0,phi+3)]) > sage: R0e2 = PET.toral_translation(Gamma0, vector((0,1)), fundamental_domain) > sage: y_le_1 = [1, 0, -1] # syntax for the inequality y <= 1 > sage: > sage: %time P1,beta0 = R0e2.induced_partition(y_le_1, P0, > substitution_type='column') > CPU times: user 4.6 s, sys: 84 ms, total: 4.68 s > Wall time: 4.64 s > sage: %prun P1,beta0 = R0e2.induced_partition(y_le_1, P0, > substitution_type='column') > > 3059637 function calls (3058959 primitive calls) in 5.373 seconds > > Ordered by: internal time > > ncalls tottime percall cumtime percall filename:lineno(function) > 4878 0.619 0.000 1.713 0.000 {method 'right_kernel' of > 'sage.matrix.matrix2.Matrix' objects} > 4184 0.392 0.000 0.489 0.000 {method 'solve_right' of > 'sage.matrix.matrix2.Matrix' objects} > 43084 0.253 0.000 0.280 0.000 matrix_space.py:720(__call__) > 9756 0.209 0.000 0.294 0.000 number_field.py:3081(_repr_) > 30698 0.191 0.000 0.253 0.000 > matrix_space.py:103(get_matrix_class) > 4184 0.166 0.000 0.182 0.000 {method 'pivots' of > 'sage.matrix.matrix0.Matrix' objects} > 4184 0.166 0.000 0.205 0.000 {method 'pivot_rows' of > 'sage.matrix.matrix2.Matrix' objects} > 5243 0.152 0.000 0.171 0.000 {method 'rank' of > 'sage.matrix.matrix0.Matrix' objects} > 5005 0.146 0.000 0.325 0.000 free_module.py:662(__init__) > 54383 0.140 0.000 0.200 0.000 > free_module.py:973(_element_constructor_) > 14168 0.138 0.000 0.197 0.000 sequence.py:80(Sequence) > 435687 0.122 0.000 0.122 0.000 {isinstance} > 35194 0.115 0.000 0.127 0.000 > representation.py:1181(evaluated_on) > 30698 0.113 0.000 0.367 0.000 > matrix_space.py:432(__classcall__) > 4184 0.106 0.000 1.284 0.000 > double_description.py:641(initial_pair) > 54383 0.102 0.000 0.304 0.000 > free_module.py:5569(_element_constructor_) > 9637 0.101 0.000 0.312 0.000 > {sage.modules.free_module_element.vector} > 8368 0.080 0.000 0.169 0.000 {method 'rows' of > 'sage.matrix.matrix1.Matrix' objects} > 41111 0.072 0.000 0.149 0.000 misc.py:295(cputime) > 10231 0.070 0.000 0.072 0.000 > double_description.py:313(R_by_sign) > 35194 0.066 0.000 0.247 0.000 representation.py:694(contains) > 41111 0.057 0.000 0.057 0.000 {resource.getrusage} > 52510 0.051 0.000 0.051 0.000 free_module.py:328(create_key) > 4593 0.050 0.000 0.112 0.000 {method 'columns' of > 'sage.matrix.matrix1.Matrix' objects} > 4878 0.045 0.000 0.156 0.000 > free_module.py:1593(basis_matrix) > 2092 0.043 0.000 0.408 0.000 > double_description_inhomogeneous.py:273(_extract_Vrep) > 4878 0.042 0.000 0.443 0.000 free_module.py:5643(__init__) > 19512 0.038 0.000 0.038 0.000 {method 'sub' of > '_sre.SRE_Pattern' objects} > 14168 0.036 0.000 0.039 0.000 sequence.py:405(__init__) > 2965 0.036 0.000 0.057 0.000 representation.py:330(_set_data) > 2092 0.036 0.000 2.732 0.001 > double_description_inhomogeneous.py:154(__init__) > 43834 0.032 0.000 0.281 0.000 base.py:587(<genexpr>) > 1882 0.031 0.000 0.063 0.000 > number_field.py:1554(_element_constructor_) > 5005 0.030 0.000 0.042 0.000 > free_module.py:7218(element_class) > 6983 0.028 0.000 0.030 0.000 {method 'inner_product' of > 'sage.modules.free_module_element.FreeModuleElement' objects} > 35194 0.028 0.000 0.028 0.000 backend_field.py:92(_is_nonneg) > 2965 0.028 0.000 0.084 0.000 representation.py:311(__init__) > 10231 0.024 0.000 0.193 0.000 > double_description.py:689(add_inequality) > 41111 0.023 0.000 0.173 0.000 misc.py:525(verbose) > 19512 0.023 0.000 0.023 0.000 re.py:230(_compile) > 1882 0.023 0.000 0.025 0.000 > polynomial_ring.py:320(_element_constructor_) > 5010 0.022 0.000 0.085 0.000 > modules.py:112(__classcall_private__) > 347 0.022 0.000 0.328 0.001 > point_configuration.py:1827(contained_simplex) > 31 0.021 0.001 4.147 0.134 > polyhedron_partition.py:1204(refinement) > 47132 0.020 0.000 0.020 0.000 > number_field.py:3792(pari_polynomial) > 1745 0.019 0.000 3.565 0.002 > backend_field.py:214(_init_from_Hrepresentation) > 6276 0.019 0.000 0.020 0.000 > double_description.py:112(__init__) > 409 0.018 0.000 0.027 0.000 {method 'inverse' of > 'sage.matrix.matrix2.Matrix' objects} > 7979 0.018 0.000 0.037 0.000 fields.py:63(__contains__) > 2092 0.018 0.000 0.747 0.000 > double_description_inhomogeneous.py:451(_init_Vrep) > 93 0.018 0.000 0.041 0.000 > point_configuration.py:332(__init__) > 4878 0.017 0.000 0.481 0.000 free_module.py:3794(span) > 