yank
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Published
20 hours ago •
choderalab
choderalab
Load() missing one argument
getting the following error when running yank analyze report --store=experiments --output=yank_output.ipynb --format ipynb:
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Rendering notebook as a .ipynb file...
Processing notebook now, this may take a while...
Traceback (most recent call last):
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/bin/yank", line 10, in <module>
sys.exit(main())
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 123, in dispatch
return dispatch_report(args)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 322, in dispatch_report
run_notebook(store, output, notebook_serial_file, **analyzer_kwargs)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 281, in run_notebook
processed_notebook, resources = ep.preprocess(loaded_notebook, resource_data)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 91, in preprocess
self.preprocess_cell(cell, resources, index)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 112, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 85, in wrapped
return just_run(coro(*args, **kwargs))
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 60, in just_run
return loop.run_until_complete(coro)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nest_asyncio.py", line 90, in run_until_complete
return f.result()
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/futures.py", line 201, in result
raise self._exception.with_traceback(self._exception_tb)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/tasks.py", line 232, in __step
result = coro.send(None)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 1019, in async_execute_cell
await self._check_raise_for_error(cell, cell_index, exec_reply)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 913, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
from matplotlib import pyplot as plt
from yank.reports import notebook
%matplotlib inline
report = notebook.HealthReportData(store_directory, **analyzer_kwargs)
report.report_version()
------------------
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In [2], line 4
2 from yank.reports import notebook
3 get_ipython().run_line_magic('matplotlib', 'inline')
----> 4 report = notebook.HealthReportData(store_directory, **analyzer_kwargs)
5 report.report_version()
File ~/.conda/envs/myenv/lib/python3.10/site-packages/yank/analyze.py:299, in ExperimentAnalyzer.__init__(self, store_directory, **analyzer_kwargs)
297 raise RuntimeError(err_msg)
298 with open(analysis_script_path, 'r') as f:
--> 299 analysis = yaml.load(f)
300 phases_names = []
301 signs = {}
TypeError: load() missing 1 required positional argument: 'Loader'
TypeError: load() missing 1 required positional argument: 'Loader'
2022-11-03 15:14:21,028: CRITICAL - mpiplus.mpiplus - MPI node 1/1 raised an exception and called Abort()! The exception traceback follows
Traceback (most recent call last):
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/bin/yank", line 10, in <module>
sys.exit(main())
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 123, in dispatch
return dispatch_report(args)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 322, in dispatch_report
run_notebook(store, output, notebook_serial_file, **analyzer_kwargs)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 281, in run_notebook
processed_notebook, resources = ep.preprocess(loaded_notebook, resource_data)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 91, in preprocess
self.preprocess_cell(cell, resources, index)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 112, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 85, in wrapped
return just_run(coro(*args, **kwargs))
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 60, in just_run
return loop.run_until_complete(coro)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nest_asyncio.py", line 90, in run_until_complete
return f.result()
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/futures.py", line 201, in result
raise self._exception.with_traceback(self._exception_tb)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/tasks.py", line 232, in __step
result = coro.send(None)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 1019, in async_execute_cell
await self._check_raise_for_error(cell, cell_index, exec_reply)
File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 913, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
from matplotlib import pyplot as plt
from yank.reports import notebook
%matplotlib inline
report = notebook.HealthReportData(store_directory, **analyzer_kwargs)
report.report_version()
------------------
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In [2], line 4
2 from yank.reports import notebook
3 get_ipython().run_line_magic('matplotlib', 'inline')
----> 4 report = notebook.HealthReportData(store_directory, **analyzer_kwargs)
5 report.report_version()
File ~/.conda/envs/myenv/lib/python3.10/site-packages/yank/analyze.py:299, in ExperimentAnalyzer.__init__(self, store_directory, **analyzer_kwargs)
297 raise RuntimeError(err_msg)
298 with open(analysis_script_path, 'r') as f:
--> 299 analysis = yaml.load(f)
300 phases_names = []
301 signs = {}
TypeError: load() missing 1 required positional argument: 'Loader'
TypeError: load() missing 1 required positional argument: 'Loader'
