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nohup.out
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Fatal Python error: init_import_site: Failed to import the site module
Python runtime state: initialized
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site.py", line 589, in <module>
main()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site.py", line 576, in main
known_paths = addsitepackages(known_paths)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site.py", line 359, in addsitepackages
addsitedir(sitedir, known_paths)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site.py", line 208, in addsitedir
addpackage(sitedir, name, known_paths)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site.py", line 169, in addpackage
exec(line)
File "<string>", line 1, in <module>
File "/home/adele/anaconda3/envs/bss/lib/python3.9/importlib/util.py", line 2, in <module>
from . import abc
File "/home/adele/anaconda3/envs/bss/lib/python3.9/importlib/abc.py", line 17, in <module>
from typing import Protocol, runtime_checkable
File "/home/adele/anaconda3/envs/bss/lib/python3.9/typing.py", line 22, in <module>
import collections.abc
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 846, in exec_module
File "<frozen importlib._bootstrap_external>", line 941, in get_code
File "<frozen importlib._bootstrap_external>", line 1040, in get_data
KeyboardInterrupt
[I 13:35:28.846 NotebookApp] Serving notebooks from local directory: /home/adele/Documents/allostery/examples/example_ptp1b
[I 13:35:28.846 NotebookApp] Jupyter Notebook 6.4.12 is running at:
[I 13:35:28.846 NotebookApp] http://localhost:8884/
[I 13:35:28.847 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 14:06:48.789 NotebookApp] 302 GET /tree (127.0.0.1) 2.130000ms
[I 14:06:53.711 NotebookApp] 302 POST /login?next=%2Ftree (127.0.0.1) 819.360000ms
[W 14:07:11.077 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:07:13.714 NotebookApp] Kernel started: bfd79334-860c-4b9c-b536-1594a8b9c561, name: python3
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: 55956333-9cd9-4b93-9040-06c6acf234e0
[I 14:09:12.775 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:09:12.783 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:09:23.985 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:09:23.987 NotebookApp] Notebook analysis/msm.ipynb is not trusted
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
[I 14:11:12.779 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:11:12.781 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:19:12.809 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:19:12.811 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:21:12.866 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:21:12.898 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:23:12.921 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:23:12.923 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:25:13.285 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:25:13.287 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:27:12.938 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:27:12.939 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:31:13.087 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:31:13.100 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:33:13.152 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:33:13.154 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:35:13.180 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:35:13.182 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:37:12.974 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:37:12.976 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:39:13.879 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:39:13.880 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:41:12.803 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:41:12.804 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:43:12.823 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:43:12.837 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:45:12.978 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:45:12.979 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:47:13.892 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:47:13.914 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:49:13.649 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:49:13.651 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:51:13.142 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:51:13.144 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:52:17.927 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:39bc1eb2e2af4b59b8f28c95f32a0d56
[I 14:52:20.684 NotebookApp] Kernel restarted: bfd79334-860c-4b9c-b536-1594a8b9c561
[I 14:52:20.771 NotebookApp] Restoring connection for bfd79334-860c-4b9c-b536-1594a8b9c561:39bc1eb2e2af4b59b8f28c95f32a0d56
[W 14:52:25.289 NotebookApp] Nudge: attempt 10 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 14:52:30.306 NotebookApp] Nudge: attempt 20 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 14:52:35.324 NotebookApp] Nudge: attempt 30 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 14:52:40.341 NotebookApp] Nudge: attempt 40 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[I 14:52:43.015 NotebookApp] Replaying 3 buffered messages
[I 14:53:12.954 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:53:12.956 NotebookApp] Notebook analysis/msm.ipynb is not trusted
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
[I 14:55:12.881 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:55:12.883 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:57:12.878 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:57:12.958 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:59:12.809 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:59:12.890 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:22:31.291 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:39bc1eb2e2af4b59b8f28c95f32a0d56
[I 15:22:34.177 NotebookApp] Kernel restarted: bfd79334-860c-4b9c-b536-1594a8b9c561
[I 15:22:34.264 NotebookApp] Restoring connection for bfd79334-860c-4b9c-b536-1594a8b9c561:39bc1eb2e2af4b59b8f28c95f32a0d56
