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Traceback (most recent call last):
File "extasy-analytics-gromacs.py", line 304, in <module>
appman.run()
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/appman/appmanager.py", line 437, in run
self.terminate()
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/appman/appmanager.py", line 479, in terminate
self._rmgr._terminate_resource_request()
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/execman/rp/resource_manager.py", line 230, in _terminate_resource_request
self._session.close(cleanup=cleanup, download=get_profiles)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/pilot/session.py", line 288, in close
self.fetch_json (tgt='%s/%s' % (tgt, self.uid))
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/pilot/session.py", line 693, in fetch_json
session=self)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/pilot/utils/session.py", line 414, in fetch_json
ru.write_json(json_docs, dst)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/utils/json_io.py", line 62, in write_json
json.dump(data, f, sort_keys=True, indent=4, ensure_ascii=False)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/json/__init__.py", line 180, in dump
fp.write(chunk)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 1050: ordinal not in range(128)
Update: pipeline.0000.stage.0002.task.0710 state: EXECUTED
Update: pipeline.0000.stage.0002.task.0710 state: DONE
close unit manager ok
wait for 1 pilot(s)
0 ok
closing session re.session.login5.hrlee.018430.0004 \
close pilot manager \
wait for 1 pilot(s)
0 ok
ok
Error: 'ascii' codec can't encode character '\u2019' in position 1050: ordinal not in range(128)
Traceback (most recent call last):
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/appman/appmanager.py", line 426, in run
self._run_workflow()
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/appman/appmanager.py", line 736, in _run_workflow
if not self._task_manager.check_heartbeat() and \
KeyboardInterrupt
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "extasy-analytics-gromacs.py", line 304, in <module>
appman.run()
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/appman/appmanager.py", line 437, in run
self.terminate()
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/appman/appmanager.py", line 479, in terminate
self._rmgr._terminate_resource_request()
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/entk/execman/rp/resource_manager.py", line 230, in _terminate_resource_request
self._session.close(cleanup=cleanup, download=get_profiles)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/pilot/session.py", line 288, in close
self.fetch_json (tgt='%s/%s' % (tgt, self.uid))
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/pilot/session.py", line 693, in fetch_json
session=self)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/pilot/utils/session.py", line 414, in fetch_json
ru.write_json(json_docs, dst)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/site-packages/radical/utils/json_io.py", line 62, in write_json
json.dump(data, f, sort_keys=True, indent=4, ensure_ascii=False)
File "/ccs/home/hrlee/.conda/envs/workflow-2/lib/python3.6/json/__init__.py", line 180, in dump
fp.write(chunk)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 1050: ordinal not in range(128)
My stack:
And the session data is at: https://github.com/radical-experiments/extasy_profiling/blob/master/data/raw_gromacs/re.session.login5.hrlee.018425.0020.tar.gz
And the script is at: https://github.com/radical-experiments/extasy_profiling/blob/master/script/extasy-analytics-gromacs.py
it runs like:
Please see the README for configuration
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