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run profiling again to ensure new CCC implementation works as expected
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@miltondp
miltondp committed Sep 11, 2023
1 parent 6670b09 commit b363465
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Showing 21 changed files with 1,202 additions and 1,202 deletions.
96 changes: 48 additions & 48 deletions nbs/others/05_clustermatch_profiling/12_cm_optimized/06-cm_many_genes.txt
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21956760 function calls (21956754 primitive calls) in 102.486 seconds
21092455 function calls (21092449 primitive calls) in 99.101 seconds

Ordered by: cumulative time
List reduced from 106 to 50 due to restriction <50>
List reduced from 167 to 50 due to restriction <50>

ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 102.486 102.486 {built-in method builtins.exec}
1 0.000 0.000 102.486 102.486 <string>:1(<module>)
1 0.000 0.000 102.486 102.486 1375007101.py:1(func)
1 0.005 0.005 102.486 102.486 impl.py:307(ccc)
2 1.512 0.756 102.174 51.087 impl.py:508(compute_coef)
124750 25.803 0.000 99.395 0.001 impl.py:154(cdist_parts_basic)
10104750 45.819 0.000 73.540 0.000 metrics.py:107(adjusted_rand_index)
10104750 27.722 0.000 27.722 0.000 metrics.py:72(get_pair_confusion_matrix)
124750 0.071 0.000 1.030 0.000 <__array_function__ internals>:2(amax)
124758 0.066 0.000 0.944 0.000 {built-in method numpy.core._multiarray_umath.implement_array_function}
124750 0.106 0.000 0.878 0.000 fromnumeric.py:2638(amax)
124750 0.213 0.000 0.772 0.000 fromnumeric.py:69(_wrapreduction)
124750 0.460 0.000 0.460 0.000 {method 'reduce' of 'numpy.ufunc' objects}
2 0.000 0.000 0.305 0.153 impl.py:476(compute_parts)
2 0.001 0.001 0.300 0.150 impl.py:478(<listcomp>)
500 0.299 0.001 0.299 0.001 impl.py:110(get_parts)
124750 0.129 0.000 0.129 0.000 {method 'argmax' of 'numpy.ndarray' objects}
124750 0.069 0.000 0.069 0.000 core.py:85(unravel_index_2d)
124754 0.052 0.000 0.052 0.000 {built-in method numpy.zeros}
124750 0.047 0.000 0.047 0.000 fromnumeric.py:70(<dictcomp>)
124750 0.039 0.000 0.039 0.000 impl.py:218(get_coords_from_index)
124751 0.037 0.000 0.037 0.000 {built-in method builtins.getattr}
124750 0.015 0.000 0.015 0.000 {method 'items' of 'dict' objects}
124750 0.015 0.000 0.015 0.000 fromnumeric.py:2633(_amax_dispatcher)
2 0.005 0.003 0.005 0.003 {built-in method numpy.array}
1 0.000 0.000 0.001 0.001 {method 'seed' of 'numpy.random.mtrand.RandomState' objects}
1 0.000 0.000 0.000 0.000 random.py:791(getrandbits)
1 0.000 0.000 0.000 0.000 {built-in method posix.urandom}
7 0.000 0.000 0.000 0.000 numeric.py:289(full)
7 0.000 0.000 0.000 0.000 <__array_function__ internals>:2(copyto)
2 0.000 0.000 0.000 0.000 impl.py:242(get_chunks)
1 0.000 0.000 99.101 99.101 {built-in method builtins.exec}
1 0.000 0.000 99.101 99.101 <string>:1(<module>)
1 0.000 0.000 99.101 99.101 1375007101.py:1(func)
1 0.008 0.008 99.101 99.101 impl.py:511(ccc)
1 0.913 0.913 98.744 98.744 impl.py:405(compute_coef)
124750 0.324 0.000 97.798 0.001 impl.py:344(compute_ccc)
124750 24.820 0.000 97.238 0.001 impl.py:191(cdist_parts_basic)
10104750 44.939 0.000 72.368 0.000 metrics.py:107(adjusted_rand_index)
