Crashed BlueSky #7
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When I tried to continue with command line, it seemed unresponsive and when I hit enter, it opened GUI with DataBroker catalog, when I tried to close it it stated it was not saved. Closed anyway, but looks like DataBroker was active and waiting for something. |
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Problem here is that matplotlib is being configured with Tk. That's the
problem to be fixed.
…On Fri, Oct 25, 2024, 9:25 AM Jan Ilavsky ***@***.***> wrote:
When I tried to continue with command line, it seemed unresponsive and
when I hit enter, it opened GUI with DataBroker catalog, when I tried to
close it it stated it was not saved. Closed anyway, but looks like
DataBroker was active and waiting for something.
—
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Matplotlib seems to be imported in generic configuration of bluesky, for notebook as well as console session. |
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Seen recently and entirely clear why. Here is the clear (to me) identification of this situation: Next, I'm going to question the steps you executed to create this conda environment. (There might be something to change in the |
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This thread from Bluesky's Mattermost discussion: The supported backends (at this time) are: I'm thinking that the conda environment did not get a requirement to install one of the Qt packages. If this is left to |
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Related to: prjemian/model_instrument#5 |
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Short version : recreating bluesky_2024_3 from yml file does not help. |
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I'm reinstalling from https://raw.githubusercontent.com/BCDA-APS/bluesky_training/refs/heads/main/bluesky/environments/environment_2024_3.yml (downloading into |
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With re-installed environment, restarted session. This is the test: In [1]: import matplotlib as mpl
In [2]: mpl.backends.backend
Out[2]: 'tkagg'Should be |
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Similar to prjemian/model_instrument#5, but not the same startup code. |
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Similar versions with that issue's solved version: In [3]: !conda list qt
/share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/IPython/core/interactiveshell.py:2673: UserWarning: You executed the system command !conda which may not work as expected. Try the IPython magic %conda instead.
warnings.warn(
# packages in environment at /share1/bluesky/conda_envs/bluesky_2024_3:
#
# Name Version Build Channel
pyqt 5.15.9 py311hf0fb5b6_5 conda-forge
pyqt5-sip 12.12.2 py311hb755f60_5 conda-forge
pyqtgraph 0.12.4 pypi_0 pypi
qt 5.15.8 hf11cfaa_0 conda-forge
qt-main 5.15.8 h374914d_26 conda-forge
qt-webengine 5.15.8 h8f589be_8 conda-forge
qtconsole 5.6.0 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
sphinxcontrib-qthelp 2.0.0 pypi_0 pypi |
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At this point: bluesky/instrument/mpl/console.py Line 17 in 2e9ba47 The backend is |
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Need more diagnostics, increasing the xmode level to (/share1/bluesky/conda_envs/bluesky_2024_3) usaxs@usaxscontrol ~/bluesky $ blueskyStarter.sh
==> CONDA_PREFIX=/share1/bluesky/conda_envs/bluesky_2024_3
/share1/bluesky/conda_envs/bluesky_2024_3/bin/python -- Python 3.11.10
Python 3.11.10 | packaged by conda-forge | (main, Oct 16 2024, 01:27:36) [GCC 13.3.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.29.0 -- An enhanced Interactive Python. Type '?' for help.
IPython profile: bluesky
Exception reporting mode: Minimal
/home/beams11/USAXS/bluesky/instrument/_iconfig.py
Activating auto-logging. Current session state plus future input saved.
