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Opened 4 years ago
Closed 3 years ago
#5670 closed defect (can't reproduce)
OpenMM: Error uploading array TabulatedFunction
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.19.0-17-amd64-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 /storage/ria2/NanoCage/iSpy/iSpyAAAA-10-04-2021/phenix-
refine/Autosharpen_9/sharpened_map.ccp4 format ccp4
Opened sharpened_map.ccp4 as #1, grid size 380,380,380, pixel 1.33, shown at
level 0.925, step 2, values float32
open /storage/ria2/NanoCage/iSpy/iSpyAAAA-10-04-2021/phenix-
refine/RealSpaceRefine_10/iSpy-AAAA_model_min_real_space_refined_010.pdb
format pdb
Chain information for iSpy-AAAA_model_min_real_space_refined_010.pdb #2
---
Chain | Description
? | No description available
volume #1 step 1
volume #1 level 13.41
ui tool show ISOLDE
set selectionWidth 4
Chain information for iSpy-AAAA_model_min_real_space_refined_010.pdb
---
Chain | Description
2.2/? | No description available
Done loading forcefield
Opened sharpened_map.ccp4 as #2.1.1.1, grid size 380,380,380, pixel 1.33,
shown at step 1, values float32
clipper spotlight radius 25.00
clipper spotlight radius 25.00
select clear
volume #2.1.1.1 level 24.07
clipper spotlight radius 26.00
clipper spotlight radius 27.00
clipper spotlight radius 28.00
clipper spotlight radius 29.00
clipper spotlight radius 30.00
clipper spotlight radius 31.00
clipper spotlight radius 32.00
clipper spotlight radius 33.00
clipper spotlight radius 34.00
clipper spotlight radius 35.00
clipper spotlight radius 36.00
clipper spotlight radius 37.00
clipper spotlight radius 38.00
clipper spotlight radius 39.00
clipper spotlight radius 40.00
select #2
4480 atoms, 4524 bonds, 292 residues, 12 models selected
~select
Nothing selected
select #2.2
4480 atoms, 4524 bonds, 292 residues, 5 models selected
Traceback (most recent call last):
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim
sm.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim
sh.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim
self._prepare_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/opt/chimerax/1.2.5-1/lib/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 "/opt/chimerax/1.2.5-1/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in init
this = _openmm.new_Context(*args)
simtk.openmm.OpenMMException: Error uploading array TabulatedFunction:
clEnqueueWriteBuffer (-4)
simtk.openmm.OpenMMException: Error uploading array TabulatedFunction:
clEnqueueWriteBuffer (-4)
File "/opt/chimerax/1.2.5-1/lib/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.
~select
Nothing selected
ui tool show ISOLDE
set selectionWidth 4
Done loading forcefield
select #2.2
4480 atoms, 4524 bonds, 292 residues, 11 models selected
Traceback (most recent call last):
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim
sm.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim
sh.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim
self._prepare_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/opt/chimerax/1.2.5-1/lib/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 "/opt/chimerax/1.2.5-1/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in init
this = _openmm.new_Context(*args)
simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6)
simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6)
File "/opt/chimerax/1.2.5-1/lib/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.
Traceback (most recent call last):
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim
sm.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim
sh.start_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim
self._prepare_sim()
File "/home/ria2/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/opt/chimerax/1.2.5-1/lib/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 "/opt/chimerax/1.2.5-1/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in init
this = _openmm.new_Context(*args)
simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6)
simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6)
File "/opt/chimerax/1.2.5-1/lib/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 460.84
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Debian GNU/Linux 10 buster
Architecture: 64bit ELF
Virutal Machine: none
CPU: 64 AMD Ryzen Threadripper 2990WX 32-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 76Gi 43Gi 367Mi 6.2Gi 47Gi
Swap: 73Gi 3.1Gi 70Gi
Graphics:
09:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 GTX 1080 Ti [10de:1b06] (rev a1)
Subsystem: ASUSTeK Computer Inc. GP102 GTX 1080 Ti [1043:85e5]
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
Change History (2)
comment:1 by , 4 years ago
| Status: | assigned → feedback |
|---|
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | feedback → closed |
Hmm... the OpenCL error codes you're getting correspond to CL_MEM_OBJECT_ALLOCATION_FAILURE and CL_OUT_OF_HOST_MEMORY (see https://streamhpc.com/blog/2013-04-28/opencl-error-codes/)... which seems strange considering your machine has impressive specs and the system you were working with is quite small. Did you have a lot of other stuff open at the same time? Does this happen every time, or was it just this once?