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XPCS bluesky instrument configuration
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nxwriter ExternalLink crash & Lambda2M HDF Plugin error #14

Open qzhang234 opened 12 months ago

qzhang234 commented 12 months ago

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.