Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6745 closed defect (fixed)

Mac M1 pytables broken: libsnappy.1.dylib not loaded

Reported by: goddard@… Owned by: Zach Pearson
Priority: normal Milestone: 1.4
Component: Platform Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.3.1-arm64-arm-64bit
ChimeraX Version: 1.4.dev202204220707 (2022-04-22 07:07:55 UTC)
Description
Mac M1 PyTables broken.  Test using these two commands

open 1080 from emdb
save test.cmap



Log:
UCSF ChimeraX version: 1.4.dev202204220707 (2022-04-22)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1080 fromDatabase emdb

Summary of feedback from opening 1080 fetched from emdb  
---  
note | Fetching compressed map 1080 from
ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-1080/map/emd_1080.map.gz  
  
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32  

> save test.cmap

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save  
save_map(session, path, _name, **kw)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/cmap/write_cmap.py", line 80, in
write_grid_as_chimera_map  
import tables  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/__init__.py", line 11, in <module>  
from .utilsextension import get_hdf5_version as _get_hdf5_version  
ImportError:
dlopen(/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/utilsextension.cpython-39-darwin.so, 0x0002): Library not
loaded: @rpath/libcrypto.3.dylib  
Referenced from:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libhdf5.200.dylib  
Reason: tried:
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.3.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libcrypto.3.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libcrypto.3.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../lib/libcrypto.3.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../Library/Frameworks/Python.framework/libcrypto.3.dylib'
(no such file), '/usr/local/lib/libcrypto.3.dylib' (no such file),
'/usr/lib/libcrypto.3.dylib' (no such file)Library not loaded:
@rpath/libsnappy.1.dylib  
Referenced from:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libblosc.1.dylib  
Reason: tried:
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libsnappy.1.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libsnappy.1.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libsnappy.1.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../lib/libsnappy.1.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../Library/Frameworks/Python.framework/libsnappy.1.dylib'
(no such file), '/usr/local/lib/libsnappy.1.dylib' (no such file),
'/usr/lib/libsnappy.1.dylib' (no such file)  
  

Populating font family aliases took 88 ms. Replace uses of missing font family
".AppleSystemUIFont" with one that exists to avoid this cost.  

ImportError:
dlopen(/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/utilsextension.cpython-39-darwin.so, 0x0002): Library not
loaded: @rpath/libcrypto.3.dylib  
Referenced from:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libhdf5.200.dylib  
Reason: tried:
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.3.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libcrypto.3.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libcrypto.3.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../lib/libcrypto.3.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../Library/Frameworks/Python.framework/libcrypto.3.dylib'
(no such file), '/usr/local/lib/libcrypto.3.dylib' (no such file),
'/usr/lib/libcrypto.3.dylib' (no such file)Library not loaded:
@rpath/libsnappy.1.dylib  
Referenced from:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libblosc.1.dylib  
Reason: tried:
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libsnappy.1.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libsnappy.1.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/../../../libsnappy.1.dylib' (no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../lib/libsnappy.1.dylib'
(no such file),
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../Library/Frameworks/Python.framework/libsnappy.1.dylib'
(no such file), '/usr/local/lib/libsnappy.1.dylib' (no such file),
'/usr/lib/libsnappy.1.dylib' (no such file)  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/__init__.py", line 11, in  
from .utilsextension import get_hdf5_version as _get_hdf5_version  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.101.3
      OS Loader Version: 7459.101.3

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 24 days 2:09

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.38.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.3
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202204220707
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.5
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.2
    funcparserlib: 1.0.0a1
    grako: 3.16.5
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2022.2.22
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.8
    PyQt6: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (13)

comment:1 by Tom Goddard, 4 years ago

Component: Unassigned → Platform
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Mac M1 pytables broken: libsnappy.1.dylib not loaded

comment:2 by Tom Goddard, 4 years ago

Milestone: → 1.4

comment:3 by Zach Pearson, 4 years ago

Nice find! I tested the tables import using just import tables -- it must not have hit a codepath that required that library. I'll get it up on the prereqs repo.

comment:4 by Zach Pearson, 4 years ago

Intel ChimeraX has libcrypto.1.1.dylib or libcrypto.dylib but not libsnappy. I wonder why arm64 ChimeraX needs it.

comment:5 by Zach Pearson, 4 years ago

But like the other ticket, even without this library it doesn't reproduce on my laptop.

comment:6 by Tom Goddard, 4 years ago

The llibhdf5.200.dylib installed by a Mac M1 Chimera build has several dependent libraries

$ otool -L libhdf5.200.dylib
libhdf5.200.dylib:

@rpath/libhdf5.200.dylib (compatibility version 202.0.0, current version 202.0.0)
@rpath/libcrypto.3.dylib (compatibility version 3.0.0, current version 3.0.0)
@rpath/libcurl.4.dylib (compatibility version 12.0.0, current version 12.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.0.0)
@rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)

$

comment:7 by Tom Goddard, 4 years ago

And libblosc.1.dylib has a missing dependency libsnappy.1.dylib.

