Reading hdf5 files broken on Mac

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202111181350 (2021-11-18 13:50:17 UTC)
Description
Can't read segger .seg file.  Apparently PyTables broken due to hdf library problem.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.4.dev202111181350 (2021-11-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Desktop/test.seg format segger

Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 333, in interceptRequest  
self._callback(info)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 366, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 468, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 397, in thread_safe  
func(*args, **kw)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 459, in defer  
cxcmd(session, topic)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 477, in cxcmd  
run(session, cmd)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2875, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2875, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/__init__.py", line 45, in open  
return open_segmentation(session, path, file_name)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segfile.py", line 116, in open_segmentation  
seg = read_segmentation(session, path, open = False)  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segfile.py", line 281, in read_segmentation  
import tables  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/__init__.py", line 99, in <module>  
from .utilsextension import (  
ImportError:
dlopen(/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/utilsextension.cpython-39-darwin.so, 0x0002): Library not
loaded: .dylibs/libhdf5.200.dylib  
Referenced from:
/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/utilsextension.cpython-39-darwin.so  
Reason: tried:
'/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/MacOS/../lib/.dylibs/libhdf5.200.dylib'
(no such file),
'/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/MacOS/../Library/Frameworks/Python.framework/.dylibs/libhdf5.200.dylib'
(no such file), '.dylibs/libhdf5.200.dylib' (no such file),
'/usr/lib/libhdf5.200.dylib' (no such file)  
  
ImportError:
dlopen(/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/utilsextension.cpython-39-darwin.so, 0x0002): Library not
loaded: .dylibs/libhdf5.200.dylib  
Referenced from:
/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/utilsextension.cpython-39-darwin.so  
Reason: tried:
'/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/MacOS/../lib/.dylibs/libhdf5.200.dylib'
(no such file),
'/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/MacOS/../Library/Frameworks/Python.framework/.dylibs/libhdf5.200.dylib'
(no such file), '.dylibs/libhdf5.200.dylib' (no such file),
'/usr/lib/libhdf5.200.dylib' (no such file)  
  
File
"/Users/goddard/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/tables/__init__.py", line 99, in  
from .utilsextension import (  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 447.40.12.0.0
      OS Loader Version: 540.40.4~45
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 20 days 19:37

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.2
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.1.7
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
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    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
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    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
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    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202111181350
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    ChimeraX-FunctionKey: 1.0
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    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
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    ChimeraX-HKCage: 1.3
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    ParmEd: 3.2.0
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    wcwidth: 0.2.5
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    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tom Goddard]

This same test works on my Mac laptop. Possibly it is using some libraries I have installed on that development machine that are not on the office iMac where the error occurs.

[Tom Goddard]

Fails on the laptop in the Nov 11 release candidate build. Not sure what is special about my development build that makes it work.

[Tom Goddard]

Fixed.

The pytables libraries on Mac were using relative runtime linking paths like .dylibs/libhdf5.200.dylib. Those needed to be @loader_path/.dylibs/libhdf5.200.dylib. I was not able to figure out why my ChimeraX development build worked with the incorrect paths while release candidate and daily builds failed as expected. But I tested the fix in the release candidate build.