markovmodel
unable to execute
I installed it using pip3. but unable to execute from jupyter notebook or from command line. the error given bellow
Command line error ~/Desktop$ python3 Python 3.9.5 (default, Jun 4 2021, 12:28:51) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.
import pyemma Traceback (most recent call last): File "
", line 1, in File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/pyemma/init.py", line 34, in from . import msm File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/pyemma/msm/init.py", line 83, in from msmtools.analysis.dense.pcca import PCCA File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/msmtools/init.py", line 41, in from . import estimation File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/msmtools/estimation/init.py", line 91, in from .api import * File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/msmtools/estimation/api.py", line 38, in from . import dense File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/msmtools/estimation/dense/init.py", line 24, in from .mle import mle_trev, mle_trev_given_pi File "msmtools/estimation/dense/mle/mle_trev.pyx", line 1, in init msmtools.estimation.dense.mle.mle_trev ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Jupyter notebook issue !pip3 install pyemma Requirement already satisfied: pyemma in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (2.5.11) Requirement already satisfied: tqdm>=4.23 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pyemma) (4.62.3) Requirement already satisfied: psutil>=3.1.1 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pyemma) (5.8.0) Requirement already satisfied: mdtraj>=1.9.2 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pyemma) (1.9.7) Requirement already satisfied: decorator>=4.0.0 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pyemma) (5.1.1) Requirement already satisfied: matplotlib in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pyemma) (3.5.0) Requirement already satisfied: bhmm<0.7,>=0.6 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pyemma) (0.6.3) Requirement already satisfied: msmtools>=1.2 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pyemma) (1.2.6) ....................... ...................... Requirement already satisfied: multiprocess>=0.70.12 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from pathos->pyemma) (0.70.12.2) Requirement already satisfied: joblib>=0.11 in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (from scikit-learn->deeptime->pyemma) (1.1.0)
import pyemma
ModuleNotFoundError Traceback (most recent call last)
/tmp/ipykernel_3014/684328617.py in
ModuleNotFoundError: No module named 'pyemma'
Same with Mdshare
It looks like this is an incompatibility issue with msmtools. Can you install msmtools with conda instead of pip and try again?
