Re: [cctbxbb] DYLD_FALLBACK_LIBRARY_PATH

Hi Billy Sorry for the slow response - needed to be near the right computer & currently bouncing between office and home for work Rebuilt base to give a clean starting point, on default Python (3.9) -> this is the package list I conda install -c c-f napari’d - getting me to here - Then silver-surfer viewer :) $ dials.python viewer.py /Users/graeme/data/i04-1-2021-run3-ins/Insulin_6_2.nxs Traceback (most recent call last): File "/Users/graeme/work/viewer/viewer.py", line 24, in <module> viewer = napari.view_image(d, title="DIALS Image Viewer", File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/_lazy.py", line 47, in __getattr__ submod = import_module(f'{module_name}.{attr_to_modules[name]}') File "/Users/graeme/git/dials/conda_base/python.app/Contents/lib/python3.9/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1030, in _gcd_import File "<frozen importlib._bootstrap>", line 1007, in _find_and_load File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 680, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 850, in exec_module File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/view_layers.py", line 17, in <module> from .viewer import Viewer File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/viewer.py", line 5, in <module> from .components.viewer_model import ViewerModel File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/components/__init__.py", line 19, in <module> from .layerlist import LayerList File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/components/layerlist.py", line 8, in <module> from ..layers import Image, Labels, Layer File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/layers/__init__.py", line 12, in <module> from .image import Image File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/layers/image/__init__.py", line 1, in <module> from .image import Image File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/layers/image/image.py", line 12, in <module> from ...utils import config File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/utils/config.py", line 5, in <module> from ._octree import get_octree_config File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/utils/_octree.py", line 11, in <module> from ..settings import get_settings File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/settings/__init__.py", line 6, in <module> from ._napari_settings import NapariSettings File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/settings/_napari_settings.py", line 9, in <module> from ._appearance import AppearanceSettings File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/settings/_appearance.py", line 4, in <module> from ..utils.theme import available_themes File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/utils/theme.py", line 20, in <module> from .._vendor import darkdetect File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/_vendor/darkdetect/__init__.py", line 17, in <module> from ._mac_detect import * File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/_vendor/darkdetect/_mac_detect.py", line 18, in <module> objc = ctypes.cdll.LoadLibrary('libobjc.dylib') File "/Users/graeme/git/dials/conda_base/python.app/Contents/lib/python3.9/ctypes/__init__.py", line 460, in LoadLibrary return self._dlltype(name) File "/Users/graeme/git/dials/conda_base/python.app/Contents/lib/python3.9/ctypes/__init__.py", line 382, in __init__ self._handle = _dlopen(self._name, mode) OSError: dlopen(libobjc.dylib, 6): image not found And silver-surfer viewer :( $ cctbx.python -c "from napari import viewer" Traceback (most recent call last): File "<string>", line 1, in <module> File "<frozen importlib._bootstrap>", line 1055, in _handle_fromlist File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/_lazy.py", line 45, in __getattr__ return import_module(f'{module_name}.{name}') File "/Users/graeme/git/dials/conda_base/python.app/Contents/lib/python3.9/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/viewer.py", line 5, in <module> from .components.viewer_model import ViewerModel File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/components/__init__.py", line 19, in <module> from .layerlist import LayerList File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/components/layerlist.py", line 8, in <module> from ..layers import Image, Labels, Layer File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/layers/__init__.py", line 12, in <module> from .image import Image File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/layers/image/__init__.py", line 1, in <module> from .image import Image File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/layers/image/image.py", line 12, in <module> from ...utils import config File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/utils/config.py", line 5, in <module> from ._octree import get_octree_config File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/utils/_octree.py", line 11, in <module> from ..settings import get_settings File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/settings/__init__.py", line 6, in <module> from ._napari_settings import NapariSettings File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/settings/_napari_settings.py", line 9, in <module> from ._appearance import AppearanceSettings File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/settings/_appearance.py", line 4, in <module> from ..utils.theme import available_themes File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/utils/theme.py", line 20, in <module> from .._vendor import darkdetect File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/_vendor/darkdetect/__init__.py", line 17, in <module> from ._mac_detect import * File "/Users/graeme/git/dials/conda_base/lib/python3.9/site-packages/napari/_vendor/darkdetect/_mac_detect.py", line 18, in <module> objc = ctypes.cdll.LoadLibrary('libobjc.dylib') File "/Users/graeme/git/dials/conda_base/python.app/Contents/lib/python3.9/ctypes/__init__.py", line 460, in LoadLibrary return self._dlltype(name) File "/Users/graeme/git/dials/conda_base/python.app/Contents/lib/python3.9/ctypes/__init__.py", line 382, in __init__ self._handle = _dlopen(self._name, mode) OSError: dlopen(libobjc.dylib, 6): image not found however silver-surfer viewer :( $ which python3 /Users/graeme/git/dials/conda_base/bin/python3 silver-surfer viewer :) $ python3 -c "from napari import viewer" silver-surfer viewer :) $ Following these instructions on macOS should reproduce the problem https://dials.github.io/documentation/installation_developer.html (with an additional conda install napari) - am running on Big Sur here. I generated this email with fresh bootstrap -> should be reproducible Thanks for any help you can offer! Graeme On 14 Dec 2021, at 19:15, Billy Poon mailto:[email protected]> wrote: Hi Graeme, The DYLD_FALLBACK_LIBRARY_PATH is prepended because we want cctbx libraries to come before any other user defined libraries when running cctbx code. Otherwise, there is no way to guarantee that any libraries that the user overrides in their environment will actually work with cctbx code. Are you using conda? How did you construct your conda environment? You should be able to use "conda install napari" in your conda_base directory or some other conda environment that you use for building. Can you list your environment (i.e. conda list)? And the explicit one so that it can be reproduced (conda list -e --explicit --md5)? Also, steps to reproduce your build would be helpful in reproducing the error. I tested "conda install -c conda-forge napari" in my Python 3.7 conda_base directory and the import works without any errors from cctbx.python. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.orghttps://phenix-online.org/ On Tue, Dec 14, 2021 at 9:30 AM Winter, Graeme (DLSLtd,RAL,LSCI) mailto:[email protected]> wrote: Hi Folks, By default cctbx dispatchers on macOS clobber DYLD_FALLBACK_LIBRARY_PATH with some stuff which means that from napari import viewer fails with a huge stack trace ending in OSError: dlopen(libobjc.dylib, 6): image not found If I comment out the clobbering in the dispatcher then everything works fine so I am fairly sure this is the problem Some questions - - why do we do this? - is there a way I can make a dispatcher not to this? or maybe leave the system DYLD… as it was and _append_ to rather than prepend? Seems like a thing I am surprised I have not broken a toe on before now Thanks Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). 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