{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/287","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/287/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/287/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/287/events","html_url":"https://github.com/Acellera/htmd/issues/287","id":215898960,"number":287,"title":"error during adaptive sampling","user":{"login":"funnybomb","id":3928507,"avatar_url":"https://avatars3.githubusercontent.com/u/3928507?v=3","gravatar_id":"","url":"https://api.github.com/users/funnybomb","html_url":"https://github.com/funnybomb","followers_url":"https://api.github.com/users/funnybomb/followers","following_url":"https://api.github.com/users/funnybomb/following{/other_user}","gists_url":"https://api.github.com/users/funnybomb/gists{/gist_id}","starred_url":"https://api.github.com/users/funnybomb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/funnybomb/subscriptions","organizations_url":"https://api.github.com/users/funnybomb/orgs","repos_url":"https://api.github.com/users/funnybomb/repos","events_url":"https://api.github.com/users/funnybomb/events{/privacy}","received_events_url":"https://api.github.com/users/funnybomb/received_events","type":"User","site_admin":false},"labels":[{"id":265455043,"url":"https://api.github.com/repos/Acellera/htmd/labels/help%20wanted","name":"help wanted","color":"159818","default":true}],"state":"open","locked":false,"assignee":{"login":"stefdoerr","id":7935362,"avatar_url":"https://avatars0.githubusercontent.com/u/7935362?v=3","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false},"assignees":[{"login":"stefdoerr","id":7935362,"avatar_url":"https://avatars0.githubusercontent.com/u/7935362?v=3","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2017-03-21T22:33:25Z","updated_at":"2017-03-26T23:25:58Z","closed_at":null,"body":"hi, I am using adaptive samplie by \r\n```python\r\n# set up\r\nfrom htmd import *\r\nfrom htmd.protocols.production_v4 import Production\r\n\r\nmd = Production()\r\nmd.runtime = 10\r\nmd.timeunits = 'ns'\r\nmd.temperature  = 300\r\nmd.acemd.bincoordinates = 'output.coor'\r\nmd.acemd.extendedsystem  = 'output.xsc'\r\nmd.acemd.binvelocities = None\r\nmd.write('equil','prod_adaptive')\r\n\r\n## run\r\nmd = AdaptiveMD()\r\nmd.nmin=3\r\nmd.nmax=5\r\nmd.nepochs = 80\r\nmd.app = AcemdLocal(datadir='./data/')\r\n#md.app = AcemdLocal()\r\nmd.generatorspath='./prod_adaptive'\r\n#md.datapath = './data/'\r\nmd.projection=[MetricDihedral()]\r\nmd.ticadim = 3\r\nmd.updateperiod = 7200 # execute every 2 hours\r\nmd.run()\r\n\r\n```\r\nI got exit and the log file is \r\n```\r\n2017-03-21 18:37:01,386 - htmd.molecule.readers - WARNING - Non-integer values were read from the PDB \"serial\" field. Dropping PDB values and assigning new ones.\r\n2017-03-21 18:37:01,389 - htmd.molecule.readers - WARNING - Non-integer values were read from the PDB \"serial\" field. Dropping PDB values and assigning new ones.\r\n2017-03-21 18:37:04,083 - htmd.molecule.readers - WARNING - Reading PDB file with more than 99999 atoms. Bond information can be wrong.\r\n2017-03-21 18:37:04,087 - htmd.molecule.readers - WARNING - Reading PDB file with more than 99999 atoms. Bond information can be wrong.\r\n\r\n2017-03-21 18:37:37,733 - htmd.projections.metric - INFO - Frame step 0.1ns was read from the trajectories. If it looks wrong, redefine it by manually setting the MetricData.fstep property.\r\n2017-03-21 18:37:37,733 - htmd.metricdata - INFO - Dropped 0 trajectories from 2 resulting in 2\r\n2017-03-21 18:39:03,815 - htmd.metricdata - INFO - Dropped 0 trajectories from 2 resulting in 2\r\n```\r\n```pytb\r\n/home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/decomposition.py:545: SpectralWarning: Multiple eigenvalues with magnitude one.\r\n  warnings.warn('Multiple eigenvalues with magnitude one.', SpectralWarning)\r\n\r\n\r\nTraceback (most recent call last):\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/pyemma/msm/models/msm.py\", line 910, in pcca\r\n    if self._pcca.n_metastable != m:\r\nAttributeError: 'MaximumLikelihoodMSM' object has no attribute '_pcca'\r\n\r\nDuring handling of the above exception, another exception occurred:\r\n\r\nTraceback (most recent call last):\r\n  File \"run_adaptive.py\", line 14, in <module>\r\n    md.run()\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/htmd/adaptive/adaptive.py\", line 99, in run\r\n    flag = self._algorithm()\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/htmd/adaptive/adaptiverun.py\", line 127, in _algorithm\r\n    self._createMSM(data)\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/htmd/adaptive/adaptiverun.py\", line 170, in _createMSM\r\n    self._model.markovModel(self.lag, self._numMacrostates(data))\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/htmd/model.py\", line 86, in markovModel\r\n    self.coarsemsm = self.msm.pcca(macronum)\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/pyemma/msm/models/msm.py\", line 915, in pcca\r\n    self._pcca = PCCA(self.transition_matrix, m)\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/api.py\", line 1450, in _pcca_object\r\n    return dense.pcca.PCCA(T, m)\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py\", line 535, in __init__\r\n    self._M = pcca(P, m)\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py\", line 430, in pcca\r\n    chi[component, ipcca:ipcca + m_by_component] = _pcca_connected(closed_components_Psub[i], m_by_component)\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py\", line 299, in _pcca_connected\r\n    (chi, rot_matrix) = _pcca_connected_isa(evecs, n)\r\n  File \"/home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py\", line 83, in _pcca_connected_isa\r\n    assert diffs[1] > 1e-6, \"An eigenvector after the first one is constant. \" \\\r\nAssertionError: An eigenvector after the first one is constant. Probably the eigenvectors are incorrectly sorted. Cannot do PCCA.\r\n```"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/289325197","html_url":"https://github.com/Acellera/htmd/issues/287#issuecomment-289325197","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/287","id":289325197,"user":{"login":"funnybomb","id":3928507,"avatar_url":"https://avatars3.githubusercontent.com/u/3928507?v=3","gravatar_id":"","url":"https://api.github.com/users/funnybomb","html_url":"https://github.com/funnybomb","followers_url":"https://api.github.com/users/funnybomb/followers","following_url":"https://api.github.com/users/funnybomb/following{/other_user}","gists_url":"https://api.github.com/users/funnybomb/gists{/gist_id}","starred_url":"https://api.github.com/users/funnybomb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/funnybomb/subscriptions","organizations_url":"https://api.github.com/users/funnybomb/orgs","repos_url":"https://api.github.com/users/funnybomb/repos","events_url":"https://api.github.com/users/funnybomb/events{/privacy}","received_events_url":"https://api.github.com/users/funnybomb/received_events","type":"User","site_admin":false},"created_at":"2017-03-26T23:25:58Z","updated_at":"2017-03-26T23:25:58Z","body":"the log is below:\r\n```\r\n2017-03-27 06:14:43,662 - conda.base.context - INFO - No cio_test package found.\r\n\r\nPlease cite HTMD: Doerr et al.(2016)JCTC,12,1845. https://dx.doi.org/10.1021/acs.jctc.6b00049\r\n\r\nHTMD Documentation at: https://www.htmd.org/docs/latest/\r\n\r\nUsing Anaconda API: https://api.anaconda.org\r\nNew devel HTMD version (1.7.14 python[==3.5,==3.6]) is available. You are currently on (1.7.13). Use 'conda update -c acellera htmd' to update to the new version. You might need to update your python version as well if there is no release for your current version.\r\n\r\n/home/funnybomb/MD/reanalysis/3rbz_run/adaptive/run_adaptive.py:7: DeprecationWarning: The `AcemdLocal` class has been deprecated since version 1.5.15. Use `htmd.queues.localqueue.LocalGPUQueue` instead.\r\n  md.app = AcemdLocal(datadir='./data/')\r\n```\r\nand I did what you told @j3mdamas , below is the result\r\n```\r\n> /home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py(83)_pcca_connected_isa()\r\n     81     assert diffs[0] < 1e-6, \"First eigenvector is not constant. This indicates that the transition matrix \" \\\r\n     82                             \"is not connected or the eigenvectors are incorrectly sorted. Cannot do PCCA.\"\r\n---> 83     assert diffs[1] > 1e-6, \"An eigenvector after the first one is constant. \" \\\r\n     84                             \"Probably the eigenvectors are incorrectly sorted. Cannot do PCCA.\"\r\n     85 \r\n\r\nipdb> \r\nipdb> up\r\n> /home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py(299)_pcca_connected()\r\n    297 \r\n    298     # create initial solution using PCCA+. This could have negative memberships\r\n--> 299     (chi, rot_matrix) = _pcca_connected_isa(evecs, n)\r\n    300 \r\n    301     #print \"initial chi = \\n\",chi\r\n\r\nipdb> up\r\n> /home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py(430)pcca()\r\n    428         elif (m_by_component > 1):\r\n    429             #print \"submatrix: \",closed_components_Psub[i]\r\n--> 430             chi[component, ipcca:ipcca + m_by_component] = _pcca_connected(closed_components_Psub[i], m_by_component)\r\n    431             ipcca += m_by_component\r\n    432         else:\r\n\r\nipdb> up\r\n> /home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/dense/pcca.py(535)__init__()\r\n    533         # PCCA memberships\r\n    534         # TODO: can be improved. pcca computes stationary distribution internally, we don't need to compute it twice.\r\n--> 535         self._M = pcca(P, m)\r\n    536 \r\n    537         # stationary distribution\r\n\r\nipdb> up\r\n> /home/funnybomb/anaconda3/lib/python3.5/site-packages/msmtools/analysis/api.py(1450)_pcca_object()\r\n   1448         T = T.toarray()\r\n   1449     T = _types.ensure_ndarray(T, ndim=2, uniform=True, kind='numeric')\r\n-> 1450     return dense.pcca.PCCA(T, m)\r\n   1451 \r\n   1452 \r\n```"}}
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