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??
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