[W 15:22:38.782 NotebookApp] Nudge: attempt 10 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 15:22:43.798 NotebookApp] Nudge: attempt 20 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 15:22:48.815 NotebookApp] Nudge: attempt 30 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 15:22:53.831 NotebookApp] Nudge: attempt 40 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[I 15:22:56.181 NotebookApp] Replaying 3 buffered messages
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
[I 15:25:12.808 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:25:12.809 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:27:12.832 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:27:12.842 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:31:13.447 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:31:13.449 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:33:12.704 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:33:12.705 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:35:12.679 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:35:12.720 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:37:12.709 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:37:12.711 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:39:12.686 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:39:12.687 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:41:12.722 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:41:12.723 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:43:12.676 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:43:12.678 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:45:12.780 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:45:12.794 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:46:56.303 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:39bc1eb2e2af4b59b8f28c95f32a0d56
[I 15:46:59.047 NotebookApp] Kernel restarted: bfd79334-860c-4b9c-b536-1594a8b9c561
[I 15:46:59.135 NotebookApp] Restoring connection for bfd79334-860c-4b9c-b536-1594a8b9c561:39bc1eb2e2af4b59b8f28c95f32a0d56
[W 15:47:03.653 NotebookApp] Nudge: attempt 10 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 15:47:08.671 NotebookApp] Nudge: attempt 20 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[I 15:47:12.742 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:47:12.744 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[W 15:47:13.689 NotebookApp] Nudge: attempt 30 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[W 15:47:18.707 NotebookApp] Nudge: attempt 40 on kernel bfd79334-860c-4b9c-b536-1594a8b9c561
[I 15:47:18.768 NotebookApp] Replaying 3 buffered messages
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
[I 15:48:31.363 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:48:31.364 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:49:12.638 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:49:12.640 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:51:12.626 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:51:12.627 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:51:38.018 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:51:38.019 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:55:12.654 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:55:12.667 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:57:12.685 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:57:12.687 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:59:12.674 NotebookApp] Saving file at /analysis/msm.ipynb
[W 15:59:12.682 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 16:01:12.631 NotebookApp] Saving file at /analysis/msm.ipynb
[W 16:01:12.632 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 16:03:12.718 NotebookApp] Saving file at /analysis/msm.ipynb
[W 16:03:12.731 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 16:05:12.737 NotebookApp] Saving file at /analysis/msm.ipynb
[W 16:05:12.738 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 16:07:12.784 NotebookApp] Saving file at /analysis/msm.ipynb
[W 16:07:12.785 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[W 19:46:59.136 NotebookApp] WebSocket ping timeout after 119937 ms.
[I 19:47:04.321 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:39bc1eb2e2af4b59b8f28c95f32a0d56
[W 14:25:30.221 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:27:32.304 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:27:32.723 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:27:59.359 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:27:59.381 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:29:04.164 NotebookApp] Saving file at /analysis/msm.ipynb
[W 14:29:04.339 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 14:29:31.800 NotebookApp] Saving file at /analysis/msm.ipynb
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[I 14:48:13.675 NotebookApp] Creating new notebook in /analysis
[I 14:48:26.298 NotebookApp] Kernel started: dfe7f99f-8abe-42f8-ac43-de1547d1ca76, name: python3
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: c7f01ec1-ac14-4ab3-b745-017ecfa793db
[I 14:50:29.265 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
[I 14:51:31.699 NotebookApp] Saving file at /analysis/msm.ipynb
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Error: Number of atoms in NetCDF file (4764) does not match number
Error: in associated topology (4770)!
Error: Could not set up '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/active.nc' for reading.
Error: Could not set up trajectory '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/active.nc'
Error: Number of atoms in NetCDF file (4764) does not match number
Error: in associated topology (4770)!
Error: Could not set up '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/inactive.nc' for reading.
Error: Could not set up trajectory '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/inactive.nc'
[I 14:59:02.268 NotebookApp] Saving file at /analysis/msm.ipynb
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[I 15:03:21.229 NotebookApp] Starting buffering for dfe7f99f-8abe-42f8-ac43-de1547d1ca76:eab2290f8cba40fa846c41cf33ef7c17
[I 15:03:21.487 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:d45b92714bbf46cca013103a952f3769
[W 15:29:25.758 NotebookApp] Notebook analysis/msm.ipynb is not trusted
[I 15:29:27.117 NotebookApp] Discarding 2 buffered messages for bfd79334-860c-4b9c-b536-1594a8b9c561:d45b92714bbf46cca013103a952f3769
Internal Error: in Frame::Frame(int,double*) pointer is NULL.
