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radical-collaboration / extasy-grlsd

Repository to hold the input data and scripts for the ExTASY gromacs-lsdmap work
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'NoneType' object has no attribute 'join' #113

Closed euhruska closed 5 years ago

euhruska commented 5 years ago 
2019-02-06 15:19:36,377: radical.entk.wfprocessor.0000: MainProcess                     : MainThread     : DEBUG   : Attempting to end WFprocessor... event: False
2019-02-06 15:19:36,424: radical.entk.wfprocessor.0000: wfprocessor                     : MainThread     : INFO    : WFprocessor started
2019-02-06 15:19:36,424: radical.entk.wfprocessor.0000: wfprocessor                     : MainThread     : INFO    : Terminating enqueue-thread
2019-02-06 15:19:36,424: radical.entk.wfprocessor.0000: wfprocessor                     : MainThread     : ERROR   : Error in wfp process: 'NoneType' object has no attribute 'join'.
 Closing enqueue, dequeue threads
2019-02-06 15:19:36,424: radical.entk.wfprocessor.0000: wfprocessor                     : MainThread     : INFO    : WFprocessor process terminated
Process wfprocessor:
Traceback (most recent call last):
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap
    self.run()
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/site-packages/radical/entk/appman/wfprocessor.py", line 557, in _wfp
    raise EnTKError(text=ex)
TypeError: __init__() got an unexpected keyword argument 'text'
Traceback (most recent call last):
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/site-packages/radical/entk/appman/wfprocessor.py", line 503, in _wfp
    self._enqueue_thread.join()
AttributeError: 'NoneType' object has no attribute 'join'

2019-02-06 15:19:36,431: radical.entk.wfprocessor.0000: MainProcess                     : MainThread     : DEBUG   : WFprocessor process terminated
2019-02-06 15:19:36,433: radical.entk.appmanager.0000: MainProcess                     : MainThread     : INFO    : Terminating synchronizer thread
2019-02-06 15:19:37,049: radical.entk.appmanager.0000: MainProcess                     : MainThread     : INFO    : Synchronizer thread terminated
2019-02-06 15:19:46,295: radical.entk.resource_manager.0000: MainProcess                     : pmgr.0000.idler._state_pull_cb: INFO    : Pilot pilot.0000 state: CANCELED
2019-02-06 15:19:52,445: radical.utils       : MainProcess                     : MainThread     : DEBUG   : lm create  pool   for gsisftp://bw.ncsa.illinois.edu/shell_file_adaptor_command_shell/ (<type 'str'>) (<radical.utils.lease_manager.LeaseManager object at 0x7f4d589dbf10>)
2019-02-06 15:19:52,445: radical.utils       : MainProcess                     : MainThread     : DEBUG   : lm create  object for gsisftp://bw.ncsa.illinois.edu/shell_file_adaptor_command_shell/
Error: [Errno 5] Input/output error
Traceback (most recent call last):
  File "extasy_tica3.py", line 322, in <module>
    appman.run()
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/site-packages/radical/entk/appman/appmanager.py", line 344, in run
    port=self._port
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/site-packages/radical/entk/execman/rp/task_manager.py", line 51, in __init__
    rts='radical.pilot')
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/site-packages/radical/entk/execman/base/task_manager.py", line 79, in __init__
    self._uid = ru.generate_id('task_manager.%(item_counter)04d', ru.ID_CUSTOM, namespace=self._sid)
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/site-packages/radical/utils/ids.py", line 179, in generate_id
    return _generate_id(template, prefix, namespace)
  File "/scratch1/eh22/conda/envs/extasy16/lib/python2.7/site-packages/radical/utils/ids.py", line 248, in _generate_id
    os.close(fd)
OSError: [Errno 5] Input/output error
vivek-bala commented 5 years ago

Hey Eugene, can you add the entire verbose log? The message from the event causing the error might be missing.

euhruska commented 5 years ago

looks like this was caused by the bluewaters storage maintenance, now fixed