OpenMM: Error compiling program: nvrtc: error: failed to open libnvrtc-builtins.so

[pett]

The following bug report has been submitted:
Platform: Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open /nfs/userdocs/sch/walsh/MwergedPDB-KKSP.pdb format pdb

Chain information for MwergedPDB-KKSP.pdb #1
---
Chain | Description
A R | No description available
B S | No description available
C T | No description available
D U | No description available
E V | No description available
F W | No description available
G X | No description available
H Y | No description available
I Z | No description available
J a | No description available
K b | No description available
L c | No description available
M d | No description available
N e | No description available
O f | No description available
P g | No description available
Q h | No description available

open /nfs/userdocs/sch/walsh/Downloads/preholo_3A_J319_C2_sharp.mrc format
mrc

Opened preholo_3A_J319_C2_sharp.mrc as #2, grid size 360,360,360, pixel 1.06,
shown at level 0.305, step 2, values float32

addh

Summary of feedback from adding hydrogens to MwergedPDB-KKSP.pdb #1
---
notes | No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain A;
guessing termini instead
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain B; guessing
termini instead
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain C; guessing
termini instead
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain D; guessing
termini instead
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain E; guessing
termini instead
29 messages similar to the above omitted
Chain-initial residues that are actual N termini: /B ASP 3, /C TYR 6, /D TYR
4, /E MET 1, /F MET 1, /G THR 2, /H VAL 21, /I ALA 2, /J SER 6, /M PHE 21, /O
MET 1, /P SER 2, /Q PRO 37, /S ASP 3, /T TYR 6, /U TYR 4, /V MET 1, /W MET 1,
/X THR 2, /Y VAL 21, /Z ALA 2, /a SER 6, /d PHE 21, /f MET 1, /g SER 2, /h PRO
37
Chain-initial residues that are not actual N termini: /A GLY 11, /A GLU 197,
/C VAL 225, /D LEU 52, /D SER 62, /D ALA 209, /E ARG 132, /G LEU 187, /G ASP
211, /H THR 132, /I THR 30, /I SER 231, /J PHE 40, /J GLY 184, /K ASP 2, /K
GLY 24, /K ASP 32, /K VAL 179, /L THR 79, /L ASP 127, /L MET 173, /L ASN 252,
/M LEU 194, /N GLY 14, /O VAL 117, /O PRO 163, /P SER 57, /P ASN 128, /P VAL
164, /P PRO 199, /P ALA 237, /Q LEU 120, /R GLY 11, /R GLU 197, /T VAL 225, /U
LEU 52, /U SER 62, /U ALA 209, /V ARG 132, /X LEU 187, /X ASP 211, /Y THR 132,
/Z THR 30, /Z SER 231, /a PHE 40, /a GLY 184, /b ASP 2, /b GLY 24, /b ASP 32,
/b VAL 179, /c THR 79, /c ASP 127, /c MET 173, /c ASN 252, /d LEU 194, /e GLY
14, /f VAL 117, /f PRO 163, /g SER 57, /g ASN 128, /g VAL 164, /g PRO 199, /g
ALA 237, /h LEU 120
Chain-final residues that are actual C termini: /A GLN 251, /B ALA 249, /C ILE
244, /F ILE 234, /H ILE 148, /I ILE 249, /K PHE 195, /M ASP 241, /N LEU 215,
/O ILE 276, /P PHE 262, /Q GLU 248, /R GLN 251, /S ALA 249, /T ILE 244, /W ILE
234, /Y ILE 148, /Z ILE 249, /b PHE 195, /d ASP 241, /e LEU 215, /f ILE 276,
/g PHE 262, /h GLU 248
Chain-final residues that are not actual C termini: /A PHE 186, /C LYS 218, /D
GLU 237, /D ARG 48, /D THR 60, /D VAL 202, /E GLU 247, /E GLY 126, /G ALA 243,
/G PRO 184, /G HIS 204, /H GLY 125, /I ASN 18, /I PRO 222, /J LYS 201, /J ASP
26, /J ALA 175, /K LYS 19, /K LEU 28, /K MET 174, /L HIS 264, /L VAL 92, /L
LYS 167, /L VAL 205, /M ASN 174, /O VAL 80, /O ALA 159, /P GLU 52, /P GLU 125,
/P PHE 145, /P LEU 193, /P GLN 231, /Q TYR 109, /R PHE 186, /T LYS 218, /U GLU
237, /U ARG 48, /U THR 60, /U VAL 202, /V GLU 247, /V GLY 126, /X ALA 243, /X
PRO 184, /X HIS 204, /Y GLY 125, /Z ASN 18, /Z PRO 222, /a LYS 201, /a ASP 26,
/a ALA 175, /b LYS 19, /b LEU 28, /b MET 174, /c HIS 264, /c VAL 92, /c LYS
167, /c VAL 205, /d ASN 174, /f VAL 80, /f ALA 159, /g GLU 52, /g GLU 125, /g
PHE 145, /g LEU 193, /g GLN 231, /h TYR 109
5569 hydrogen bonds
/D GLU 237 is not terminus, removing H atom from 'C'
/E GLU 247 is not terminus, removing H atom from 'C'
/G ALA 243 is not terminus, removing H atom from 'C'
/J LYS 201 is not terminus, removing H atom from 'C'
/L HIS 264 is not terminus, removing H atom from 'C'
5 messages similar to the above omitted
46 hydrogens added

