{"action":"created","issue":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/9","labels_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/9/comments","events_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/9/events","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/9","id":42061581,"number":9,"title":"Inchworm CPU option not filling out all files","user":{"login":"benfulton","id":46128,"avatar_url":"https://avatars.githubusercontent.com/u/46128?v=3","gravatar_id":"","url":"https://api.github.com/users/benfulton","html_url":"https://github.com/benfulton","followers_url":"https://api.github.com/users/benfulton/followers","following_url":"https://api.github.com/users/benfulton/following{/other_user}","gists_url":"https://api.github.com/users/benfulton/gists{/gist_id}","starred_url":"https://api.github.com/users/benfulton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benfulton/subscriptions","organizations_url":"https://api.github.com/users/benfulton/orgs","repos_url":"https://api.github.com/users/benfulton/repos","events_url":"https://api.github.com/users/benfulton/events{/privacy}","received_events_url":"https://api.github.com/users/benfulton/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"benfulton","id":46128,"avatar_url":"https://avatars.githubusercontent.com/u/46128?v=3","gravatar_id":"","url":"https://api.github.com/users/benfulton","html_url":"https://github.com/benfulton","followers_url":"https://api.github.com/users/benfulton/followers","following_url":"https://api.github.com/users/benfulton/following{/other_user}","gists_url":"https://api.github.com/users/benfulton/gists{/gist_id}","starred_url":"https://api.github.com/users/benfulton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benfulton/subscriptions","organizations_url":"https://api.github.com/users/benfulton/orgs","repos_url":"https://api.github.com/users/benfulton/repos","events_url":"https://api.github.com/users/benfulton/events{/privacy}","received_events_url":"https://api.github.com/users/benfulton/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2014-09-05T16:01:14Z","updated_at":"2015-09-22T15:56:51Z","closed_at":null,"body":"User reports requesting 24 CPU but in working directory only 2 files are filled. He was able to work around the issue by setting OpenMP variables on the cluster:\r\n\r\nexport OMP_NUM_THREADS=28\r\nexport OMP_THREAD_LIMIT=29\r\n\r\nIn IRKE.cpp, the number of files created is equal to the return value of omp_get_max_threads().\r\nThis is an upper bound on the number of threads that can be created in a subsequent\r\nparallel region; however, the requested number of threads is not guaranteed to be created unless\r\nunless the dynamic adjustment of threads is disabled, either via the omp_dynamic(false) routine,\r\nor by setting the OMP_DYNAMIC environment variable to \"false\".\r\n\r\nThis generally isn't an issue on systems that don't have other concurrent users, but\r\nthe OpenMP specification does allow an implementation to create any number of threads\r\nless than or equal to the number of threads requested unless the dynamic adjustment of\r\nthreads is disabled.\r\n"},"comment":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/comments/142332289","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/9#issuecomment-142332289","issue_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/9","id":142332289,"user":{"login":"benfulton","id":46128,"avatar_url":"https://avatars.githubusercontent.com/u/46128?v=3","gravatar_id":"","url":"https://api.github.com/users/benfulton","html_url":"https://github.com/benfulton","followers_url":"https://api.github.com/users/benfulton/followers","following_url":"https://api.github.com/users/benfulton/following{/other_user}","gists_url":"https://api.github.com/users/benfulton/gists{/gist_id}","starred_url":"https://api.github.com/users/benfulton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benfulton/subscriptions","organizations_url":"https://api.github.com/users/benfulton/orgs","repos_url":"https://api.github.com/users/benfulton/repos","events_url":"https://api.github.com/users/benfulton/events{/privacy}","received_events_url":"https://api.github.com/users/benfulton/received_events","type":"User","site_admin":false},"created_at":"2015-09-22T15:56:51Z","updated_at":"2015-09-22T15:56:51Z","body":"I would prefer to change the iworm code. Setting the dynamic would be suboptimal for the system as a whole."}}