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ccc profiling: run existing notebooks
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@miltondp
miltondp committed Sep 7, 2023
1 parent 9cace44 commit ddb2f5f
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Showing 10 changed files with 1,063 additions and 998 deletions.
100 changes: 50 additions & 50 deletions nbs/others/05_ccc_profiling/12_cm_optimized/06-cm_many_genes.txt
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Original file line number Diff line number Diff line change
@@ -1,56 +1,56 @@
1021 function calls (1015 primitive calls) in 432.044 seconds
226019 function calls (226013 primitive calls) in 21.329 seconds

Ordered by: cumulative time
List reduced from 133 to 50 due to restriction <50>
List reduced from 138 to 50 due to restriction <50>

ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 432.044 432.044 {built-in method builtins.exec}
1 0.000 0.000 432.044 432.044 <string>:1(<module>)
1 0.000 0.000 432.044 432.044 1750096170.py:1(func)
1 0.005 0.005 432.044 432.044 coef.py:275(cm)
26 0.000 0.000 432.037 16.617 threading.py:280(wait)
79 432.037 5.469 432.037 5.469 {method 'acquire' of '_thread.lock' objects}
20 0.000 0.000 432.037 21.602 _base.py:601(result_iterator)
18 0.000 0.000 432.036 24.002 _base.py:417(result)
2 0.000 0.000 0.001 0.000 _base.py:572(map)
2 0.000 0.000 0.001 0.000 _base.py:597(<listcomp>)
18 0.000 0.000 0.001 0.000 thread.py:155(submit)
18 0.000 0.000 0.001 0.000 thread.py:174(_adjust_thread_count)
2 0.001 0.000 0.001 0.000 {built-in method numpy.zeros}
3 0.000 0.000 0.000 0.000 threading.py:873(start)
3 0.000 0.000 0.000 0.000 threading.py:556(wait)
1 0.000 0.000 0.000 0.000 numeric.py:289(full)
1 0.000 0.000 0.000 0.000 <__array_function__ internals>:2(copyto)
1 0.000 0.000 0.000 0.000 {built-in method numpy.core._multiarray_umath.implement_array_function}
1 0.000 0.000 0.000 0.000 _base.py:635(__exit__)
1 0.000 0.000 0.000 0.000 thread.py:210(shutdown)
3 0.000 0.000 0.000 0.000 threading.py:1021(join)
3 0.000 0.000 0.000 0.000 threading.py:1059(_wait_for_tstate_lock)
1 0.000 0.000 21.329 21.329 {built-in method builtins.exec}
1 0.000 0.000 21.329 21.329 <string>:1(<module>)
1 0.000 0.000 21.329 21.329 1375007101.py:1(func)
1 0.023 0.023 21.328 21.328 impl.py:367(ccc)
5052 0.009 0.000 21.271 0.004 _base.py:602(result_iterator)
5050 0.014 0.000 21.262 0.004 _base.py:418(result)
10001 0.015 0.000 21.251 0.002 threading.py:280(wait)
29905 21.226 0.001 21.226 0.001 {method 'acquire' of '_thread.lock' objects}
2 0.000 0.000 0.033 0.017 _base.py:573(map)
2 0.001 0.001 0.033 0.017 _base.py:598(<listcomp>)
5050 0.005 0.000 0.032 0.000 thread.py:161(submit)
5050 0.002 0.000 0.019 0.000 thread.py:180(_adjust_thread_count)
5050 0.004 0.000 0.017 0.000 threading.py:404(acquire)
5050 0.002 0.000 0.007 0.000 _base.py:318(__init__)
10101 0.004 0.000 0.005 0.000 threading.py:256(__enter__)
5052 0.004 0.000 0.005 0.000 threading.py:228(__init__)
10101 0.003 0.000 0.004 0.000 threading.py:259(__exit__)
5050 0.004 0.000 0.004 0.000 {method '_acquire_restore' of '_thread.RLock' objects}
10004 0.001 0.000 0.001 0.000 {built-in method _thread.allocate_lock}
5050 0.001 0.000 0.001 0.000 {method '_release_save' of '_thread.RLock' objects}
5050 0.001 0.000 0.001 0.000 _base.py:388(__get_result)
