Re: [cctbxbb] DYLD_FALLBACK_LIBRARY_PATH

Hi Graeme, Are you normally setting DYLD_FALLBACK_LIBRARY_PATH in your environment? When I run python3 -c 'import os; print(os.environ["DYLD_FALLBACK_LIBRARY_PATH"])' I get a KeyError since I do not have anything defined. If you are setting DYLD_FALLBACK_LIBRARY_PATH normally for builds, then this does require special handling and the general solution is to add those paths to your dispatchers using the "dispatcher_include_template.sh" in your build directory. I generally would not recommend defining that environment variable since it will override some of the libraries that are linked during the build phase (also depends on the Xcode version since /usr/lib for Xcode 13 is very different from Xcode 11). This is especially important if you are using conda packages for dependencies since the conda environment is essentially self-contained. I was only able to reproduce the crash by setting DYLD_FALLBACK_LIBRARY_PATH before building. To make the import work, I have attached a modified "dispatcher_include_template.sh" which defines DYLD_FALLBACK_LIBRARY_PATH=/usr/X11/lib:/usr/lib prior to the check for DYLD_FALLBACK_LIBRARY_PATH. Put this file in your build directory and run "libtbx.refresh" to regenerate your dispatchers with the new setting. You should be able to see the change in the dispatcher for cctbx.python. It should look like this LIBTBX_DISPATCHER_NAME="cctbx.python" export LIBTBX_DISPATCHER_NAME # ---------------------------------------------------------------------------------------- # included from /Users/bkpoon/software/dials/build/dispatcher_include_DYLD_LIBRARY_PATH.sh # Commands to be executed at the start of the # auto-generated dispatchers in bin. export DYLD_FALLBACK_LIBRARY_PATH=/usr/X11/lib:/usr/lib # # ---------------------------------------------------------------------------------------- We use this approach for linking certain libraries on HPC builds since those systems usually have some optimized libraries that we want to use. The "disptacher_include_template.sh" approach also allows you to choose where in the dispatcher to add the changes so that the order of the paths can be customized. Let me know if that does not work. -- 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.org On Thu, Dec 16, 2021 at 2:46 AM Winter, Graeme (DLSLtd,RAL,LSCI) < [email protected]> wrote:

OK, this is to do with macOS and SIP - I suspect you may have disabled this at some point in the past perhaps?

Anyhow, I found a workaround, PR in https://github.com/cctbx/cctbx_project/pull/702

To my eyeballs at least it seems relatively harmless since it is largely restoring the behaviour we would have expected anyway

Thanks and cheerio Graeme

On 16 Dec 2021, at 07:03, Winter, Graeme (DLSLtd,RAL,LSCI) < [email protected]> wrote:

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 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.org

On Tue, Dec 14, 2021 at 9:30 AM Winter, Graeme (DLSLtd,RAL,LSCI) < [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

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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). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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