Internal Error: Size of atoms array is 4770, Frame size is 0
Internal Error: in Frame::Frame(int,double*) pointer is NULL.
Internal Error: Size of atoms array is 4770, Frame size is 0
[I 15:31:27.689 NotebookApp] Saving file at /analysis/msm.ipynb
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[I 15:31:31.335 NotebookApp] Kernel started: 0a49a69d-b439-45ee-a12d-959a22ac7dec, name: python3
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: 6181230d-037a-4193-997a-dfa9eab14455
Error: Number of atoms in NetCDF file (4764) does not match number
Error: in associated topology (4770)!
Error: Could not set up '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/active.nc' for reading.
Error: Could not set up trajectory '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/active.nc'
Error: Number of atoms in NetCDF file (4764) does not match number
Error: in associated topology (4770)!
Error: Could not set up '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/inactive.nc' for reading.
Error: Could not set up trajectory '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/inactive.nc'
[I 15:33:27.173 NotebookApp] Saving file at /analysis/msm.ipynb
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[I 15:33:31.586 NotebookApp] Saving file at /analysis/new_divergence.ipynb
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Error: Number of atoms in NetCDF file (4764) does not match number
Error: in associated topology (4770)!
Error: Could not set up '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/active.nc' for reading.
Error: Could not set up trajectory '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/active.nc'
Error: Number of atoms in NetCDF file (4764) does not match number
Error: in associated topology (4770)!
Error: Could not set up '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/inactive.nc' for reading.
Error: Could not set up trajectory '/home/adele/Documents/allostery/examples/example_ptp1b/systems/reference/inactive.nc'
Internal Error: in Frame::Frame(int,double*) pointer is NULL.
Internal Error: Size of atoms array is 4770, Frame size is 0
Internal Error: in Frame::Frame(int,double*) pointer is NULL.
Internal Error: Size of atoms array is 4770, Frame size is 0
[I 15:35:27.166 NotebookApp] Saving file at /analysis/msm.ipynb
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[I 15:38:02.315 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:ef26e2ef45964d5b82366b228c92a87a
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[I 15:38:11.984 NotebookApp] Kernel started: 62937f19-649a-4c88-99bd-f8dc5b8dbf09, name: python3
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: 895513d5-c0ae-42f4-9111-8b366ce9fce9
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: c9d9776a-05f9-4e8f-9392-c42bd245a473
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/pyemma/util/log.py:41: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(yaml.__version__) >= LooseVersion('5.1'):
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/pyemma/util/log.py:41: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(yaml.__version__) >= LooseVersion('5.1'):
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/analysis/sparse/assessment.py:24: DeprecationWarning: Please use `isdense` from the `scipy.sparse` namespace, the `scipy.sparse.sputils` namespace is deprecated.
from scipy.sparse.sputils import isdense
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/analysis/sparse/assessment.py:25: DeprecationWarning: Please use `diags` from the `scipy.sparse` namespace, the `scipy.sparse.construct` namespace is deprecated.
from scipy.sparse.construct import diags
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/analysis/sparse/expectations.py:29: DeprecationWarning: Please use `diags` from the `scipy.sparse` namespace, the `scipy.sparse.construct` namespace is deprecated.
from scipy.sparse.construct import diags
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/api.py:36: DeprecationWarning: Please use `isdense` from the `scipy.sparse` namespace, the `scipy.sparse.sputils` namespace is deprecated.
from scipy.sparse.sputils import isdense
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/dense/tmat_sampling/tmatrix_sampler.py:37: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
from . sampler_revpi import SamplerRevPi
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py:32: DeprecationWarning: Please use `csr_matrix` from the `scipy.sparse` namespace, the `scipy.sparse.csr` namespace is deprecated.
from scipy.sparse.csr import csr_matrix
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/flux/api.py:28: DeprecationWarning: Please use `issparse` from the `scipy.sparse` namespace, the `scipy.sparse.base` namespace is deprecated.
from scipy.sparse.base import issparse
/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/flux/api.py:29: DeprecationWarning: Please use `isdense` from the `scipy.sparse` namespace, the `scipy.sparse.sputils` namespace is deprecated.