Filename : /home/beams11/USAXS/bluesky/.logs/ipython_console.log
Mode : rotate
Output logging : True
Raw input log : False
Timestamping : True
State : active
I Sun-17:24:43 - ############################################################ startup
I Sun-17:24:43 - logging started
I Sun-17:24:43 - logging level = 10
I Sun-17:24:43 - /home/beams11/USAXS/bluesky/instrument/session_logs.py
I Sun-17:24:43 - /home/beams11/USAXS/bluesky/instrument/collection.py
I Sun-17:24:43 - CONDA_PREFIX = /share1/bluesky/conda_envs/bluesky_2024_3
Exception reporting mode: Verbose
I Sun-17:24:43 - xmode exception level: 'Verbose'
I Sun-17:24:43 - /home/beams11/USAXS/bluesky/instrument/mpl/console.py
PyQt5.__file__='/share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/PyQt5/__init__.py'
matplotlib.backends.backend='tkagg'
[TerminalIPythonApp] WARNING | Unknown error in handling startup files:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/IPython/core/shellapp.py:403, in InteractiveShellApp._exec_file(self=<IPython.terminal.ipapp.TerminalIPythonApp object>, fname='/home/beams/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py', shell_futures=False)
399 self.shell.safe_execfile_ipy(full_filename,
400 shell_futures=shell_futures)
401 else:
402 # default to python, even without extension
--> 403 self.shell.safe_execfile(full_filename,
full_filename = '/home/beams/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py'
self = <IPython.terminal.ipapp.TerminalIPythonApp object at 0x7f7bf35a6990>
shell_futures = False
404 self.shell.user_ns,
405 shell_futures=shell_futures,
406 raise_exceptions=True)
407 finally:
408 sys.argv = save_argv
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/IPython/core/interactiveshell.py:2932, in InteractiveShell.safe_execfile(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, fname=PosixPath('/home/beams11/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py'), exit_ignore=False, raise_exceptions=True, shell_futures=False, *where=({'In': [''], 'Out': {}, '_': '', '__': '', '___': '', '__builtin__': <module 'builtins' (built-in)>, '__builtins__': <module 'builtins' (built-in)>, '__doc__': '\nstart bluesky in IPython session\n', '__loader__': None, '__name__': '__main__', ...},))
2930 try:
2931 glob, loc = (where + (None, ))[:2]
-> 2932 py3compat.execfile(
py3compat = <module 'IPython.utils.py3compat' from '/share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/IPython/utils/py3compat.py'>
fname = PosixPath('/home/beams11/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py')
glob = {'__name__': '__main__', '__doc__': '\nstart bluesky in IPython session\n', '__package__': None, '__loader__': None, '__spec__': None, '__builtin__': <module 'builtins' (built-in)>, '__builtins__': <module 'builtins' (built-in)>, '_ih': [''], '_oh': {}, '_dh': [PosixPath('/home/beams11/USAXS/bluesky')], 'In': [''], 'Out': {}, 'get_ipython': <bound method InteractiveShell.get_ipython of <IPython.terminal.interactiveshell.TerminalInteractiveShell object at 0x7f7bf125af10>>, 'exit': <IPython.core.autocall.ExitAutocall object at 0x7f7bf1143dd0>, 'quit': <IPython.core.autocall.ExitAutocall object at 0x7f7bf1143dd0>, 'open': <function open at 0x7f7bf1b85260>, '_': '', '__': '', '___': '', 'faulthandler': <module 'faulthandler' (built-in)>, 'pathlib': <module 'pathlib' from '/share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/pathlib.py'>, 'sys': <module 'sys' (built-in)>, 'path': PosixPath('/home/beams/USAXS/bluesky')}
loc = None
self = <IPython.terminal.interactiveshell.TerminalInteractiveShell object at 0x7f7bf125af10>
shell_futures = False
self.compile = <IPython.core.compilerop.CachingCompiler object at 0x7f7bf1335e90>
2933 fname, glob, loc,
2934 self.compile if shell_futures else None)
2935 except SystemExit as status:
2936 # If the call was made with 0 or None exit status (sys.exit(0)
2937 # or sys.exit() ), don't bother showing a traceback, as both of
(...)
2943 # For other exit status, we show the exception unless
2944 # explicitly silenced, but only in short form.
