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January 21, 2016 11:24
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| [ExTASY-tools-21Jan16] ardita@moriarty 143% python extasy_amber_coco.py --RPconfig archer.rcfg --Kconfig cocoamber.wcfg | |
| ================================================================================ | |
| EnsembleMD (0.3.14) | |
| ================================================================================ | |
| Starting Allocation ok | |
| Verifying pattern ok | |
| Starting pattern execution ok | |
| -------------------------------------------------------------------------------- | |
| Executing simulation-analysis loop with 2 iterations on 24 allocated core(s) on 'epsrc.archer' | |
| Job waiting on queue... | |
| Job is now running ! | |
| Waiting for pre_loop step to complete.2016-01-21 11:21:52,070: radical.saga.cpi : MainProcess : InputFileTransferWorker-2: ERROR : Could not detect shell prompt (timeout) (/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py +288 (_initialize_pty) : raise se.NoSuccess ("Could not detect shell prompt (timeout)")) | |
| Traceback (most recent call last): | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py", line 288, in _initialize_pty | |
| raise se.NoSuccess ("Could not detect shell prompt (timeout)") | |
| NoSuccess: Could not detect shell prompt (timeout) (/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py +288 (_initialize_pty) : raise se.NoSuccess ("Could not detect shell prompt (timeout)")) | |
| 2016-01-21 11:21:52,071: radical.pilot : MainProcess : InputFileTransferWorker-2: ERROR : Error: Could not detect shell prompt (timeout) (/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py +288 (_initialize_pty) : raise se.NoSuccess ("Could not detect shell prompt (timeout)")) | |
| Traceback (most recent call last): | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/pilot/controller/input_file_transfer_worker.py", line 140, in run | |
| session=self._session) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/filesystem/directory.py", line 95, in __init__ | |
| _adaptor, _adaptor_state, _ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/namespace/directory.py", line 95, in __init__ | |
| _adaptor, _adaptor_state, _ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/namespace/entry.py", line 89, in __init__ | |
| url, flags, session, ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/base.py", line 101, in __init__ | |
| self._init_task = self._adaptor.init_instance (adaptor_state, *args, **kwargs) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/adaptors/cpi/decorators.py", line 57, in wrap_function | |
| return sync_function (self, *args, **kwargs) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/adaptors/shell/shell_file.py", line 292, in init_instance | |
| self._logger) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell.py", line 244, in __init__ | |
| self.pty_shell = self.factory.run_shell (self.pty_info) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py", line 448, in run_shell | |
| self._initialize_pty (sh_slave, info) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py", line 411, in _initialize_pty | |
| raise ptye.translate_exception (e) | |
| NoSuccess: Could not detect shell prompt (timeout) (/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py +288 (_initialize_pty) : raise se.NoSuccess ("Could not detect shell prompt (timeout)")) | |
| 2016-01-21 11:21:52,086: radical.pilot : MainProcess : InputFileTransferWorker-2: ERROR : {'timestamp': 1453375312.071581, 'message': 'Input transfer failed: Could not detect shell prompt (timeout) (/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py +288 (_initialize_pty) : raise se.NoSuccess ("Could not detect shell prompt (timeout)"))'} | |
| Traceback (most recent call last): | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/pilot/controller/input_file_transfer_worker.py", line 140, in run | |
| session=self._session) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/filesystem/directory.py", line 95, in __init__ | |
| _adaptor, _adaptor_state, _ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/namespace/directory.py", line 95, in __init__ | |
| _adaptor, _adaptor_state, _ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/namespace/entry.py", line 89, in __init__ | |
| url, flags, session, ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/base.py", line 101, in __init__ | |
| self._init_task = self._adaptor.init_instance (adaptor_state, *args, **kwargs) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/adaptors/cpi/decorators.py", line 57, in wrap_function | |
| return sync_function (self, *args, **kwargs) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/adaptors/shell/shell_file.py", line 292, in init_instance | |
| self._logger) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell.py", line 244, in __init__ | |
| self.pty_shell = self.factory.run_shell (self.pty_info) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py", line 448, in run_shell | |
| self._initialize_pty (sh_slave, info) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py", line 411, in _initialize_pty | |
| raise ptye.translate_exception (e) | |
| NoSuccess: Could not detect shell prompt (timeout) (/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py +288 (_initialize_pty) : raise se.NoSuccess ("Could not detect shell prompt (timeout)")) | |
| Exception in thread InputFileTransferWorker-2: | |
| Traceback (most recent call last): | |
| File "/usr/remote/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner | |
| self.run() | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/pilot/controller/input_file_transfer_worker.py", line 140, in run | |
| session=self._session) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/filesystem/directory.py", line 95, in __init__ | |
| _adaptor, _adaptor_state, _ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/namespace/directory.py", line 95, in __init__ | |
| _adaptor, _adaptor_state, _ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/namespace/entry.py", line 89, in __init__ | |
| url, flags, session, ttype=_ttype) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/base.py", line 101, in __init__ | |
| self._init_task = self._adaptor.init_instance (adaptor_state, *args, **kwargs) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/adaptors/cpi/decorators.py", line 57, in wrap_function | |
| return sync_function (self, *args, **kwargs) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/adaptors/shell/shell_file.py", line 292, in init_instance | |
| self._logger) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell.py", line 244, in __init__ | |
| self.pty_shell = self.factory.run_shell (self.pty_info) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py", line 448, in run_shell | |
| self._initialize_pty (sh_slave, info) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py", line 411, in _initialize_pty | |
| raise ptye.translate_exception (e) | |
| NoSuccess: Could not detect shell prompt (timeout) (/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/saga/utils/pty_shell_factory.py +288 (_initialize_pty) : raise se.NoSuccess ("Could not detect shell prompt (timeout)")) | |
| 2016-01-21 11:21:54,020: radical.enmd.simulation_analysis_loop.static.default: MainProcess : Thread-3 : ERROR : ComputeUnit error: STDERR: None, STDOUT: None | |
| 2016-01-21 11:21:54,021: radical.enmd.simulation_analysis_loop.static.default: MainProcess : Thread-3 : ERROR : Pattern execution FAILED. | |
| 2016-01-21 11:21:54,021: radical.pilot : MainProcess : Thread-3 : ERROR : unit manager controller thread caught system exit -- forcing application shutdown | |
| Traceback (most recent call last): | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/pilot/controller/unit_manager_controller.py", line 261, in run | |
| self.call_unit_state_callbacks(unit_id, new_state) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/pilot/controller/unit_manager_controller.py", line 198, in call_unit_state_callbacks | |
| cb(self._shared_data[unit_id]['facade_object'], new_state) | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/ensemblemd/exec_plugins/simulation_analysis_loop/static.py", line 141, in unit_state_cb | |
| sys.exit(1) | |
| SystemExit: 1 | |
| Execution interuptedTraceback (most recent call last): | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/ensemblemd/exec_plugins/simulation_analysis_loop/static.py", line 209, in execute_pattern | |
| resource._umgr.wait_units() | |
| File "/users/ardita/ExTASY-tools-21Jan16/lib/python2.7/site-packages/radical/pilot/unit_manager.py", line 697, in wait_units | |
| time.sleep (0.5) | |
| KeyboardInterrupt | |
| Starting Deallocationdone |
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