5050 0.001 0.000 0.001 0.000 {method '__enter__' of '_thread.RLock' objects}
4951 0.001 0.000 0.001 0.000 threading.py:271(_is_owned)
4951 0.001 0.000 0.001 0.000 threading.py:265(_release_save)
5050 0.001 0.000 0.001 0.000 threading.py:82(RLock)
5051 0.001 0.000 0.001 0.000 {method '__exit__' of '_thread.RLock' objects}
10001 0.001 0.000 0.001 0.000 {method 'append' of 'collections.deque' objects}
5050 0.001 0.000 0.001 0.000 {method 'pop' of 'list' objects}
4951 0.001 0.000 0.001 0.000 threading.py:268(_acquire_restore)
5050 0.001 0.000 0.001 0.000 thread.py:47(__init__)
15153 0.001 0.000 0.001 0.000 {method '__exit__' of '_thread.lock' objects}
5050 0.001 0.000 0.001 0.000 {method '_is_owned' of '_thread.RLock' objects}
9900 0.001 0.000 0.001 0.000 {built-in method time.monotonic}
5051 0.000 0.000 0.000 0.000 {method 'put' of '_queue.SimpleQueue' objects}
5051 0.000 0.000 0.000 0.000 {method '__enter__' of '_thread.lock' objects}
4950 0.000 0.000 0.000 0.000 {method 'remove' of 'collections.deque' objects}
4952 0.000 0.000 0.000 0.000 {method 'release' of '_thread.lock' objects}
4951 0.000 0.000 0.000 0.000 {built-in method builtins.len}
1 0.000 0.000 0.000 0.000 {method 'seed' of 'numpy.random.mtrand.RandomState' objects}
1 0.000 0.000 0.000 0.000 _base.py:636(__exit__)
1 0.000 0.000 0.000 0.000 thread.py:216(shutdown)
2 0.000 0.000 0.000 0.000 {built-in method numpy.zeros}
9 0.000 0.000 0.000 0.000 typedlist.py:341(append)
2 0.000 0.000 0.000 0.000 coef.py:233(get_chunks)
1 0.000 0.000 0.000 0.000 threading.py:873(start)
1 0.000 0.000 0.000 0.000 threading.py:1021(join)
1 0.000 0.000 0.000 0.000 threading.py:1059(_wait_for_tstate_lock)
1 0.000 0.000 0.000 0.000 typedlist.py:298(_initialise_list)
18 0.000 0.000 0.000 0.000 threading.py:404(acquire)
3 0.000 0.000 0.000 0.000 threading.py:795(__init__)
18 0.000 0.000 0.000 0.000 _base.py:317(__init__)
22 0.000 0.000 0.000 0.000 threading.py:228(__init__)
2 0.000 0.000 0.000 0.000 {built-in method numpy.arange}
3 0.000 0.000 0.000 0.000 {built-in method _thread.start_new_thread}
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)
39 0.000 0.000 0.000 0.000 threading.py:259(__exit__)
2 0.000 0.000 0.000 0.000 functools.py:872(wrapper)
1 0.000 0.000 0.000 0.000 typedlist.py:270(_parse_arg)
39 0.000 0.000 0.000 0.000 threading.py:256(__enter__)
2 0.000 0.000 0.000 0.000 abstract.py:48(_intern)
3 0.000 0.000 0.000 0.000 threading.py:985(_stop)
2 0.000 0.000 0.000 0.000 {method 'get' of 'dict' objects}
1 0.000 0.000 0.000 0.000 dispatcher.py:677(typeof_pyval)
1 0.000 0.000 0.000 0.000 thread.py:117(__init__)
14 0.000 0.000 0.000 0.000 {method '_acquire_restore' of '_thread.RLock' objects}
18 0.000 0.000 0.000 0.000 _base.py:387(__get_result)
12 0.000 0.000 0.000 0.000 threading.py:268(_acquire_restore)
1 0.000 0.000 0.000 0.000 parallel.py:596(get_num_threads)
12/10 0.000 0.000 0.000 0.000 abstract.py:120(__eq__)
1 0.000 0.000 0.000 0.000 typeof.py:257(_typeof_nb_type)
1 0.000 0.000 0.000 0.000 typedlist.py:228(__init__)
1 0.000 0.000 0.000 0.000 containers.py:618(__init__)
1 0.000 0.000 0.000 0.000 threading.py:556(wait)
1 0.000 0.000 0.000 0.000 impl.py:75(get_range_n_clusters)
1 0.000 0.000 0.000 0.000 random.py:791(getrandbits)
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