2945 if status.code:
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/IPython/utils/py3compat.py:55, in execfile(fname=PosixPath('/home/beams11/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py'), glob={'In': [''], 'Out': {}, '_': '', '__': '', '___': '', '__builtin__': <module 'builtins' (built-in)>, '__builtins__': <module 'builtins' (built-in)>, '__doc__': '\nstart bluesky in IPython session\n', '__loader__': None, '__name__': '__main__', ...}, loc={'In': [''], 'Out': {}, '_': '', '__': '', '___': '', '__builtin__': <module 'builtins' (built-in)>, '__builtins__': <module 'builtins' (built-in)>, '__doc__': '\nstart bluesky in IPython session\n', '__loader__': None, '__name__': '__main__', ...}, compiler=<built-in function compile>)
53 with open(fname, "rb") as f:
54 compiler = compiler or compile
---> 55 exec(compiler(f.read(), fname, "exec"), glob, loc)
loc = {'__name__': '__main__', '__doc__': '\nstart bluesky in IPython session\n', '__package__': None, '__loader__': None, '__spec__': None, '__builtin__': <module 'builtins' (built-in)>, '__builtins__': <module 'builtins' (built-in)>, '_ih': [''], '_oh': {}, '_dh': [PosixPath('/home/beams11/USAXS/bluesky')], 'In': [''], 'Out': {}, 'get_ipython': <bound method InteractiveShell.get_ipython of <IPython.terminal.interactiveshell.TerminalInteractiveShell object at 0x7f7bf125af10>>, 'exit': <IPython.core.autocall.ExitAutocall object at 0x7f7bf1143dd0>, 'quit': <IPython.core.autocall.ExitAutocall object at 0x7f7bf1143dd0>, 'open': <function open at 0x7f7bf1b85260>, '_': '', '__': '', '___': '', 'faulthandler': <module 'faulthandler' (built-in)>, 'pathlib': <module 'pathlib' from '/share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/pathlib.py'>, 'sys': <module 'sys' (built-in)>, 'path': PosixPath('/home/beams/USAXS/bluesky')}
glob = {'__name__': '__main__', '__doc__': '\nstart bluesky in IPython session\n', '__package__': None, '__loader__': None, '__spec__': None, '__builtin__': <module 'builtins' (built-in)>, '__builtins__': <module 'builtins' (built-in)>, '_ih': [''], '_oh': {}, '_dh': [PosixPath('/home/beams11/USAXS/bluesky')], 'In': [''], 'Out': {}, 'get_ipython': <bound method InteractiveShell.get_ipython of <IPython.terminal.interactiveshell.TerminalInteractiveShell object at 0x7f7bf125af10>>, 'exit': <IPython.core.autocall.ExitAutocall object at 0x7f7bf1143dd0>, 'quit': <IPython.core.autocall.ExitAutocall object at 0x7f7bf1143dd0>, 'open': <function open at 0x7f7bf1b85260>, '_': '', '__': '', '___': '', 'faulthandler': <module 'faulthandler' (built-in)>, 'pathlib': <module 'pathlib' from '/share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/pathlib.py'>, 'sys': <module 'sys' (built-in)>, 'path': PosixPath('/home/beams/USAXS/bluesky')}
f = <_io.BufferedReader name='/home/beams11/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py'>
compiler = <built-in function compile>
fname = PosixPath('/home/beams11/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py')
File /home/beams11/USAXS/.ipython-bluesky/profile_bluesky/startup/__start_instrument__.py:21
18 # terse error dumps
19 get_ipython().run_line_magic('xmode', 'Minimal')
---> 21 from instrument.collection import *
File /home/beams11/USAXS/bluesky/instrument/collection.py:27
24 logger.info("xmode exception level: '%s'", _xmode_level)
25 del _ip
---> 27 from . import mpl
29 logger.info("#### Bluesky Framework ####")
30 from .framework import *
File /home/beams11/USAXS/bluesky/instrument/mpl/__init__.py:31
29 from .notebook import *
30 else:
---> 31 from .console import *
File /home/beams11/USAXS/bluesky/instrument/mpl/console.py:23
20 plt.ion()
22 print(f"{matplotlib.backends.backend=!r}")
---> 23 matplotlib.use("qtAgg")
24 if matplotlib.backends.backend not in ("qtagg"):
25 raise RuntimeError(
26 f"Wrong MatPlotLib backend: {matplotlib.backends.backend=!r}"
27 )
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/matplotlib/__init__.py:1255, in use(backend='qtAgg', force=True)
1250 if plt is not None:
1251 try:
1252 # we need this import check here to re-raise if the
1253 # user does not have the libraries to support their
1254 # chosen backend installed.
