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

[venkatareddy@…]

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

[Tristan Croll]

This appears to be an error with your system CUDA installation. libnvrtc-builtins.so is a companion library to libnvrtc.so, Nvidia's CUDA runtime compiler. libnvrtc.so isn't bundled with OpenMM (although in theory it could be, but I don't have control over that), so it looks for a copy matching the version it was compiled against in the usual locations (typically /usr/local/cuda, but I think it will also check the LD_LIBRARY_PATH). If it doesn't find it at all it will fall back to using nvcc (the Nvidia command-line compiler) or OpenCL - but in your case it's finding a broken copy leading to this failure. I'll see if I can add some code to give a more graceful fallback in this case, but it won't happen immediately.

The version you have installed requires CUDA 11.0 to use nvrtc - but there's a new version of ISOLDE out (1.3, which requires the ChimeraX 1.3 release candidate) which uses CUDA 11.2. I'd strongly recommend updating to that.