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20 hours ago •
MDAnalysis
MDAnalysis
asv: fix GeoSelectionBench.time_geometric_selections
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Expected behavior
All ASV benchmarks for the latest develop run (see benchmarks.benchmarks for the code and the MDAnalysis/benchmarks repo + the benchmarks wiki for more details.)
Actual behavior
All GeoSelectionBench.time_geometric_selections tests fail as shown below (recent output from nightly run on Python 3.6). This seems to be related to the removal of the flags #782 .
[ 97.44%] ··· ....GeoSelectionBench.time_geometric_selections failed
[ 97.44%] ··· ============================ =================== ==================== ========
selection_string dynamic_selection periodic_selection
---------------------------- ------------------- -------------------- --------
around 5.0 resid 1 True [False, True] failed
around 5.0 resid 1 True [True, False] failed
around 5.0 resid 1 False [False, True] failed
around 5.0 resid 1 False [True, False] failed
sphlayer 2.4 6.0 (protein) True [False, True] failed
sphlayer 2.4 6.0 (protein) True [True, False] failed
sphlayer 2.4 6.0 (protein) False [False, True] failed
sphlayer 2.4 6.0 (protein) False [True, False] failed
sphzone 6.0 (protein) True [False, True] failed
sphzone 6.0 (protein) True [True, False] failed
sphzone 6.0 (protein) False [False, True] failed
sphzone 6.0 (protein) False [True, False] failed
cylayer 5 10 10 -8 protein True [False, True] failed
cylayer 5 10 10 -8 protein True [True, False] failed
cylayer 5 10 10 -8 protein False [False, True] failed
cylayer 5 10 10 -8 protein False [True, False] failed
cyzone 15 4 -8 protein True [False, True] failed
cyzone 15 4 -8 protein True [True, False] failed
cyzone 15 4 -8 protein False [False, True] failed
cyzone 15 4 -8 protein False [True, False] failed
point 5.0 5.0 5.0 3.5 True [False, True] failed
point 5.0 5.0 5.0 3.5 True [True, False] failed
point 5.0 5.0 5.0 3.5 False [False, True] failed
point 5.0 5.0 5.0 3.5 False [True, False] failed
prop z >= 5.0 True [False, True] failed
prop z >= 5.0 True [True, False] failed
prop z >= 5.0 False [False, True] failed
prop z >= 5.0 False [True, False] failed
prop abs z <= 5.0 True [False, True] failed
prop abs z <= 5.0 True [True, False] failed
prop abs z <= 5.0 False [False, True] failed
prop abs z <= 5.0 False [True, False] failed
============================ =================== ==================== ========
[ 97.44%] ···· For parameters: 'around 5.0 resid 1', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'around 5.0 resid 1', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'around 5.0 resid 1', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'around 5.0 resid 1', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphlayer 2.4 6.0 (protein)', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphlayer 2.4 6.0 (protein)', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphlayer 2.4 6.0 (protein)', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphlayer 2.4 6.0 (protein)', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphzone 6.0 (protein)', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphzone 6.0 (protein)', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphzone 6.0 (protein)', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'sphzone 6.0 (protein)', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cylayer 5 10 10 -8 protein', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cylayer 5 10 10 -8 protein', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cylayer 5 10 10 -8 protein', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cylayer 5 10 10 -8 protein', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cyzone 15 4 -8 protein', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cyzone 15 4 -8 protein', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cyzone 15 4 -8 protein', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'cyzone 15 4 -8 protein', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'point 5.0 5.0 5.0 3.5', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'point 5.0 5.0 5.0 3.5', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'point 5.0 5.0 5.0 3.5', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'point 5.0 5.0 5.0 3.5', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop z >= 5.0', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop z >= 5.0', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop z >= 5.0', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop z >= 5.0', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop abs z <= 5.0', True, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop abs z <= 5.0', True, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop abs z <= 5.0', False, [False, True]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
For parameters: 'prop abs z <= 5.0', False, [True, False]
Traceback (most recent call last):
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1184, in main_run_server
main_run(run_args)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 1058, in main_run
result = benchmark.do_run()
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 537, in do_run
return self.run(*self._current_params)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 631, in run
min_run_count=self.min_run_count)
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 663, in benchmark_timing
timing = timer.timeit(number)
File "~/mdanalysis/benchmarks/env/80c5ba7efaa89366b97da3ced85c0c44/lib/python3.6/timeit.py", line 178, in timeit
timing = self.inner(it, self.timer)
File "<timeit-src>", line 6, in inner
File "~/miniconda3/envs/benchmark/lib/python3.6/site-packages/asv/benchmark.py", line 599, in <lambda>
func = lambda: self.func(*param)
File "~/mdanalysis/benchmarks/benchmarks/selections.py", line 76, in time_geometric_selections
MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
AttributeError: module 'MDAnalysis.core' has no attribute 'flags'
So as far as I can tell (I might be missing something obvious), there no longer is a means by which we can set the search method in a selection call, so I guess that needs removing?
