{"action":"closed","issue":{"url":"https://api.github.com/repos/radical-cybertools/radical.ensemblemd/issues/128","repository_url":"https://api.github.com/repos/radical-cybertools/radical.ensemblemd","labels_url":"https://api.github.com/repos/radical-cybertools/radical.ensemblemd/issues/128/labels{/name}","comments_url":"https://api.github.com/repos/radical-cybertools/radical.ensemblemd/issues/128/comments","events_url":"https://api.github.com/repos/radical-cybertools/radical.ensemblemd/issues/128/events","html_url":"https://github.com/radical-cybertools/radical.ensemblemd/issues/128","id":131292120,"number":128,"title":"RP workflow on ARCHER gromacs/lsdmap for (0.3.14-27-g65bc062) ","user":{"login":"ebreitmo","id":4025281,"avatar_url":"https://avatars.githubusercontent.com/u/4025281?v=3","gravatar_id":"","url":"https://api.github.com/users/ebreitmo","html_url":"https://github.com/ebreitmo","followers_url":"https://api.github.com/users/ebreitmo/followers","following_url":"https://api.github.com/users/ebreitmo/following{/other_user}","gists_url":"https://api.github.com/users/ebreitmo/gists{/gist_id}","starred_url":"https://api.github.com/users/ebreitmo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ebreitmo/subscriptions","organizations_url":"https://api.github.com/users/ebreitmo/orgs","repos_url":"https://api.github.com/users/ebreitmo/repos","events_url":"https://api.github.com/users/ebreitmo/events{/privacy}","received_events_url":"https://api.github.com/users/ebreitmo/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-02-04T09:41:53Z","updated_at":"2016-02-04T13:49:34Z","closed_at":"2016-02-04T13:49:34Z","body":"Hi,\r\n\r\nI started with a clean virtualenv, did\r\n\r\n```\r\npip install --upgrade git+https://github.com/radical-cybertools/radical.ensemblemd.git@master#egg=radical.ensemblemd \r\n```\r\ngot the latest grls-on-archer.tar.gz\r\n```\r\npython extasy_gromacs_lsdmap.py --RPconfig archer.rcfg --Kconfig gromacslsdmap.wcfg\r\n\r\n================================================================================\r\n EnsembleMD (0.3.14-27-g65bc062)                                                \r\n================================================================================\r\n\r\nStarting Allocation                                                           ok\r\nVerifying pattern                                                             ok\r\nStarting pattern execution                                                    ok\r\n--------------------------------------------------------------------------------\r\nExecuting simulation-analysis loop with 1 iterations on 24 allocated core(s) on 'epsrc.archer'\r\n\r\nJob waiting on queue...\r\nJob is now running !\r\nWaiting for pre_loop step to complete.                                      done\r\nIteration 1: Waiting for 8 simulation tasks: custom.gromacs to complete     done\r\nIteration 1: Waiting for analysis tasks: custom.pre_lsdmap to complete2016-02-04 09:26:25,515: radical.enmd.simulation_analysis_loop.static.default: MainProcess                     : Thread-4       : ERROR   : ComputeUnit error: STDERR: [... CONTENT SHORTENED ...]\r\nute of Technology, Sweden.\r\ncheck out http://www.gromacs.org for more information.\r\n\r\nGROMACS is free software; you can redistribute it and/or modify it\r\nunder the terms of the GNU Lesser General Public License\r\nas published by the Free Software Foundation; either version 2.1\r\nof the License, or (at your option) any later version.\r\n\r\nGROMACS:      gmx trjconv, VERSION 5.1\r\nExecutable:   /work/y07/y07/gmx/5.1-phase2/bin/gmx\r\nData prefix:  /work/y07/y07/gmx/5.1-phase2\r\nCommand line:\r\n  gmx trjconv -f tmp.gro -s tmp.gro -o tmpha.gro\r\n\r\nWill write gro: Coordinate file in Gromos-87 format\r\n\r\n-------------------------------------------------------\r\nProgram gmx trjconv, VERSION 5.1\r\nSource code file: /work/y07/y07/gmx/5.1-phase2/source/src/gromacs/fileio/confio.c, line: 907\r\n\r\nFatal error:\r\ngro file does not have the number of atoms on the second line\r\nFor more information and tips for troubleshooting, please check the GROMACS\r\nwebsite at http://www.gromacs.org/Documentation/Errors\r\n-------------------------------------------------------\r\n\r\n, STDOUT: [... CONTENT SHORTENED ...]\r\nute of Technology, Sweden.\r\ncheck out http://www.gromacs.org for more information.\r\n\r\nGROMACS is free software; you can redistribute it and/or modify it\r\nunder the terms of the GNU Lesser General Public License\r\nas published by the Free Software Foundation; either version 2.1\r\nof the License, or (at your option) any later version.\r\n\r\nGROMACS:      gmx trjconv, VERSION 5.1\r\nExecutable:   /work/y07/y07/gmx/5.1-phase2/bin/gmx\r\nData prefix:  /work/y07/y07/gmx/5.1-phase2\r\nCommand line:\r\n  gmx trjconv -f tmp.gro -s tmp.gro -o tmpha.gro\r\n\r\nWill write gro: Coordinate file in Gromos-87 format\r\n\r\n-------------------------------------------------------\r\nProgram gmx trjconv, VERSION 5.1\r\nSource code file: /work/y07/y07/gmx/5.1-phase2/source/src/gromacs/fileio/confio.c, line: 907\r\n\r\nFatal error:\r\ngro file does not have the number of atoms on the second line\r\nFor more information and tips for troubleshooting, please check the GROMACS\r\nwebsite at http://www.gromacs.org/Documentation/Errors\r\n-------------------------------------------------------\r\n\r\n\r\n2016-02-04 09:26:25,515: radical.enmd.simulation_analysis_loop.static.default: MainProcess                     : Thread-4       : ERROR   : Pattern execution FAILED.