Opened 10 months ago

Closed 10 months ago

#16637 closed defect (can't reproduce)

Session restore: HDF5: file signature not found

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.12.9-arch1-1.2-g14-x86_64-with-glibc2.40
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /home/aaron/LocalSend/pollo.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Log from Thu Jan 16 17:52:49 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /data/ScipionUserData/projects/aaron_y_boris/Runs/000585_EmanProtInitModel/extra/initial_models/model_00_01.hdf

Opened model_00_01.hdf as #1, grid size 120,120,120, pixel 1.77, shown at
level 3.97, step 1, values float32  

> save /home/scipion/Downloads/pollo.cxs

——— End of log from Thu Jan 16 17:52:49 2025 ———

opened ChimeraX session  

> open /home/aaron/LocalSend/pollo.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/core/session.py",
line 757, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/map/session.py",
line 231, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/map/session.py",
line 412, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/map/session.py",
line 483, in open_data  
grids, error_message = opendialog.open_grid_files(paths_and_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/opendialog.py", line 38, in open_grid_files  
glist = open_file(path, file_type, log = log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 171, in open_file  
data = open_func(apath, **okw)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 58, in __init__  
f = tables.open_file(path)  
^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/tables/file.py", line 300, in
open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/tables/file.py", line 750, in
__init__  
self._g_new(filename, mode, **params)  
File "tables/hdf5extension.pyx", line 484, in tables.hdf5extension.File._g_new  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "H5F.c", line 620, in H5Fopen  
unable to open file  
File "H5VLcallback.c", line 3501, in H5VL_file_open  
failed to iterate over available VOL connector plugins  
File "H5PLpath.c", line 578, in H5PL__path_table_iterate  
can't iterate over plugins in plugin path '(null)'  
File "H5PLpath.c", line 620, in H5PL__path_table_iterate_process_path  
can't open directory: /usr/local/hdf5/lib/plugin  
File "H5VLcallback.c", line 3351, in H5VL__file_open  
open failed  
File "H5VLnative_file.c", line 97, in H5VL__native_file_open  
unable to open file  
File "H5Fint.c", line 1990, in H5F_open  
unable to read superblock  
File "H5Fsuper.c", line 405, in H5F__super_read  
file signature not found  
  
End of HDF5 error back trace  
  
Unable to open/create file '/home/aaron/LocalSend/pollo.cxs'  
  
opened ChimeraX session  

> open /home/aaron/LocalSend/pollo.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/core/session.py",
line 757, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/map/session.py",
line 231, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/map/session.py",
line 412, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/chimerax/map/session.py",
line 483, in open_data  
grids, error_message = opendialog.open_grid_files(paths_and_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/opendialog.py", line 38, in open_grid_files  
glist = open_file(path, file_type, log = log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 171, in open_file  
data = open_func(apath, **okw)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 58, in __init__  
f = tables.open_file(path)  
^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/tables/file.py", line 300, in
open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/opt/chimerax/lib/python3.11/site-packages/tables/file.py", line 750, in
__init__  
self._g_new(filename, mode, **params)  
File "tables/hdf5extension.pyx", line 484, in tables.hdf5extension.File._g_new  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "H5F.c", line 620, in H5Fopen  
unable to open file  
File "H5VLcallback.c", line 3501, in H5VL_file_open  
failed to iterate over available VOL connector plugins  
File "H5PLpath.c", line 578, in H5PL__path_table_iterate  
can't iterate over plugins in plugin path '(null)'  
File "H5PLpath.c", line 620, in H5PL__path_table_iterate_process_path  
can't open directory: /usr/local/hdf5/lib/plugin  
File "H5VLcallback.c", line 3351, in H5VL__file_open  
open failed  
File "H5VLnative_file.c", line 97, in H5VL__native_file_open  
unable to open file  
File "H5Fint.c", line 1990, in H5F_open  
unable to read superblock  
File "H5Fsuper.c", line 405, in H5F__super_read  
file signature not found  
  
End of HDF5 error back trace  
  
Unable to open/create file '/home/aaron/LocalSend/pollo.cxs'  
  
opened ChimeraX session  




OpenGL version: 4.6 (Core Profile) Mesa 24.3.3-arch1.2
OpenGL renderer: AMD Radeon 660M (radeonsi, rembrandt, LLVM 19.1.6, DRM 3.59, 6.12.9-arch1-1.2-g14)
OpenGL vendor: AMD

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasmax11
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming A15 FA506NF_FA506NF
OS: Arch Linux rolling n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 AMD Ryzen 5 7535HS with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            22Gi       9.5Gi        10Gi       484Mi       3.9Gi        13Gi
	Swap:           19Gi        32Mi        19Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA107 [GeForce RTX 2050] [10de:25ad] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:1dc3]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 10 months ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session restore: HDF5: file signature not found

comment:2 by Tom Goddard, 10 months ago

Resolution: → can't reproduce
Status: assigned → closed

Online posts say this HDF "file signature not found" error means either the HDF5 files is corrupted, or not an HDF5 file or is an HDF4 file. The file is being referenced from a ChimeraX session file so ChimeraX must have opened it in the past. But maybe the file has changed and the session now points to a corrupted file.

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