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nxwriter ExternalLink crash & Lambda2M HDF Plugin error #14

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qzhang234 opened this issue Aug 29, 2023 · 0 comments
Open

nxwriter ExternalLink crash & Lambda2M HDF Plugin error #14

qzhang234 opened this issue Aug 29, 2023 · 0 comments
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@prjemian @sureshnaps @qzhang234

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@qzhang234
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qzhang234 commented Aug 29, 2023 •
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Nxwriter crashed due to ExternalLink error.

Terminal output 
In [1]: %run -i /home/8ididata/2023-2/pvaccess_test/bp_Nexus_Lambda2M.py

In [2]: RE(nexus_test())


Transient Scan ID: 38056     Time: 2023-08-29 15:00:24
Persistent Unique Scan ID: 'e5f7d283-353f-4e8f-acc4-d127a6d91c1e'
New stream: 'primary'
+-----------+------------+
|   seq_num |       time |
+-----------+------------+
|         1 | 15:00:40.5 |
Exception in thread Thread-84 (_threaded_writer):
Traceback (most recent call last):
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
    self.run()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/threading.py", line 953, in run
    self._target(*self._args, **self._kwargs)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/apstools/callbacks/nexus_writer.py", line 290, in _threaded_writer
    self.write_root(fname)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/apstools/callbacks/nexus_writer.py", line 541, in write_root
    self.write_entry()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/apstools/callbacks/nexus_writer.py", line 394, in write_entry
    self.write_instrument(nxentry)  # also writes streams and metadata
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/apstools/callbacks/nexus_writer.py", line 805, in write_instrument
    nxinstrument = super().write_instrument(parent)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/apstools/callbacks/nexus_writer.py", line 427, in write_instrument
    self.write_streams(bluesky_group)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/apstools/callbacks/nexus_writer.py", line 730, in write_streams
    self.write_stream_external(parent, d, subgroup, stream_name, k, v)
  File "/home/beams10/8IDIUSER/bluesky/instrument/callbacks/nexus_data_file_writer.py", line 50, in write_stream_external
    ds.attrs["image_file"] = str(fname)
AttributeError: 'ExternalLink' object has no attribute 'attrs'
+-----------+------------+
generator count ['e5f7d283'] (scan num: 38056)
lambda2M_hdf1_capture: _set_and_wait(value=0, timeout=3, atol=None, rtol=None, kwargs={})
Run aborted
Traceback (most recent call last):
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 1523, in _run
    msg = self._plan_stack[-1].send(resp)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 1307, in __call__
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 1160, in baseline_wrapper
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 803, in monitor_during_wrapper
    return (yield from plan2)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 861, in fly_during_wrapper
    return (yield from plan2)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/utils/__init__.py", line 1147, in dec_inner
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 382, in subs_wrapper
    return (yield from finalize_wrapper(_inner_plan(),
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 509, in finalize_wrapper
    ret = yield from plan
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 380, in _inner_plan
    return (yield from plan)
  File "/home/8ididata/2023-2/pvaccess_test/bp_Nexus_Lambda2M.py", line 8, in nexus_test
    yield from bp.count([lambda2M])
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/plans.py", line 77, in count
    return (yield from inner_count())
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/utils/__init__.py", line 1147, in dec_inner
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 952, in stage_wrapper
    return (yield from finalize_wrapper(inner(), unstage_devices()))
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 528, in finalize_wrapper
    yield from ensure_generator(final_plan_instance)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 946, in unstage_devices
    yield Msg('unstage', d)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
    inner_ret = yield msg
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
    inner_ret = yield msg
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
    inner_ret = yield msg
  [Previous line repeated 1 more time]
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 1583, in _run
    new_response = await coro(msg)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 2352, in _unstage
    result = obj.unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/trigger_mixins.py", line 133, in unstage
    super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/device.py", line 726, in unstage
    device.unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/filestore_mixins.py", line 677, in unstage
    super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/filestore_mixins.py", line 394, in unstage
    return super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/device.py", line 732, in unstage
    sig.set(val).wait()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/status.py", line 434, in wait
    raise self._exception
ophyd.utils.errors.UnknownStatusFailure: The status Status(obj=EpicsSignalWithRBV(read_pv='8idLambda2m:HDF1:Capture_RBV', name='lambda2M_hdf1_capture', parent='lambda2M_hdf1', value=1, timestamp=1693339224.0346959, auto_monitor=True, string=False, write_pv='8idLambda2m:HDF1:Capture', limits=False, put_complete=False), done=False, success=False) has failed. To obtain more specific, helpful errors in the future, update the Device to use set_exception(...) instead of _finished(success=False).
lambda2M_hdf1_capture: _set_and_wait(value=0, timeout=3, atol=None, rtol=None, kwargs={})
Failed to unstage Lambda2MDetector(prefix='8idLambda2m:', name='lambda2M', read_attrs=['hdf1'], configuration_attrs=['cam', 'cam.acquire_period', 'cam.acquire_time', 'cam.image_mode', 'cam.manufacturer', 'cam.model', 'cam.num_exposures', 'cam.num_images', 'cam.trigger_mode', 'hdf1']).
Traceback (most recent call last):
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 1663, in _run
    raise err
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 1523, in _run
    msg = self._plan_stack[-1].send(resp)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 1307, in __call__
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 1160, in baseline_wrapper
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 803, in monitor_during_wrapper
    return (yield from plan2)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 861, in fly_during_wrapper
    return (yield from plan2)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 170, in plan_mutator
    raise ex
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 123, in plan_mutator
    msg = plan_stack[-1].send(ret)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/utils/__init__.py", line 1147, in dec_inner
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 382, in subs_wrapper
    return (yield from finalize_wrapper(_inner_plan(),
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 509, in finalize_wrapper
    ret = yield from plan
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 380, in _inner_plan
    return (yield from plan)
  File "/home/8ididata/2023-2/pvaccess_test/bp_Nexus_Lambda2M.py", line 8, in nexus_test
    yield from bp.count([lambda2M])
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/plans.py", line 77, in count
    return (yield from inner_count())
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/utils/__init__.py", line 1147, in dec_inner
    return (yield from plan)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 952, in stage_wrapper
    return (yield from finalize_wrapper(inner(), unstage_devices()))
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 528, in finalize_wrapper
    yield from ensure_generator(final_plan_instance)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 946, in unstage_devices
    yield Msg('unstage', d)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
    inner_ret = yield msg
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
    inner_ret = yield msg
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
    inner_ret = yield msg
  [Previous line repeated 1 more time]
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 1583, in _run
    new_response = await coro(msg)
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 2352, in _unstage
    result = obj.unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/trigger_mixins.py", line 133, in unstage
    super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/device.py", line 726, in unstage
    device.unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/filestore_mixins.py", line 677, in unstage
    super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/filestore_mixins.py", line 394, in unstage
    return super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/device.py", line 732, in unstage
    sig.set(val).wait()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/status.py", line 434, in wait
    raise self._exception
ophyd.utils.errors.UnknownStatusFailure: The status Status(obj=EpicsSignalWithRBV(read_pv='8idLambda2m:HDF1:Capture_RBV', name='lambda2M_hdf1_capture', parent='lambda2M_hdf1', value=1, timestamp=1693339224.0346959, auto_monitor=True, string=False, write_pv='8idLambda2m:HDF1:Capture', limits=False, put_complete=False), done=False, success=False) has failed. To obtain more specific, helpful errors in the future, update the Device to use set_exception(...) instead of _finished(success=False).