10104750 27.430 0.000 27.430 0.000 metrics.py:72(get_pair_confusion_matrix)
1 0.016 0.016 0.343 0.343 impl.py:154(get_feature_parts)
4500 0.324 0.000 0.324 0.000 impl.py:110(get_parts)
124750 0.114 0.000 0.114 0.000 {method 'argmax' of 'numpy.ndarray' objects}
124750 0.072 0.000 0.072 0.000 core.py:85(unravel_index_2d)
124750 0.050 0.000 0.050 0.000 {built-in method builtins.max}
124754 0.050 0.000 0.050 0.000 {built-in method numpy.zeros}
124750 0.032 0.000 0.032 0.000 impl.py:255(get_coords_from_index)
4500 0.003 0.000 0.003 0.000 {built-in method numpy.array}
1 0.003 0.003 0.003 0.003 impl.py:688(<listcomp>)
1 0.000 0.000 0.001 0.001 impl.py:699(<listcomp>)
1 0.001 0.001 0.001 0.001 impl.py:700(<listcomp>)
5 0.000 0.000 0.001 0.000 numeric.py:289(full)
6 0.001 0.000 0.001 0.000 {built-in method numpy.core._multiarray_umath.implement_array_function}
5 0.000 0.000 0.001 0.000 <__array_function__ internals>:2(copyto)
1 0.000 0.000 0.000 0.000 process.py:573(__init__)
2 0.000 0.000 0.000 0.000 impl.py:279(get_chunks)
1 0.000 0.000 0.000 0.000 {built-in method numpy.arange}
5 0.000 0.000 0.000 0.000 synchronize.py:50(__init__)
1 0.000 0.000 0.000 0.000 impl.py:713(<listcomp>)
4 0.000 0.000 0.000 0.000 context.py:65(Lock)
1 0.000 0.000 0.000 0.000 process.py:160(__init__)
4 0.000 0.000 0.000 0.000 synchronize.py:161(__init__)
1 0.000 0.000 0.000 0.000 queues.py:37(__init__)
1 0.000 0.000 0.000 0.000 {method 'seed' of 'numpy.random.mtrand.RandomState' objects}
2 0.000 0.000 0.000 0.000 _base.py:636(__exit__)
1 0.000 0.000 0.000 0.000 process.py:731(shutdown)
1 0.000 0.000 0.000 0.000 impl.py:714(<listcomp>)
9 0.000 0.000 0.000 0.000 typedlist.py:341(append)
1 0.000 0.000 0.000 0.000 typedlist.py:298(_initialise_list)
1 0.000 0.000 0.000 0.000 context.py:110(SimpleQueue)
1 0.000 0.000 0.000 0.000 contextlib.py:76(inner)
2 0.000 0.000 0.000 0.000 {built-in method numpy.arange}
1 0.000 0.000 0.000 0.000 {function SeedSequence.generate_state at 0x7fd0685e59d0}
1 0.000 0.000 0.000 0.000 queues.py:340(__init__)
5 0.000 0.000 0.000 0.000 synchronize.py:114(_make_name)
11 0.000 0.000 0.000 0.000 {built-in method builtins.next}
5 0.000 0.000 0.000 0.000 tempfile.py:149(__next__)
1 0.000 0.000 0.000 0.000 {function SeedSequence.generate_state at 0x7f75101d79d0}
5 0.000 0.000 0.000 0.000 tempfile.py:152(<listcomp>)
40 0.000 0.000 0.000 0.000 random.py:343(choice)
2 0.000 0.000 0.000 0.000 abstract.py:60(__call__)
2 0.000 0.000 0.000 0.000 typeof.py:25(typeof)
1 0.000 0.000 0.000 0.000 typedlist.py:270(_parse_arg)
2 0.000 0.000 0.000 0.000 functools.py:883(wrapper)
1 0.000 0.000 0.000 0.000 dispatcher.py:677(typeof_pyval)
2 0.000 0.000 0.000 0.000 abstract.py:48(_intern)
1 0.000 0.000 0.000 0.000 thread.py:123(__init__)
2 0.000 0.000 0.000 0.000 {method 'get' of 'dict' objects}
1 0.000 0.000 0.000 0.000 containers.py:618(__init__)
1 0.000 0.000 0.000 0.000 typeof.py:257(_typeof_nb_type)
7 0.000 0.000 0.000 0.000 {built-in method numpy.empty}
1 0.000 0.000 0.000 0.000 _base.py:636(__exit__)
2 0.000 0.000 0.000 0.000 _ufunc_config.py:32(seterr)
1 0.000 0.000 0.000 0.000 _ufunc_config.py:429(__enter__)
1 0.000 0.000 0.000 0.000 context.py:85(BoundedSemaphore)
1 0.000 0.000 0.000 0.000 random.py:791(getrandbits)
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