$ otool -L libblosc.1.dylib
libblosc.1.dylib:

@rpath/libblosc.1.dylib (compatibility version 1.0.0, current version 1.21.1)
@rpath/libsnappy.1.dylib (compatibility version 1.0.0, current version 1.1.8)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.0.0)

$

comment:8 by Zach Pearson, 4 years ago

This should be fixed, but before I close the ticket if you could go to prereqs/pips and make app-install that would be helpful. The tarballs I downloaded contained unsigned libraries, but libraries from the conda package manager are signed for some reason. I want to make sure this isn't specific to a machine before closing the ticket.

comment:9 by Tom Goddard, 4 years ago

I did make app-install in prereqs/pips and see that it installed libsnappy. But the test case still fails, now with libcrypto.3.dylib missing. Did you run the test case given in this ticket?

UCSF ChimeraX version: 1.4.dev202204220707 (2022-04-22)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open 1080 format ccp4 fromDatabase emdb
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68, step 1, values float32
save test.cmap
Traceback (most recent call last):
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run
    result = ci.function(session, **kw_args)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75, in cmd_save
    Command(session, registry=registry).run(provider_cmd_text, log=log)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run
    result = ci.function(session, **kw_args)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 89, in provider_save
    saver_info.save(session, path, **provider_kw)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/__init__.py", line 185, in save
    save_map(session, path, _name, **kw)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 3972, in save_map
    save_grid_data(grids, path, session, format_name, options)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
    ff.save_func(garg, tpath, options = options, progress = p)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map_data/cmap/write_cmap.py", line 80, in write_grid_as_chimera_map
    import tables
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/__init__.py", line 11, in <module>
    from .utilsextension import get_hdf5_version as _get_hdf5_version
ImportError: dlopen(/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/utilsextension.cpython-39-darwin.so, 0x0002): Library not loaded: @rpath/libcrypto.3.dylib
  Referenced from: /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libhdf5.200.dylib
  Reason: tried: '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/../../../libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/../../../libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../lib/libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../Library/Frameworks/Python.framework/libcrypto.3.dylib' (no such file), '/usr/local/lib/libcrypto.3.dylib' (no such file), '/usr/lib/libcrypto.3.dylib' (no such file)

Populating font family aliases took 87 ms. Replace uses of missing font family ".AppleSystemUIFont" with one that exists to avoid this cost.
ImportError: dlopen(/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/utilsextension.cpython-39-darwin.so, 0x0002): Library not loaded: @rpath/libcrypto.3.dylib
Referenced from: /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libhdf5.200.dylib
Reason: tried: '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/../../../libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/../../../libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../lib/libcrypto.3.dylib' (no such file), '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/../Library/Frameworks/Python.framework/libcrypto.3.dylib' (no such file), '/usr/local/lib/libcrypto.3.dylib' (no such file), '/usr/lib/libcrypto.3.dylib' (no such file)

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tables/__init__.py", line 11, in
from .utilsextension import get_hdf5_version as _get_hdf5_version

See log for complete Python traceback.
Last edited 4 years ago by Tom Goddard (previous) (diff)

comment:10 by Zach Pearson, 4 years ago

Yes, but between netcdf and pytables, copying dylibs into my build and then to plato, I thought it would be likely that I missed one. Thanks!

in reply to:  11 ; comment:11 by goddard@…, 4 years ago 

Best to test yourself.  It becomes rather inefficient for one person to make changes and another person test.  Do a fresh build and test.  Once it works for you in a fresh build then it is fine to ask others to test.

comment:12 by Zach Pearson, 4 years ago

Resolution: → fixed
Status: assigned → closed

Sure, never meant to interrupt your flow. ​This should take care of it. Tested on a fresh build.

in reply to:  13 ; comment:13 by goddard@…, 4 years ago 

Works for me too.
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