5629 0.017 0.000 0.017 0.000 {hasattr} > 9675 0.017 0.000 0.018 0.000 free_module.py:2371(zero_vector) > > > > ┌────────────────────────────────────────────────────────────────────┐ > │ SageMath version 8.8.rc1, Release Date: 2019-06-13 │ > │ Using Python 2.7.15. Type "help()" for help. │ > └────────────────────────────────────────────────────────────────────┘ > sage: from slabbe import PolyhedronPartition > sage: from slabbe import PolyhedronExchangeTransformation as PET > sage: from slabbe import Substitution2d > sage: z = polygen(QQ, 'z') > sage: K = NumberField(z**2-z-1, 'phi', embedding=RR(1.6)) > sage: phi = K.gen() > sage: P0 = PolyhedronPartition.jeandel_rao_tilings_partition() > sage: Gamma0 = matrix.column([(phi,0), (1,phi+3)]) > sage: fundamental_domain = polytopes.parallelotope([(phi,0), (0,phi+3)]) > sage: R0e2 = PET.toral_translation(Gamma0, vector((0,1)), fundamental_domain) > sage: y_le_1 = [1, 0, -1] # syntax for the inequality y <= 1 > sage: > sage: %time P1,beta0 = R0e2.induced_partition(y_le_1, P0, > substitution_type='column') > CPU times: user 12.9 s, sys: 2.62 s, total: 15.6 s > Wall time: 1min 27s > sage: %prun P1,beta0 = R0e2.induced_partition(y_le_1, P0, > substitution_type='column') > > 4286879 function calls (4284765 primitive calls) in 89.043 seconds > > Ordered by: internal time > > ncalls tottime percall cumtime percall filename:lineno(function) > 1388 69.712 0.050 69.712 0.050 {time.sleep} > 1041 1.724 0.002 1.724 0.002 {posix.read} > 4878 1.427 0.000 7.762 0.002 {method 'right_kernel' of > 'sage.matrix.matrix2.Matrix' objects} > 347 1.270 0.004 1.270 0.004 {posix.forkpty} > 9756 0.998 0.000 2.509 0.000 > number_field.py:2955(gen_embedding) > 19512 0.998 0.000 1.740 0.000 {method 'format' of 'str' > objects} > 4184 0.671 0.000 0.845 0.000 {method 'solve_right' of > 'sage.matrix.matrix2.Matrix' objects} > 43035 0.554 0.000 0.631 0.000 matrix_space.py:720(__call__) > 111653 0.521 0.000 0.906 0.000 copy.py:66(copy) > 1388 0.447 0.000 0.447 0.000 {select.select} > 30669 0.424 0.000 0.551 0.000 > matrix_space.py:103(get_matrix_class) > 4951 0.387 0.000 0.835 0.000 free_module.py:662(__init__) > 4184 0.320 0.000 0.390 0.000 {method 'pivot_rows' of > 'sage.matrix.matrix2.Matrix' objects} > 4184 0.312 0.000 0.345 0.000 {method 'pivots' of > 'sage.matrix.matrix0.Matrix' objects} > 5243 0.302 0.000 0.334 0.000 {method 'rank' of > 'sage.matrix.matrix0.Matrix' objects} > 530292 0.279 0.000 0.279 0.000 {isinstance} > 54201 0.270 0.000 0.373 0.000 > free_module.py:973(_element_constructor_) > 14168 0.258 0.000 0.365 0.000 sequence.py:80(Sequence) > 30669 0.250 0.000 0.801 0.000 > matrix_space.py:432(__classcall__) > 13844 0.223 0.000 0.231 0.000 > polynomial_ring.py:320(_element_constructor_) > 19512 0.214 0.000 0.436 0.000 qqbar.py:4023(interval) > 11962 0.212 0.000 0.617 0.000 rings.py:845(__getitem__) > 11962 0.195 0.000 0.338 0.000 > polynomial_ring_constructor.py:52(PolynomialRing) > 4184 0.193 0.000 2.282 0.001 > double_description.py:640(initial_pair) > 54201 0.186 0.000 0.562 0.000 > free_module.py:5584(_element_constructor_) > 9637 0.178 0.000 0.520 0.000 > {sage.modules.free_module_element.vector} > 39121 0.172 0.000 0.359 0.000 homset.py:84(Hom) > 41104 0.147 0.000 0.303 0.000 misc.py:295(cputime) > 347 0.142 0.000 3.001 0.009 > point_configuration.py:1829(contained_simplex) > 8368 0.140 0.000 0.308 0.000 {method 'rows' of > 'sage.matrix.matrix1.Matrix' objects} > 48780 0.137 0.000 0.137 0.000 > sets_cat.py:974(_element_constructor_from_element_class) > 35194 0.130 0.000 0.218 0.000 > representation.py:1200(evaluated_on) > 10231 0.130 0.000 0.133 0.000 > double_description.py:313(R_by_sign) > 41104 0.110 0.000 0.110 0.000 {resource.getrusage} > 1882 0.108 0.000 0.210 0.000 > number_field.py:1554(_element_constructor_) > > > I do not know where these sleep calls come from?? >
I guess it's from posix.forkpty, or related to multi-processing in some other way. > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/sage-devel. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/618fa213-bef5-4b57-88e3-8a79c784d090%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/sage-devel. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq3YP60fab3B8c0Q5%2BuKzADaSX0PVWu3ZuitON%2BNwMjZXg%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