-> 1255 plt.switch_backend(name)
name = 'qtAgg'
plt = <module 'matplotlib.pyplot' from '/share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/matplotlib/pyplot.py'>
1256 except ImportError:
1257 if force:
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/matplotlib/pyplot.py:415, in switch_backend(newbackend='qtAgg')
412 # have to escape the switch on access logic
413 old_backend = dict.__getitem__(rcParams, 'backend')
--> 415 module = backend_registry.load_backend_module(newbackend)
newbackend = 'qtAgg'
backend_registry = <matplotlib.backends.registry.BackendRegistry object at 0x7f7b79a918d0>
416 canvas_class = module.FigureCanvas
418 required_framework = canvas_class.required_interactive_framework
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/matplotlib/backends/registry.py:323, in BackendRegistry.load_backend_module(self=<matplotlib.backends.registry.BackendRegistry object>, backend='qtAgg')
309 """
310 Load and return the module containing the specified backend.
311
(...)
320 Module containing backend.
321 """
322 module_name = self._backend_module_name(backend)
--> 323 return importlib.import_module(module_name)
module_name = 'matplotlib.backends.backend_qtagg'
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/importlib/__init__.py:126, in import_module(name='matplotlib.backends.backend_qtagg', package=None)
124 break
125 level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)
level = 0
name = 'matplotlib.backends.backend_qtagg'
name[level:] = 'matplotlib.backends.backend_qtagg'
package = None
_bootstrap = <module '_frozen_importlib' (frozen)>
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/matplotlib/backends/backend_qtagg.py:9
5 import ctypes
7 from matplotlib.transforms import Bbox
----> 9 from .qt_compat import QT_API, QtCore, QtGui
10 from .backend_agg import FigureCanvasAgg
11 from .backend_qt import _BackendQT, FigureCanvasQT
File /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/matplotlib/backends/qt_compat.py:130
128 break
129 else:
--> 130 raise ImportError(
QT_API = 'PySide2'
_candidates = [(<function _setup_pyqt5plus at 0x7f7b66dcd3a0>, 'PyQt6'), (<function _setup_pyqt5plus at 0x7f7b66dcd3a0>, 'PySide6'), (<function _setup_pyqt5plus at 0x7f7b66dcd3a0>, 'PyQt5'), (<function _setup_pyqt5plus at 0x7f7b66dcd3a0>, 'PySide2')]
131 "Failed to import any of the following Qt binding modules: {}"
132 .format(", ".join([QT_API for _, QT_API in _candidates]))
133 )
134 else: # We should not get there.