I’m not sure how to write the tests so that they work with different call signatures across different versions. Try/except? @tylerjereddy , any hints? You have a lot of experience with asv?
You can use a try/except to get the benchmarks running again--I just tried the diff below locally (the flags are part of the setup, so they should be moved to setup() as well I think).
That said, I do share some of @IAlibay concerns re: semantics before and after--do we actually preserve an identical calculation type over history here with modern MDA not using those flags? If not, producing a plot with performance before/after the transition for the same benchmark name may be dubious.
If the meaning of the benchmark has changed after removal of flags, the "failing" benchmark still has a 0 exit code (shouldn't prevent the overall asv run), so could just be left as is I suppose, or eventually removed.
Could maybe consider adding i.e., time_geometric_selections_modern() or something, but actually even writing a new benchmark may be tricky to have "fair" over time if the defaults under the hood are different because flags were removed.
Well, I guess not that hard to check--just debug print the results (atomgroups/sizes) over various versions of MDA; a little tedious though.
diff --git a/benchmarks/benchmarks/selections.py b/benchmarks/benchmarks/selections.py
index b07fc7348..c6afa3c6b 100644
--- a/benchmarks/benchmarks/selections.py
+++ b/benchmarks/benchmarks/selections.py
@@ -66,16 +66,19 @@ class GeoSelectionBench(object):
dynamic_selection,
periodic_selection):
self.u = MDAnalysis.Universe(GRO)
+ try:
+ # set core flags for PBC accounting
+ MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
+ MDAnalysis.core.flags['use_KDTree_routines'] = periodic_selection[1]
+ except AttributeError:
+ # modern MDAnalysis
+ pass
def time_geometric_selections(self,
selection_string,
dynamic_selection,
periodic_selection):
- # set core flags for PBC accounting
- MDAnalysis.core.flags['use_periodic_selections'] = periodic_selection[0]
- MDAnalysis.core.flags['use_KDTree_routines'] = periodic_selection[1]
-
if hasattr(MDAnalysis.Universe, 'select_atoms'):
self.u.select_atoms(selection_string, updating=dynamic_selection)
else:
@richardjgowers or @lilyminium may be able to tell at a glance which subsets of calculations are actually the same before/after flags were in place? I suspect just leaving the benchmark alone may be the way forward, with a new time_ benchmark for "modern" selections.
I don't think we use pkdtree anywhere unless it's explicitly passed in as the chosen method, which as @IAlibay points out we can't do with atom selections. Distance and geometry selections are either brute force or NSGrid depending on how many atoms are involved (<10 = bruteforce) or how big the box is relative to the cutoff. This part of the code doesn't seem to have been changed for 2 years, so I think the tests that don't set 'use_KDTree_routines'=True should still be the same as the versions that have come out since.
https://github.com/MDAnalysis/mdanalysis/blob/343e10a257690e4312673f2a0fa4703b31b2e223/package/MDAnalysis/lib/distances.py#L405
