New OpenMM 7.7 on Linux import error

[goddard@…]

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 "<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 666, in _load_unlocked  
File "<frozen importlib._bootstrap>", line 565, in module_from_spec  
File "<frozen importlib._bootstrap_external>", line 1173, in create_module  
File "<frozen importlib._bootstrap>", 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 <lambda>  
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 <module>  
from openmm.openmm import *  
File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site-
packages/openmm/openmm.py", line 17, in <module>  
_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 "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 666, in _load_unlocked  
File "<frozen importlib._bootstrap>", line 565, in module_from_spec  
File "<frozen importlib._bootstrap_external>", line 1173, in create_module  
File "<frozen importlib._bootstrap>", 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 <module>  
from openmm import _openmm  
File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site-
packages/openmm/__init__.py", line 19, in <module>  
from openmm.openmm import *  
File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.9/site-
packages/openmm/openmm.py", line 17, in <module>  
_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
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    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
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    PyQt6-sip: 13.4.0
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    python-dateutil: 2.8.2
    pytz: 2022.5
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    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
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    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
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    sphinxcontrib-jsmath: 1.0.1
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    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

[Tom Goddard]

This is a test of the new Linux OpenMM 7.7.0 library that Tristan provided in ticket #7857.

The error in all those tracebacks is

ImportError: libOpenMM.so.7.7: cannot open shared object file: No such file or directory

I'm not sure if the error message is wrong and it finds the file and fails to load it (Linux is prone to give misleading error messages) or if it really cannot find the library. The library is in the ChimeraX lib directory exactly where it was in the previous OpenMM 7.7.0 build we have been using.

[Tristan Croll]

Hmm… that’s a worry. In my experience Python in Linux gives that error if
any dependency of the library in question is missing. Could you run ‘ldd
libOpenMM.so.7.7’ and see what it says?

On Fri, 28 Oct 2022 at 22:49, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

For my tests today, I just removed the existing OpenMM libraries from lib
and lib/plugins, and _openmm.cpython… from lib/site-packages/openmm, and it
ran flawlessly. I feel like I need to understand more about how Singularity
works - is the container fully self-contained, or is it using some elements
of the host OS (e.g. a newer glibc)?

On Fri, 28 Oct 2022 at 23:15, Tristan Croll <tcroll@altoslabs.com> wrote:

[Tom Goddard]

The ldd output is in the original description in this ticket at the top.

[Tom Goddard]

If I replace the new

site-packages/openmm/_openmm.cpython-39-x86_64-linux-gnu.so

with the old one then it finds the libOpenMM.so.7.7 but not surprisingly gives a missing symbol error probably because the lib/libOpenMM.so.7.7 uses different name mangling.

So it appears that the new _openmm.cpython-39-x86_64-linux-gnu.so somehow can't find the libraries that are in the ChimeraX.app/lib directory. I thought those were found via RPATH set on the Python executable to that lib directory. So how could the new _openmm.cpython-39-x86_64-linux-gnu.so not find it? ldd on the new and old _openmm.cpython....so library did not reveal anything.

It seems we are in the age-old idiotic problem of knowing intricate details of how Linux finds its dynamic libraries. I've added Greg and Zach to the ticket since they may have an idea.

I also tried without stripping the openmm libraries you gave me. Made no difference.

[Greg Couch]

Use ldd to confirm that it needs a shared library from 
ChimeraX.app/lib.  I would not expect it to.  But if it does, use 
objdump and confirm that it is using RPATH and not RUNPATH.  If it is 
using RUNPATH, you can fix it with build/bin/chrpath.  The system 
chrpath does not work.

[Tom Goddard]

Thanks for the tip Greg. The problem is that the new openmm from Tristan has a RUNPATH set to /home/tcroll/openmm_build_env/install/lib.

If I delete that with "chrpath -d _openmm...so" then OpenMM can be imported.

$ readelf -d _openmm.cpython-39-x86_64-linux-gnu.so.new 

Dynamic section at offset 0x2bde70 contains 35 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libOpenMM.so.7.7]
 0x0000000000000001 (NEEDED)             Shared library: [libOpenMMAmoeba.so]
 0x0000000000000001 (NEEDED)             Shared library: [libOpenMMRPMD.so]
 0x0000000000000001 (NEEDED)             Shared library: [libOpenMMDrude.so]
 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 0x000000000000001d (RUNPATH)            Library runpath: [/home/tcroll/openmm_build_env/install/lib]
 0x000000000000000c (INIT)               0x62000
 0x000000000000000d (FINI)               0x19b544
 0x0000000000000019 (INIT_ARRAY)         0x2bd8e0
 0x000000000000001b (INIT_ARRAYSZ)       16 (bytes)
 0x000000000000001a (FINI_ARRAY)         0x2bd8f0
 0x000000000000001c (FINI_ARRAYSZ)       8 (bytes)
 0x000000006ffffef5 (GNU_HASH)           0x2f0
 0x0000000000000005 (STRTAB)             0xd990
 0x0000000000000006 (SYMTAB)             0x1cd8
 0x000000000000000a (STRSZ)              155214 (bytes)
 0x000000000000000b (SYMENT)             24 (bytes)
 0x0000000000000003 (PLTGOT)             0x2bf0e0
 0x0000000000000002 (PLTRELSZ)           28344 (bytes)
 0x0000000000000014 (PLTREL)             RELA
 0x0000000000000017 (JMPREL)             0x5a6f0
 0x0000000000000007 (RELA)               0x348a8
 0x0000000000000008 (RELASZ)             155208 (bytes)
 0x0000000000000009 (RELAENT)            24 (bytes)
 0x000000000000001e (FLAGS)              BIND_NOW
 0x000000006ffffffb (FLAGS_1)            Flags: NOW
 0x000000006ffffffe (VERNEED)            0x34798
 0x000000006fffffff (VERNEEDNUM)         4
 0x000000006ffffff0 (VERSYM)             0x337de
 0x000000006ffffff9 (RELACOUNT)          5500
 0x0000000000000000 (NULL)               0x0

[Tom Goddard]

Ok, so this problem importing OpenMM is solved with chrpath. But then tug mouse mode fails because the CPU platform is not supported, ticket #7916.

[Tristan Croll]

Sorry about all the hassle. I managed to lose track of the scripts I used
for the previous builds in the move from Cambridge Uni to Altos, so had to
(apparently not quite successfully) re-create them. The issue that I ran
into is that the scripts I started from (the same ones as last time) used
the "make PythonInstall" target to build the _openmm library - which also
attempts to install into the Python site-packages directory. That doesn't
work in a read-only Singularity container (although I vaguely remember
working around it before somehow), so I tried using the "make PythonBdist"
target instead, which bundles the Python component into a tarball. Rather
than extract that and then re-compress with the main compiled libraries, I
just grabbed everything from the build/lib.cpython... directory. I suspect
the version of _openmm actually inside the tarball probably has the RUNPATH
corrected.

On Sat, Oct 29, 2022 at 12:15 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote: