{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank/issues/1100","repository_url":"https://api.github.com/repos/choderalab/yank","labels_url":"https://api.github.com/repos/choderalab/yank/issues/1100/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank/issues/1100/comments","events_url":"https://api.github.com/repos/choderalab/yank/issues/1100/events","html_url":"https://github.com/choderalab/yank/issues/1100","id":366073095,"node_id":"MDU6SXNzdWUzNjYwNzMwOTU=","number":1100,"title":"Yank 0.23.5 netCDF4 Index Error","user":{"login":"nividic","id":12229053,"node_id":"MDQ6VXNlcjEyMjI5MDUz","avatar_url":"https://avatars1.githubusercontent.com/u/12229053?v=4","gravatar_id":"","url":"https://api.github.com/users/nividic","html_url":"https://github.com/nividic","followers_url":"https://api.github.com/users/nividic/followers","following_url":"https://api.github.com/users/nividic/following{/other_user}","gists_url":"https://api.github.com/users/nividic/gists{/gist_id}","starred_url":"https://api.github.com/users/nividic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nividic/subscriptions","organizations_url":"https://api.github.com/users/nividic/orgs","repos_url":"https://api.github.com/users/nividic/repos","events_url":"https://api.github.com/users/nividic/events{/privacy}","received_events_url":"https://api.github.com/users/nividic/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-10-02T20:47:10Z","updated_at":"2018-10-02T20:56:00Z","closed_at":null,"author_association":"NONE","body":"Hi there, I was testing the latest Yank release 0.23.5. I was performing solvation free energy calculation on phenol. I stopped the system after 100 iterations to compute the free energy and then I restarted the system till 300 yank iterations. Unfortunately around 200 iterations, Yank was generating the following error:\r\n\r\n```Traceback (most recent call last):\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/bin/yank\", line 11, in <module>\r\n   load_entry_point('yank==0.23.5', 'console_scripts', 'yank')()\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/cli.py\", line 73, in main\r\n   dispatched = getattr(commands, command).dispatch(command_args)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/commands/script.py\", line 138, in dispatch\r\n   yaml_builder.run_experiments()\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/experiment.py\", line 791, in run_experiments\r\n   completed[exp_index] = self._run_experiment(exp)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/experiment.py\", line 3124, in _run_experiment\r\n   built_experiment.run(n_iterations=switch_experiment_interval)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/experiment.py\", line 476, in run\r\n   alchemical_phase.run(n_iterations=iterations_to_run)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/yank.py\", line 1209, in run\r\n   self._sampler.run(n_iterations=n_iterations)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/multistate/multistatesampler.py\", line 685, in run\r\n   self._report_iteration()\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/mpi.py\", line 271, in _wrapper\r\n   return run_single_node(rank, task, *args, **kwargs)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/mpi.py\", line 220, in run_single_node\r\n   result = task(*args, **kwargs)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/mpi.py\", line 621, in _delayed_termination\r\n   return func(*args, **kwargs)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/openmmtools/utils.py\", line 87, in _wrapper\r\n   return func(*args, **kwargs)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/multistate/multistatesampler.py\", line 1104, in _report_iteration\r\n   self._reporter.write_timestamp(self._iteration)\r\n File \"/home/gcalabro/local/miniconda3/envs/openeye_data_record/lib/python3.5/site-packages/yank/multistate/multistatereporter.py\", line 996, in write_timestamp\r\n   self._storage_checkpoint.variables['timestamp'][checkpoint_iteration] = timestamp\r\n File \"netCDF4/_netCDF4.pyx\", line 4299, in netCDF4._netCDF4.Variable.__setitem__\r\n File \"netCDF4/_netCDF4.pyx\", line 4213, in netCDF4._netCDF4.Variable._assign_vlen\r\nIndexError: data can only be assigned to VLEN variables using integer indices\r\n2018-10-02 14:35:36,695: Single node: executing <bound method MultiStateReporter.close of <yank.multistate.multistatereporter.MultiStateReporter object at 0x7f9279adf400>>\r\n```\r\n\r\nThis has happened multiple times already at different number of Yank iterations in different runs. I have attached the last yank run data here: \r\n\r\nhttps://drive.google.com/open?id=1-4_d-cNyx2SWqlr2s4DGoQ2GuBIkewO9\r\n\r\nPlease let me know if you need further info"},"comment":{"url":"https://api.github.com/repos/choderalab/yank/issues/comments/426427036","html_url":"https://github.com/choderalab/yank/issues/1100#issuecomment-426427036","issue_url":"https://api.github.com/repos/choderalab/yank/issues/1100","id":426427036,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNjQyNzAzNg==","user":{"login":"andrrizzi","id":1682142,"node_id":"MDQ6VXNlcjE2ODIxNDI=","avatar_url":"https://avatars3.githubusercontent.com/u/1682142?v=4","gravatar_id":"","url":"https://api.github.com/users/andrrizzi","html_url":"https://github.com/andrrizzi","followers_url":"https://api.github.com/users/andrrizzi/followers","following_url":"https://api.github.com/users/andrrizzi/following{/other_user}","gists_url":"https://api.github.com/users/andrrizzi/gists{/gist_id}","starred_url":"https://api.github.com/users/andrrizzi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrrizzi/subscriptions","organizations_url":"https://api.github.com/users/andrrizzi/orgs","repos_url":"https://api.github.com/users/andrrizzi/repos","events_url":"https://api.github.com/users/andrrizzi/events{/privacy}","received_events_url":"https://api.github.com/users/andrrizzi/received_events","type":"User","site_admin":false},"created_at":"2018-10-02T20:56:00Z","updated_at":"2018-10-02T20:56:00Z","author_association":"CONTRIBUTOR","body":"I've noticed this\r\n```yaml\r\noptions:\r\n    ...\r\n    checkpoint_interval: 300\r\n```\r\nDid you change the `checkpoint_interval` after running the first 100 iterations? If so, it should be ignored, but maybe it's causing some problems we haven't seen before."}}
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