{"action":"created","issue":{"url":"https://api.github.com/repos/radical-cybertools/radical.repex/issues/79","repository_url":"https://api.github.com/repos/radical-cybertools/radical.repex","labels_url":"https://api.github.com/repos/radical-cybertools/radical.repex/issues/79/labels{/name}","comments_url":"https://api.github.com/repos/radical-cybertools/radical.repex/issues/79/comments","events_url":"https://api.github.com/repos/radical-cybertools/radical.repex/issues/79/events","html_url":"https://github.com/radical-cybertools/radical.repex/issues/79","id":149467662,"number":79,"title":"TUU stuck in first cycle","user":{"login":"haoyuanchen","id":7672745,"avatar_url":"https://avatars.githubusercontent.com/u/7672745?v=3","gravatar_id":"","url":"https://api.github.com/users/haoyuanchen","html_url":"https://github.com/haoyuanchen","followers_url":"https://api.github.com/users/haoyuanchen/followers","following_url":"https://api.github.com/users/haoyuanchen/following{/other_user}","gists_url":"https://api.github.com/users/haoyuanchen/gists{/gist_id}","starred_url":"https://api.github.com/users/haoyuanchen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/haoyuanchen/subscriptions","organizations_url":"https://api.github.com/users/haoyuanchen/orgs","repos_url":"https://api.github.com/users/haoyuanchen/repos","events_url":"https://api.github.com/users/haoyuanchen/events{/privacy}","received_events_url":"https://api.github.com/users/haoyuanchen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":12,"created_at":"2016-04-19T13:53:12Z","updated_at":"2016-04-21T00:47:30Z","closed_at":null,"body":"In a TUU production run, after all replicas finished their first MD cycle, the simulation just stopped and doing nothing there. No errors were reported in the log file. Also, it seems that a CU for exchange calculation were not created.\r\n\r\nInput:\r\n\r\n{\r\n    \"remd.input\": {\r\n        \"re_pattern\": \"S\",\r\n        \"number_of_cycles\": \"39\",\r\n        \"input_folder\": \"tuu_remd_inputs\",\r\n        \"input_file_basename\": \"ace_ala_nme_remd\",\r\n        \"amber_input\": \"ace_ala_nme.mdin\",\r\n        \"us_template\": \"ace_ala_nme_double.RST\",\r\n        \"amber_parameters\": \"ace_ala_nme.parm7\",\r\n        \"amber_coordinates_folder\": \"ace_ala_nme_coors_8x8\",\r\n        \"same_coordinates\": \"False\",\r\n        \"group_exec\": \"False\",\r\n        \"init_temp\": \"300.0\",\r\n        \"replica_mpi\": \"False\",\r\n        \"replica_cores\": \"1\",\r\n        \"steps_per_cycle\": \"10000\",\r\n        \"download_mdinfo\": \"False\",\r\n        \"download_mdout\" : \"False\"\r\n        },\r\n    \"dim.input\": {\r\n        \"d1\": {\r\n            \"type\" : \"umbrella\",\r\n            \"number_of_replicas\": \"8\",\r\n            \"min_us_param\": \"45.0\",\r\n            \"max_us_param\": \"360.0\"\r\n            },\r\n        \"d2\": {\r\n            \"type\" : \"temperature\",\r\n            \"number_of_replicas\": \"11\",\r\n            \"min_temperature\": \"273.0\",\r\n            \"max_temperature\": \"373.0\"\r\n            },\r\n        \"d3\": {\r\n            \"type\" : \"umbrella\",\r\n            \"number_of_replicas\": \"8\",\r\n            \"min_us_param\": \"45.0\",\r\n            \"max_us_param\": \"360.0\"\r\n            }\r\n    }\r\n}\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/radical-cybertools/radical.repex/issues/comments/212672575","html_url":"https://github.com/radical-cybertools/radical.repex/issues/79#issuecomment-212672575","issue_url":"https://api.github.com/repos/radical-cybertools/radical.repex/issues/79","id":212672575,"user":{"login":"antonst","id":3586211,"avatar_url":"https://avatars.githubusercontent.com/u/3586211?v=3","gravatar_id":"","url":"https://api.github.com/users/antonst","html_url":"https://github.com/antonst","followers_url":"https://api.github.com/users/antonst/followers","following_url":"https://api.github.com/users/antonst/following{/other_user}","gists_url":"https://api.github.com/users/antonst/gists{/gist_id}","starred_url":"https://api.github.com/users/antonst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antonst/subscriptions","organizations_url":"https://api.github.com/users/antonst/orgs","repos_url":"https://api.github.com/users/antonst/repos","events_url":"https://api.github.com/users/antonst/events{/privacy}","received_events_url":"https://api.github.com/users/antonst/received_events","type":"User","site_admin":false},"created_at":"2016-04-21T00:47:30Z","updated_at":"2016-04-21T00:47:30Z","body":"I have double checked: all CUs have finished their execution and generated their ```matrix_column``` file, but RP's um.wait_units() call does not return. In terminal log about 1/2 of CU's are not reported as finished by RP. Nothing fails and no errors are reported. Also according to callbacks, only about 1/2 of replicas got to AgentStagingOutput stage.    "}}