Closed yingioi0 closed 1 year ago
Hi, does it work when you set n_jobs=1
, i.e., pyemma.msm.its(cluster.dtrajs, lags=[1, 2, 5, 10, 20, 50], nits=4, errors='bayes', n_jobs=1)
?
Thanks a million! It works immediately. Now all goes well : )
You're welcome, happy to hear that it works :)
Hi, when I follow the jupyter notebook tutorials, I got no return after a very long time in estimating implied timescales from discrete trajectories at the section of MSM estimation and validation ( Case 2 ). Then I have to press ctrl + C and the trace back show below:
The full command history is here ( I just copy it from html document): pdb = mdshare.fetch('alanine-dipeptide-nowater.pdb', working_directory='data') files = mdshare.fetch('alanine-dipeptide-*-250ns-nowater.xtc', working_directory='data') feat = pyemma.coordinates.featurizer(pdb) feat.add_backbone_torsions(periodic=False) data = pyemma.coordinates.load(files, features=feat) data_concatenated = np.concatenate(data) cluster = pyemma.coordinates.cluster_kmeans(data, k=200, max_iter=50, stride=10) its = pyemma.msm.its(cluster.dtrajs, lags=[1, 2, 5, 10, 20, 50], nits=4, errors='bayes')
My related environment list here ( I install PyEMMA via conda ): PyEMMA 2.5.12 numpy 1.23.3 pyemma 2.5.12 mdshare 0.4.2 scipy 1.9.1 IPython : 8.5.0 ipykernel : 6.15.3 ipywidgets : 7.7.2 jupyter_client : 7.3.5 jupyter_core : 4.11.1 jupyter_server : 1.18.1 jupyterlab : 3.4.7 nbclient : 0.6.8 nbconvert : 7.0.0 nbformat : 5.5.0 notebook : 6.4.12 qtconsole : 5.3.2 traitlets : 5.4.0 Python 3.10.6
Any one help me? Thank you!