135 raise AssertionError(f"Unexpected QT_API: {QT_API}")
ImportError: Failed to import any of the following Qt binding modules: PyQt6, PySide6, PyQt5, PySide2 |
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A clue comes from another discussion. Testing with this console command: In [3]: %gui qt
ERROR:root:/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /share1/bluesky/conda_envs/bluesky_2024_3/lib/python3.11/site-packages/PyQt5/../../../libQt5Core.so.5)Is the library file |
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That library is already installed under (/share1/bluesky/conda_envs/bluesky_2024_3) usaxs@usaxscontrol ~/bluesky $ strings $CONDA_PREFIX/lib/libstdc++.so | grep GLIBCXX | grep 26
GLIBCXX_3.4.26
_ZNSbIwSt11char_traitsIwESaIwEE4_Rep26_M_set_length_and_sharableEm@@GLIBCXX_3.4.5
_ZNSs4_Rep26_M_set_length_and_sharableEm@GLIBCXX_3.4
_ZNSbIwSt11char_traitsIwESaIwEE4_Rep26_M_set_length_and_sharableEm@GLIBCXX_3.4
_ZNSs4_Rep26_M_set_length_and_sharableEm@@GLIBCXX_3.4.5
GLIBCXX_3.4.26Solution to this problemDefine in bash shell: |
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Test proper operation using simulator: Start console session as usual: Load ophyd simulator and scan it: In [1]: from ophyd.sim import noisy_det, motor
In [2]: RE(bp.scan([noisy_det], motor, -3, 3, 31))
Transient Scan ID: 14 Time: 2024-10-27 18:21:44
Persistent Unique Scan ID: '3236f8b2-93d1-4d55-8f89-f91f29b55b02'
New stream: 'baseline'
New stream: 'primary'
+-----------+------------+------------+------------+
| seq_num | time | motor | noisy_det |
+-----------+------------+------------+------------+
| 1 | 18:21:44.3 | -3.000 | 0.009 |
| 2 | 18:21:45.3 | -2.800 | 0.022 |
| 3 | 18:21:45.3 | -2.600 | 0.085 |
| 4 | 18:21:45.3 | -2.400 | 0.105 |
| 5 | 18:21:45.3 | -2.200 | 0.149 |
| 6 | 18:21:45.3 | -2.000 | 0.186 |
| 7 | 18:21:45.3 | -1.800 | 0.267 |
| 8 | 18:21:45.3 | -1.600 | 0.335 |
| 9 | 18:21:45.3 | -1.400 | 0.410 |
| 10 | 18:21:45.3 | -1.200 | 0.405 |
| 11 | 18:21:45.3 | -1.000 | 0.629 |
| 12 | 18:21:45.3 | -0.800 | 0.704 |
| 13 | 18:21:45.4 | -0.600 | 0.867 |
| 14 | 18:21:45.4 | -0.400 | 0.843 |
| 15 | 18:21:45.4 | -0.200 | 0.983 |
| 16 | 18:21:45.4 | 0.000 | 0.999 |
| 17 | 18:21:45.4 | 0.200 | 0.911 |
| 18 | 18:21:45.4 | 0.400 | 0.958 |
| 19 | 18:21:45.4 | 0.600 | 0.804 |
| 20 | 18:21:45.4 | 0.800 | 0.751 |
| 21 | 18:21:45.4 | 1.000 | 0.663 |
| 22 | 18:21:45.4 | 1.200 | 0.445 |
| 23 | 18:21:45.4 | 1.400 | 0.468 |
| 24 | 18:21:45.4 | 1.600 | 0.374 |
| 25 | 18:21:45.4 | 1.800 | 0.295 |
| 26 | 18:21:45.4 | 2.000 | 0.218 |
| 27 | 18:21:45.5 | 2.200 | 0.042 |
| 28 | 18:21:45.5 | 2.400 | 0.150 |
| 29 | 18:21:45.5 | 2.600 | -0.009 |
| 30 | 18:21:45.5 | 2.800 | 0.074 |
| 31 | 18:21:45.5 | 3.000 | -0.076 |
+-----------+------------+------------+------------+
generator scan ['3236f8b2'] (scan num: 14)
Out[2]: ('3236f8b2-93d1-4d55-8f89-f91f29b55b02',)MatPlotLib/Qt screen from BestEffortCallback: |
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I'll try to explore why this library was not found by default. It should have been found with no additional help. Not obvious why. |
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This issue is fixed, scan verified to be working as expected. Thank you! |
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Was trying to run scan on monochromator, but it was hanging likely due to tolerance issue. Didctrl-C. 2x and RE.abort. After this run scan on s_stage.x which worked fine, but after that looks like BS crashed:
The text was updated successfully, but these errors were encountered: