{"action":"created","issue":{"url":"https://api.github.com/repos/FoldingAtHome/openmm/issues/3","labels_url":"https://api.github.com/repos/FoldingAtHome/openmm/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/FoldingAtHome/openmm/issues/3/comments","events_url":"https://api.github.com/repos/FoldingAtHome/openmm/issues/3/events","html_url":"https://github.com/FoldingAtHome/openmm/pull/3","id":100136528,"number":3,"title":"Ensure neighbor list is large enough on first step","user":{"login":"peastman","id":4379786,"avatar_url":"https://avatars.githubusercontent.com/u/4379786?v=3","gravatar_id":"","url":"https://api.github.com/users/peastman","html_url":"https://github.com/peastman","followers_url":"https://api.github.com/users/peastman/followers","following_url":"https://api.github.com/users/peastman/following{/other_user}","gists_url":"https://api.github.com/users/peastman/gists{/gist_id}","starred_url":"https://api.github.com/users/peastman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peastman/subscriptions","organizations_url":"https://api.github.com/users/peastman/orgs","repos_url":"https://api.github.com/users/peastman/repos","events_url":"https://api.github.com/users/peastman/events{/privacy}","received_events_url":"https://api.github.com/users/peastman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-08-10T18:30:36Z","updated_at":"2015-08-11T21:53:44Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/FoldingAtHome/openmm/pulls/3","html_url":"https://github.com/FoldingAtHome/openmm/pull/3","diff_url":"https://github.com/FoldingAtHome/openmm/pull/3.diff","patch_url":"https://github.com/FoldingAtHome/openmm/pull/3.patch"},"body":"I believe this fixes https://github.com/FoldingAtHome/openmm-core/issues/56.  *Please test this*.  I verified that similar changes in the master version fix the problem with John's Python script, but I'm not set up to be able to easily run Python scripts against the core21 code."},"comment":{"url":"https://api.github.com/repos/FoldingAtHome/openmm/issues/comments/130089557","html_url":"https://github.com/FoldingAtHome/openmm/pull/3#issuecomment-130089557","issue_url":"https://api.github.com/repos/FoldingAtHome/openmm/issues/3","id":130089557,"user":{"login":"peastman","id":4379786,"avatar_url":"https://avatars.githubusercontent.com/u/4379786?v=3","gravatar_id":"","url":"https://api.github.com/users/peastman","html_url":"https://github.com/peastman","followers_url":"https://api.github.com/users/peastman/followers","following_url":"https://api.github.com/users/peastman/following{/other_user}","gists_url":"https://api.github.com/users/peastman/gists{/gist_id}","starred_url":"https://api.github.com/users/peastman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peastman/subscriptions","organizations_url":"https://api.github.com/users/peastman/orgs","repos_url":"https://api.github.com/users/peastman/repos","events_url":"https://api.github.com/users/peastman/events{/privacy}","received_events_url":"https://api.github.com/users/peastman/received_events","type":"User","site_admin":false},"created_at":"2015-08-11T21:53:44Z","updated_at":"2015-08-11T21:53:44Z","body":"The best thing is to run it on Windows.  If this were the CUDA platform, you could use nvprof or nvvp to get the kernel execution time, but that doesn't support OpenCL anymore.\r\n\r\nBy the way, instead of calling step(1), I'd suggest called getState(getForces=True).  That makes it return the forces back to the host, which ensures all the kernels have really executed.  step(1) can potentially just add the kernels to the queue and return immediately."}}