{"action":"opened","number":261,"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/261","id":34347697,"html_url":"https://github.com/MDAnalysis/mdanalysis/pull/261","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/261.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/261.patch","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/261","number":261,"state":"open","locked":false,"title":"Parallel distance calculations","user":{"login":"richardjgowers","id":9249543,"avatar_url":"https://avatars.githubusercontent.com/u/9249543?v=3","gravatar_id":"","url":"https://api.github.com/users/richardjgowers","html_url":"https://github.com/richardjgowers","followers_url":"https://api.github.com/users/richardjgowers/followers","following_url":"https://api.github.com/users/richardjgowers/following{/other_user}","gists_url":"https://api.github.com/users/richardjgowers/gists{/gist_id}","starred_url":"https://api.github.com/users/richardjgowers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richardjgowers/subscriptions","organizations_url":"https://api.github.com/users/richardjgowers/orgs","repos_url":"https://api.github.com/users/richardjgowers/repos","events_url":"https://api.github.com/users/richardjgowers/events{/privacy}","received_events_url":"https://api.github.com/users/richardjgowers/received_events","type":"User","site_admin":false},"body":"So currently we have a parallel version of distance_array, but these are done in Cython, and only exist if someone does a separate piece of code for a parallel version.\r\n\r\nBy putting openmp statements behind conditional compilation options, we can use the same C code twice, and this then generates a serial and parallel version of each function.  This is nice as it keeps the code DRY, and also all functions exist in the serial/parallel namespace, regardless of whether the directives have been written yet.\r\n\r\nThis needs to have a separate .pyx file, and will generate a different submodule.  This is a little confusing, and arguably there should be a single point of reference for people accessing these functions.  It would be nice to change the call signature to something like\r\n``` python \r\nMDAnalysis.analysis.distances.distance_array(a, b, parallel=True)\r\n```\r\nThen in analysis.distances it chooses one of the correct Cython backends.  Using Flags to default to parallel/not is also possible.\r\n\r\nSo questions that need answering are:\r\n * Will this approach work on all platforms?\r\n * Will it fail properly on platforms without openmp support?\r\n    * I've tried to make it just compile serially if it can't do openmp\r\n * How should we managed serial/parallel versions of identical functions in our 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