id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7915 New OpenMM 7.7 on Linux import error goddard@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-120-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.6.dev202210281747 (2022-10-28 17:47:30 UTC) Description Tristan's new Linux OpenMM library does not work in this Ubuntu 20.04 build of ChimeraX from today's develop branch code. It seems it can't find libOpenMM.so.7.7. But that library is in the ChimeraX lib directory exactly where the previous OpenMM library is with the same name. The previous OpenMM works fine in this build. It does not appear that an dependencies are missing: goddard@beetracker:~/ucsf/chimerax/ChimeraX.app/lib$ ldd libOpenMM.so.7.7 linux-vdso.so.1 (0x00007ffffa7dc000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fef34af9000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fef34af3000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fef34ad0000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fef348ee000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fef3479f000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fef34784000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fef34590000) /lib64/ld-linux-x86-64.so.2 (0x00007fef34ebc000) Log: UCSF ChimeraX version: 1.6.dev202210281747 (2022-10-28) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1mtx format mmcif fromDatabase pdb 1mtx title: Determination of the three-dimensional structure of margatoxin by 1H, 13C, 15N triple-resonance nuclear magnetic resonance spectroscopy [more info...] Chain information for 1mtx --- Chain | Description | UniProt 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A | MARGATOXIN | SCKM_CENMA > close #1.2-30 > hide cartoons > show atoms > ui mousemode right tug Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 14, in swig_import_helper return importlib.import_module(mname) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 666, in _load_unlocked File """", line 565, in module_from_spec File """", line 1173, in create_module File """", line 228, in _call_with_frames_removed ImportError: libOpenMM.so.7.7: cannot open shared object file: No such file or directory During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/mouse_modes/mousemodes.py"", line 637, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 77, in mouse_down self._pick_atom(pick) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 86, in _pick_atom self._tugger = st = StructureTugger(a.structure) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 231, in __init__ from openmm import unit File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/__init__.py"", line 19, in from openmm.openmm import * File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 17, in _openmm = swig_import_helper() File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 16, in swig_import_helper return importlib.import_module('_openmm') File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) ModuleNotFoundError: No module named '_openmm' ModuleNotFoundError: No module named '_openmm' File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) See log for complete Python traceback. > open /home/goddard/Downloads/test_openmm.py Traceback (most recent call last): File """", line 986, in _find_and_load_unlocked File """", line 666, in _load_unlocked File """", line 565, in module_from_spec File """", line 1173, in create_module File """", line 228, in _call_with_frames_removed ImportError: libOpenMM.so.7.7: cannot open shared object file: No such file or directory During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/goddard/Downloads/test_openmm.py"", line 1, in from openmm import _openmm File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/__init__.py"", line 19, in from openmm.openmm import * File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 17, in _openmm = swig_import_helper() File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site- packages/openmm/openmm.py"", line 16, in swig_import_helper return importlib.import_module('_openmm') File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) ModuleNotFoundError: No module named '_openmm' Error opening python file /home/goddard/Downloads/test_openmm.py OpenGL version: 4.6 (Core Profile) Mesa 21.2.6 OpenGL renderer: Mesa Intel(R) HD Graphics 6000 (BDW GT3) OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:0 Manufacturer: unknown Model: unknown OS: Ubuntu 20.04 Focal Fossa Architecture: 64bit ELF Virtual Machine: none CPU: 4 Intel(R) Core(TM) i5-5250U CPU @ 1.60GHz Cache Size: 3072 KB Memory: total used free shared buff/cache available Mem: 15Gi 1.6Gi 274Mi 604Mi 13Gi 13Gi Swap: 2.0Gi 2.0Mi 2.0Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 6000 [8086:1626] (rev 09) Subsystem: Intel Corporation HD Graphics 6000 [8086:2057] Kernel driver in use: i915 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.43.3 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202210281747 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.25.1 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 entrypoints: 0.4 executing: 1.1.1 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.2 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 prompt-toolkit: 3.0.31 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.5 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.2.1 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.5.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.10.0 }}} " defect closed normal Platform fixed Greg Couch Zach Pearson all ChimeraX