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/bluesky/run_engine.py", line 1682, in _run
    obj.unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/trigger_mixins.py", line 133, in unstage
    super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/device.py", line 726, in unstage
    device.unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/filestore_mixins.py", line 677, in unstage
    super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/areadetector/filestore_mixins.py", line 394, in unstage
    return super().unstage()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/device.py", line 732, in unstage
    sig.set(val).wait()
  File "/home/beams/8IDIUSER/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/status.py", line 434, in wait
    raise self._exception
ophyd.utils.errors.UnknownStatusFailure: The status Status(obj=EpicsSignalWithRBV(read_pv='8idLambda2m:HDF1:Capture_RBV', name='lambda2M_hdf1_capture', parent='lambda2M_hdf1', value=1, timestamp=1693339224.0346959, auto_monitor=True, string=False, write_pv='8idLambda2m:HDF1:Capture', limits=False, put_complete=False), done=False, success=False) has failed. To obtain more specific, helpful errors in the future, update the Device to use set_exception(...) instead of _finished(success=False).
UnknownStatusFailure: The status Status(obj=EpicsSignalWithRBV(read_pv='8idLambda2m:HDF1:Capture_RBV', name='lambda2M_hdf1_capture', parent='lambda2M_hdf1', value=1, timestamp=1693339224.0346959, auto_monitor=True, string=False, write_pv='8idLambda2m:HDF1:Capture', limits=False, put_complete=False), done=False, success=False) has failed. To obtain more specific, helpful errors in the future, update the Device to use set_exception(...) instead of _finished(success=False).


In [3]: 

In [3]:

There is also issue with HDF plugin of Lambda2M, will talk to @sureshnaps separately in person.
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