clipper associate #2 toModel #1

Opened preholo_3A_J319_C2_sharp.mrc as #1.1.1.1, grid size 360,360,360, pixel
1.06, shown at level 0.779, step 1, values float32
Chain information for MwergedPDB-KKSP.pdb
---
Chain | Description
1.2/A 1.2/R | No description available
1.2/B 1.2/S | No description available
1.2/C 1.2/T | No description available
1.2/D 1.2/U | No description available
1.2/E 1.2/V | No description available
1.2/F 1.2/W | No description available
1.2/G 1.2/X | No description available
1.2/H 1.2/Y | No description available
1.2/I 1.2/Z | No description available
1.2/J 1.2/a | No description available
1.2/K 1.2/b | No description available
1.2/L 1.2/c | No description available
1.2/M 1.2/d | No description available
1.2/N 1.2/e | No description available
1.2/O 1.2/f | No description available
1.2/P 1.2/g | No description available
1.2/Q 1.2/h | No description available

isolde start

set selectionWidth 4

Done loading forcefield
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2726, in
_start_sim_or_toggle_pause
self.start_sim()
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2780, in
start_sim
sm.start_sim()
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim
sh.start_sim()
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim
self._prepare_sim()
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line
105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 17752, in
init
this = _openmm.new_Context(*args)
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: failed to
open libnvrtc-builtins.so.
Make sure that libnvrtc-builtins.so is installed correctly.

simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: failed to
open libnvrtc-builtins.so.
Make sure that libnvrtc-builtins.so is installed correctly.

File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 17752, in
init
this = _openmm.new_Context(*args)

See log for complete Python traceback.

OpenGL version: 3.3.0 NVIDIA 450.80.02
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:

total used free shared buff/cache available

Mem: 31G 8.5G 252M 272M 22G 22G
Swap: 2.0G 61M 1.9G

Graphics:

01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11a3]
Kernel driver in use: nvidia

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:

alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0

[pett]

Had to inject ticket by hand into Trac

[Tristan Croll]

Looks like a bad CUDA installation - OpenMM still relies on the libnvrtc.so provided by CUDA rather than bundling its own, and obviously expects that if it finds that then the associated dependency libraries will still be there. Will see what I can do about adding a graceful fallback with a warning (to nvcc first, then to OpenCL if that fails). Not immediately, though - fellowship deadline is looming!
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 08 December 2021 18:54
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5745: OpenMM: Error compiling program: nvrtc: error: failed to open libnvrtc-builtins.so

#5745: OpenMM: Error compiling program: nvrtc: error: failed to open libnvrtc-
builtins.so
----------------------------------+---------------------------
          Reporter:  pett         |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  moderate     |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by pett):

 Had to inject ticket by hand into Trac

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5745#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

Long since fixed - ISOLDE now automatically falls back to using OpenCL if the CUDA platform exists but throws an exception on trying to start a simulation.