{"action":"opened","issue":{"url":"https://api.github.com/repos/msmbuilder/msmbuilder/issues/662","labels_url":"https://api.github.com/repos/msmbuilder/msmbuilder/issues/662/labels{/name}","comments_url":"https://api.github.com/repos/msmbuilder/msmbuilder/issues/662/comments","events_url":"https://api.github.com/repos/msmbuilder/msmbuilder/issues/662/events","html_url":"https://github.com/msmbuilder/msmbuilder/issues/662","id":110430527,"number":662,"title":"Memory error using command line msmb AtomPairsFeaturizer","user":{"login":"jeiros","id":10696140,"avatar_url":"https://avatars.githubusercontent.com/u/10696140?v=3","gravatar_id":"","url":"https://api.github.com/users/jeiros","html_url":"https://github.com/jeiros","followers_url":"https://api.github.com/users/jeiros/followers","following_url":"https://api.github.com/users/jeiros/following{/other_user}","gists_url":"https://api.github.com/users/jeiros/gists{/gist_id}","starred_url":"https://api.github.com/users/jeiros/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeiros/subscriptions","organizations_url":"https://api.github.com/users/jeiros/orgs","repos_url":"https://api.github.com/users/jeiros/repos","events_url":"https://api.github.com/users/jeiros/events{/privacy}","received_events_url":"https://api.github.com/users/jeiros/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-10-08T11:43:53Z","updated_at":"2015-10-08T11:43:53Z","closed_at":null,"body":"Hi eveyone, \r\n\r\nI've encountered the following error when trying to apply the same commands as the command line tutorial http://msmbuilder.org/latest/commandline.html on my data (larger than the alanine-dipeptide)\r\n\r\nTraceback (most recent call last):\r\n  File \"/home/je714/anaconda3/bin/msmb\", line 6, in <module>\r\n    sys.exit(main())\r\n  File \"/home/je714/anaconda3/lib/python3.4/site-packages/msmbuilder-3.3.0-py3.4-linux-x86_64.egg/msmbuilder/scripts/msmb.py\", line 28, in main\r\n    app.start()\r\n  File \"/home/je714/anaconda3/lib/python3.4/site-packages/msmbuilder-3.3.0-py3.4-linux-x86_64.egg/msmbuilder/cmdline.py\", line 440, in start\r\n    instance.start()\r\n  File \"/home/je714/anaconda3/lib/python3.4/site-packages/msmbuilder-3.3.0-py3.4-linux-x86_64.egg/msmbuilder/commands/featurizer.py\", line 62, in start\r\n    trajectory.append(self.instance.partial_transform(chunk))\r\n  File \"/home/je714/anaconda3/lib/python3.4/site-packages/msmbuilder-3.3.0-py3.4-linux-x86_64.egg/msmbuilder/featurizer/featurizer.py\", line 250, in partial_transform\r\n    d = md.geometry.compute_distances(traj, self.pair_indices, periodic=self.periodic)\r\n  File \"/home/je714/anaconda3/lib/python3.4/site-packages/mdtraj/geometry/distance.py\", line 84, in compute_distances\r\n    out = np.empty((xyz.shape[0], pairs.shape[0]), dtype=np.float32)\r\nMemoryError\r\n\r\nIs the command line only suitable for small subsets of MD data? I've tried feeding the same MD data with one big file or in different chunks, makes no difference. Actually this is only a small subset of my complete dataset, is my only option to use the python API and mdtraj's iterload? For quick trials the command line is actually more suitable... \r\n\r\nThanks in advance\r\n"}}