\r\n2016-02-04 09:26:25,515: radical.pilot       : MainProcess                     : Thread-4       : ERROR   : unit manager controller thread caught system exit -- forcing application shutdown\r\nTraceback (most recent call last):\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/controller/unit_manager_controller.py\", line 262, in run\r\n    self.call_unit_state_callbacks(unit_id, new_state)\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/controller/unit_manager_controller.py\", line 199, in call_unit_state_callbacks\r\n    cb(self._shared_data[unit_id]['facade_object'], new_state)\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/ensemblemd/exec_plugins/simulation_analysis_loop/static.py\", line 318, in unit_state_cb\r\n    sys.exit(1)\r\nSystemExit: 1\r\nExecution interuptedTraceback (most recent call last):\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/ensemblemd/exec_plugins/simulation_analysis_loop/static.py\", line 603, in execute_pattern\r\n    resource._umgr.wait_units(uids)\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/unit_manager.py\", line 698, in wait_units\r\n    time.sleep (0.5)\r\nKeyboardInterrupt\r\n\r\nStarting Deallocation..\r\n2016-02-04 09:26:36,007: radical.enmd.SingleClusterEnvironment: MainProcess                     : Thread-1       : ERROR   : Resource error: \r\n2016-02-04 09:26:36,007: radical.enmd.SingleClusterEnvironment: MainProcess                     : Thread-1       : ERROR   : Pattern execution FAILED.\r\n2016-02-04 09:26:36,007: radical.pilot       : MainProcess                     : Thread-1       : ERROR   : sys.exit from callback\r\nTraceback (most recent call last):\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/controller/pilot_manager_controller.py\", line 258, in call_callbacks\r\n    cb(self._shared_data[pilot_id]['facade_object'](), new_state)\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/ensemblemd/single_cluster_environment.py\", line 168, in pilot_state_cb\r\n    sys.exit(1)\r\nSystemExit: 1\r\nTraceback (most recent call last):\r\n  File \"extasy_gromacs_lsdmap.py\", line 271, in <module>\r\n    cluster.deallocate()\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/ensemblemd/single_cluster_environment.py\", line 117, in deallocate\r\n    self._session.close(cleanup=self._cleanup)\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/session.py\", line 304, in close\r\n    pmgr.close (terminate=terminate)\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/pilot_manager.py\", line 175, in close\r\n    self.cancel_pilots()\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/pilot_manager.py\", line 579, in cancel_pilots\r\n    self._worker.register_cancel_pilots_request(pilot_ids=pilot_ids)\r\n  File \"/Users/elenabreitmoser/04Feb/lib/python2.7/site-packages/radical/pilot/controller/pilot_manager_controller.py\", line 608, in register_cancel_pilots_request\r\n    time.sleep(0.3)\r\nKeyboardInterrupt\r\n```\r\n\r\n\r\nOn ARCHER \r\n```\r\nmore unit.000009/STDERR \r\n                   :-) GROMACS - gmx trjconv, VERSION 5.1 (-:\r\n\r\n                            GROMACS is written by:\r\n     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   \r\n Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch \r\n  Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen\r\n Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner  \r\n    Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff \r\n   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   \r\n   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  \r\n   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   \r\n                           and the project leaders:\r\n        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\r\n\r\nCopyright (c) 1991-2000, University of Groningen, The Netherlands.\r\nCopyright (c) 2001-2015, The GROMACS development team at\r\nUppsala University, Stockholm University and\r\nthe Royal Institute of Technology, Sweden.\r\ncheck out http://www.gromacs.org for more information.\r\n\r\nGROMACS is free software; you can redistribute it and/or modify it\r\nunder the terms of the GNU Lesser General Public License\r\nas published by the Free Software Foundation; either version 2.1\r\nof the License, or (at your option) any later version.\r\n\r\nGROMACS:      gmx trjconv, VERSION 5.1\r\nExecutable:   /work/y07/y07/gmx/5.1-phase2/bin/gmx\r\nData prefix:  /work/y07/y07/gmx/5.1-phase2\r\nCommand line:\r\n  gmx trjconv -f tmp.gro -s tmp.gro -o tmpha.gro\r\n\r\nWill write gro: Coordinate file in Gromos-87 format\r\n\r\n-------------------------------------------------------\r\nProgram gmx trjconv, VERSION 5.1\r\nSource code file: /work/y07/y07/gmx/5.1-phase2/source/src/gromacs/fileio/confio.c, line: 907\r\n\r\nFatal error:\r\ngro file does not have the number of atoms on the second line\r\nFor more information and tips for troubleshooting, please check the GROMACS\r\nwebsite at http://www.gromacs.org/Documentation/Errors\r\n-------------------------------------------------------\r\n```\r\n\r\n\r\n\r\n"}}