[cctbxbb] DYLD_FALLBACK_LIBRARY_PATH

Winter, Graeme (DLSLtd,RAL,LSCI) Graeme.Winter at diamond.ac.uk
Tue Jan 4 01:23:37 PST 2022 

OK, I can confirm that the dispatcher_thing_workaround.sh works - I cannot work out where the need for the environment variable comes from but I suspect someone who has built some of the packages napari depends on (ohai ctypes) had it set…

Cheers G

On 4 Jan 2022, at 08:54, Winter, Graeme (DLSLtd,RAL,LSCI) <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> wrote:

Hi Billy

Sorry for the slow reply - long down time over the festive break (much needed)

Reloading the pages now

One thing which occurs to me is that this is a build-dependent solution - so would not be portable to the general end user in the event that we ship something which depends on this (e.g. in this case, napari)

I will see if I can get a “clean build” which works without this being set in the first place then investigate some more. I have no idea where the variable is coming from…

Cheers Graeme

On 17 Dec 2021, at 20:12, Billy Poon <bkpoon at lbl.gov<mailto:bkpoon at lbl.gov>> wrote:

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<https://phenix-online.org/>


On Thu, Dec 16, 2021 at 2:46 AM Winter, Graeme (DLSLtd,RAL,LSCI) <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> 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) <graeme.winter at diamond.ac.uk<mailto:graeme.winter at diamond.ac.uk>> 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 <bkpoon at lbl.gov<mailto:bkpoon at lbl.gov>> 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<https://phenix-online.org/>


On Tue, Dec 14, 2021 at 9:30 AM Winter, Graeme (DLSLtd,RAL,LSCI) <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> 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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