OpenMM compiler failure on Windows

[cwa5555@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.dev202509190047 (2025-09-19 00:47:43 UTC)
Description
i installed the latest Intel Graphics Driver
and
repeated the miimization

got the same error as previous bug report :
error: midlevel compiler failed build.

openmm.OpenMMException: Error compiling kernel: :204:24: warning: double precision constant requires cl_khr_fp64, casting to single precision
const real PI = (real) 3.14159265358979323846;
^
fcl build 1 succeeded.
error: undefined reference to `_Z8atom_addPU3AS1mm()'

error: midlevel compiler failed build.

File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-packages\openmm\openmm.py", line 5082, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.11.dev202509190047 (2025-09-19)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/jl80/Documents/10mer_2.pdb format pdb

Chain information for 10mer_2.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> show atoms

> hide cartoons

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 10mer_2.pdb #1  
---  
notes | No usable SEQRES records for 10mer_2.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A HIS 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A 11  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
72 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\jl80\AppData\Local\Temp\tmptax_kifo\ante.in.mol2 -fi mol2 -o
C:\Users\jl80\AppData\Local\Temp\tmptax_kifo\ante.out.mol2 -fo mol2 -c bcc -nc
0 -j 5 -s 2 -dr n  
() ``  
() `Welcome to antechamber 20.0: molecular input file processor.`  
() ``  
() `Info: Finished reading file
(C:\Users\jl80\AppData\Local\Temp\tmptax_kifo\ante.in.mol2); atoms read (9),
bonds read (8).`  
() `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Info: Total number of electrons: 32; net charge: 0`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
Charges for residue determined  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 216, in _minimize  
context = Context(system, integrator)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 10.18.10.5161
OpenGL renderer: Intel(R) HD Graphics
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_US.cp65001
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: HP
Model: HP 15 Notebook PC
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 4,179,574,784
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Pentium(R) CPU  N3540  @ 2.16GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.8.0
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.16
    ChimeraX-AtomicLibrary: 14.2
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
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    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
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    ChimeraX-ButtonPanel: 1.0.1
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    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202509190047
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
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    ChimeraX-MapFit: 2.0
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    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
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    ChimeraX-ModelPanel: 1.6
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    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
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    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
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    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    ChimeraX-Shape: 1.1
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    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
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    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.4.1
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.10.6
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
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    h5py: 3.14.0
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    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
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    PyOpenGL-accelerate: 3.1.10
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    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
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    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
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    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1
File attachment: 10mer_2.pdb

10mer_2.pdb​

[cwa5555@…]

Added by email2trac

[Eric Pettersen]

Followup to #18851

[Tom Goddard]

It is possible that your 2014 CPU 4 Intel(R) Pentium(R) CPU N3540 cannot handle double precision values OpenCL, so no driver can fix it because the hardware does not have the capability. Having ChimeraX allow changing the OpenMM platform to "CPU" instead of "OpenCL" is the only likely fix. It is likely to be extremely slow on such an old CPU.

[Eric Pettersen]

Hi Web,

I have made a change to the code so that if the minimization fails in the way reported here, minimization switches to using the CPU. Please let me know if the change gets minimization to work for you. As Tom Goddard said, it's likely to be quite slow on the CPU.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[cwa5555@…]

hi Eric,
am having trouble downloading the daily release, but no trouble downloading the production release
any suggestions ?
ty,
Clarence

Sent from Yahoo Mail for iPhone


On Thursday, September 25, 2025, 18:09, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#18869: OpenMM compiler failure on Windows
----------------------------------------+----------------------
          Reporter:  cwa5555@…          |      Owner:  pett
              Type:  defect            |    Status:  feedback
          Priority:  normal            |  Milestone:
        Component:  Structure Editing  |    Version:
        Resolution:                    |  Keywords:
        Blocked By:                    |  Blocking:
Notify when closed:                    |  Platform:  all
          Project:  ChimeraX          |
----------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback

Comment:

 Hi Web,
        I have made a change to the code so that if the minimization fails
 in the way reported here, minimization switches to using the CPU.  Please
 let me know if the change gets minimization to work for you.  As Tom
 Goddard said, it's likely to be quite slow on the CPU.

 --Eric

        Eric Pettersen
        UCSF Computer Graphics Lab

[Eric Pettersen]

What exactly happens when you try to download the daily build? What browser are you using?

[cwa5555@…]

the download just hangs
MS Edge


Sent from Yahoo Mail for iPhone


On Thursday, October 16, 2025, 19:19, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#18869: OpenMM compiler failure on Windows
----------------------------------------+----------------------
          Reporter:  cwa5555@…          |      Owner:  pett
              Type:  defect            |    Status:  feedback
          Priority:  normal            |  Milestone:
        Component:  Structure Editing  |    Version:
        Resolution:                    |  Keywords:
        Blocked By:                    |  Blocking:
Notify when closed:                    |  Platform:  all
          Project:  ChimeraX          |
----------------------------------------+----------------------
Comment (by pett):

 What exactly happens when you try to download the daily build?  What
 browser are you using?

[Eric Pettersen]

I had no problem downloading it just now. Just to be clear, you do see the license-agreement page and when you click "Accept" then it hangs? Can you try a different browser?

[cwa5555@…]

yes, it hangs after i click accept
i’ll try opera


Sent from Yahoo Mail for iPhone


On Thursday, October 16, 2025, 19:29, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#18869: OpenMM compiler failure on Windows
----------------------------------------+----------------------
          Reporter:  cwa5555@…          |      Owner:  pett
              Type:  defect            |    Status:  feedback
          Priority:  normal            |  Milestone:
        Component:  Structure Editing  |    Version:
        Resolution:                    |  Keywords:
        Blocked By:                    |  Blocking:
Notify when closed:                    |  Platform:  all
          Project:  ChimeraX          |
----------------------------------------+----------------------
Comment (by pett):

 I had no problem downloading it just now.  Just to be clear, you do see
 the license-agreement page and when you click "Accept" then it hangs?  Can
 you try a different browser?

[Eric Pettersen]

Download worked in Opera; problem now being handled in ticket #19172

[cwa5555@…]

hi Support,
i cannot tell if this email means the bug is fixed or waiting to be fixed.
should i download the daily version ?
ThanksWeb Andrews


Sent from Yahoo Mail for iPhone


On Monday, October 20, 2025, 13:56, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#18869: OpenMM compiler failure on Windows
----------------------------------------+--------------------
          Reporter:  cwa5555@…          |      Owner:  pett
              Type:  defect            |    Status:  closed
          Priority:  normal            |  Milestone:
        Component:  Structure Editing  |    Version:
        Resolution:  duplicate          |  Keywords:
        Blocked By:                    |  Blocking:
Notify when closed:                    |  Platform:  all
          Project:  ChimeraX          |
----------------------------------------+--------------------
Changes (by pett):

 * resolution:  => duplicate
 * status:  accepted => closed

[Eric Pettersen]

No it is not fixed, but since there is more info in ticket #19172, I am tracking this problem with that ticket and closing this one, instead of having two tickets open for the same problem.

--Eric