from scipy.sparse.sputils import isdense
[I 15:40:11.786 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[I 15:44:12.336 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
[I 15:45:51.208 NotebookApp] Saving file at /analysis/02_collective_variables.ipynb
[I 15:45:51.829 NotebookApp] Starting buffering for 62937f19-649a-4c88-99bd-f8dc5b8dbf09:e1a4a83e042842ef87f28859e688549a
[I 15:45:58.340 NotebookApp] Kernel shutdown: 62937f19-649a-4c88-99bd-f8dc5b8dbf09
[W 15:45:58.344 NotebookApp] delete /analysis/02_collective_variables.ipynb
[I 15:46:12.478 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[I 15:48:06.415 NotebookApp] Kernel started: 6febe0f4-071e-4701-8757-06945649f8d9, name: python3
[I 15:48:12.423 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: 581714fb-e154-49ce-9107-50bab6095a80
[I 15:50:06.558 NotebookApp] Saving file at /analysis/05_steering_loop_only.ipynb
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[I 15:52:06.538 NotebookApp] Saving file at /analysis/05_steering_loop_only.ipynb
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[I 15:53:57.585 NotebookApp] Starting buffering for dfe7f99f-8abe-42f8-ac43-de1547d1ca76:cba0e6484fce458a99dc0d4c1c0e166e
[I 15:53:57.613 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:32549b98f1ac460586560411d9902b5b
[I 15:53:57.614 NotebookApp] Starting buffering for 6febe0f4-071e-4701-8757-06945649f8d9:cd4a69c9d0574fab8cd793ada87c9c2c
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[IPKernelApp] WARNING | No such comm: 44b64e0a-a819-4b52-8f58-9ed5f6304c78
[I 11:57:38.556 NotebookApp] Saving file at /analysis/05_steering_loop_only.ipynb
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[I 11:58:09.633 NotebookApp] New terminal with automatic name: 1
[I 11:59:37.287 NotebookApp] Saving file at /analysis/05_steering_loop_only.ipynb
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[I 12:01:38.220 NotebookApp] Saving file at /analysis/05_steering_loop_only.ipynb
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[I 12:03:37.381 NotebookApp] Saving file at /analysis/05_steering_loop_only.ipynb
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[I 12:09:37.482 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[I 12:10:31.966 NotebookApp] Saving file at /analysis/05_steering_loop_only.ipynb
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[I 12:11:37.479 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[I 12:20:14.619 NotebookApp] Starting buffering for 6febe0f4-071e-4701-8757-06945649f8d9:45edeea7c83d460d9f22c9b632dc97e9
[I 12:20:21.256 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[I 12:20:30.281 NotebookApp] Kernel shutdown: 6febe0f4-071e-4701-8757-06945649f8d9
[W 12:20:30.281 NotebookApp] delete /analysis/05_steering_loop_only.ipynb
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[W 12:20:42.110 NotebookApp] Notebook analysis/07_more_clusters.ipynb is not trusted
[I 12:20:42.803 NotebookApp] Kernel started: 53e472ea-b57a-42e9-ba83-6b914f3436cd, name: python3
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: 60606c85-f151-40f3-bc91-992a97c809aa
[I 12:21:37.896 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[W 12:34:37.302 NotebookApp] WebSocket ping timeout after 119946 ms.
[W 12:34:37.787 NotebookApp] WebSocket ping timeout after 119932 ms.
[I 12:34:42.306 NotebookApp] Starting buffering for 53e472ea-b57a-42e9-ba83-6b914f3436cd:b7858cf8d8af4c12874401be8a1e7d6d
[I 12:34:42.790 NotebookApp] Starting buffering for dfe7f99f-8abe-42f8-ac43-de1547d1ca76:3e1fd3968b3549b9916e61ccf8c186a3
[W 12:34:52.863 NotebookApp] WebSocket ping timeout after 111132 ms.
[I 12:34:57.865 NotebookApp] Starting buffering for bfd79334-860c-4b9c-b536-1594a8b9c561:06e3ee5f257a4f5dbb7d559d768fe398
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[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: a3457c13-9841-423a-a0cb-1b742d51237f
[I 14:16:01.427 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[I 14:19:41.943 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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[I 14:19:43.745 NotebookApp] Starting buffering for 53e472ea-b57a-42e9-ba83-6b914f3436cd:2e8de89ad06d4c1b937f481b969df370
[I 14:19:48.348 NotebookApp] Saving file at /analysis/msm.ipynb
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[I 14:19:49.325 NotebookApp] Kernel shutdown: 53e472ea-b57a-42e9-ba83-6b914f3436cd
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[I 14:19:59.273 NotebookApp] Kernel started: 5a74d6e3-6276-4cb1-81b8-365b9d6f3258, name: python3
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.control
[IPKernelApp] WARNING | No such comm: 456692ba-467a-49e0-bdd2-c13f76fdd839
[I 14:21:41.819 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
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Process ForkPoolWorker-236:
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Process ForkPoolWorker-232:
Process ForkPoolWorker-226:
Process ForkPoolWorker-234:
Process ForkPoolWorker-224:
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "<__array_function__ internals>", line 177, in sum
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 231, in statistical_inefficiency
prod = x[:Nx-lag] * x[lag:]
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 231, in statistical_inefficiency
prod = x[:Nx-lag] * x[lag:]
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "<__array_function__ internals>", line 177, in sum
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 231, in statistical_inefficiency
prod = x[:Nx-lag] * x[lag:]
KeyboardInterrupt
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 365, in get
res = self._reader.recv_bytes()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/connection.py", line 221, in recv_bytes
buf = self._recv_bytes(maxlength)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/connection.py", line 419, in _recv_bytes
buf = self._recv(4)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/connection.py", line 384, in _recv
chunk = read(handle, remaining)
KeyboardInterrupt
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "<__array_function__ internals>", line 180, in sum
File "<__array_function__ internals>", line 180, in sum
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
File "<__array_function__ internals>", line 180, in sum
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 73, in _wrapreduction
if type(obj) is not mu.ndarray:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "<__array_function__ internals>", line 180, in sum
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
KeyboardInterrupt
KeyboardInterrupt
KeyboardInterrupt
KeyboardInterrupt
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "<__array_function__ internals>", line 180, in sum
File "<__array_function__ internals>", line 180, in sum
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 70, in _wrapreduction
passkwargs = {k: v for k, v in kwargs.items()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 71, in <dictcomp>
if v is not np._NoValue}
KeyboardInterrupt
KeyboardInterrupt
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "<__array_function__ internals>", line 180, in sum
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 70, in _wrapreduction
passkwargs = {k: v for k, v in kwargs.items()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 71, in <dictcomp>
if v is not np._NoValue}
KeyboardInterrupt
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "<__array_function__ internals>", line 180, in sum
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 69, in _wrapreduction
def _wrapreduction(obj, ufunc, method, axis, dtype, out, **kwargs):
KeyboardInterrupt
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/estimation/sparse/effective_counts.py", line 107, in _wrapper
partial[n] = statistical_inefficiency(s, truncate_acf=truncate_acf, mact=mact)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/msmtools/util/statistics.py", line 232, in statistical_inefficiency
acf += np.sum(prod)
File "<__array_function__ internals>", line 180, in sum
File "<__array_function__ internals>", line 180, in sum
File "<__array_function__ internals>", line 180, in sum
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2296, in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 70, in _wrapreduction
passkwargs = {k: v for k, v in kwargs.items()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 71, in <dictcomp>
if v is not np._NoValue}
KeyboardInterrupt
KeyboardInterrupt
KeyboardInterrupt
[I 15:03:41.318 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
[W 15:03:41.320 NotebookApp] Notebook analysis/supplementary_information.ipynb is not trusted
[I 15:05:08.909 NotebookApp] Kernel interrupted: dfe7f99f-8abe-42f8-ac43-de1547d1ca76
[I 15:05:41.343 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
[W 15:05:41.344 NotebookApp] Notebook analysis/supplementary_information.ipynb is not trusted
[I 15:06:02.253 NotebookApp] Saving file at /analysis/supplementary_information.ipynb
[W 15:06:02.254 NotebookApp] Notebook analysis/supplementary_information.ipynb is not trusted
Process ForkPoolWorker-250:
Process ForkPoolWorker-252:
Process ForkPoolWorker-258:
Process ForkPoolWorker-241:
Process ForkPoolWorker-251:
Process ForkPoolWorker-244:
Process ForkPoolWorker-257:
Process ForkPoolWorker-247:
Process ForkPoolWorker-254:
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Process ForkPoolWorker-243:
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
KeyboardInterrupt
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
Traceback (most recent call last):
KeyboardInterrupt
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Process ForkPoolWorker-256:
Process ForkPoolWorker-245:
Process ForkPoolWorker-253:
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Process ForkPoolWorker-249:
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Process ForkPoolWorker-248:
Process ForkPoolWorker-242:
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/synchronize.py", line 95, in __enter__
return self._semlock.__enter__()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/adele/anaconda3/envs/bss/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)