Opened 3 years ago

Closed 3 years ago

#6996 closed defect (duplicate)

OpenMMException: Error uploading array TabulatedFunction

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-180-generic-x86_64-with-glibc2.23
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde tutorial

> open 1a0m structureFactors true

Summary of feedback from opening 1a0m fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 475 free from 9265 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 1.0944213038232693  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 72,72,74, pixel
0.347,0.347,0.326, shown at level 2.37, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 72,72,74, pixel
0.347,0.347,0.326, shown at level -0.301,0.301, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_27 as #1.1.1.4, grid size 72,72,74, pixel
0.347,0.347,0.326, shown at level 0.832, step 1, values float32  
1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | α-conotoxin [TYR15]-epi | CXA1_CONEP  
  
Non-standard residues in 1a0m #1.2  
---  
NH2 — amino group  
  

> save /home/dennis/Desktop/1a0m.mtz #1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  

> set bgColor white

> set bgColor black

> clipper spotlight radius 15

> cview #1.3

No displayed objects specified.  

> cview #1.2

> clipper isolate #1/A&protein

> usage clipper isolate

clipper isolate atoms [surroundDistance a number] [contextDistance a number]
[maskRadius a number] [hideSurrounds true or false] [focus true or false]  
— Visually isolate the selected atoms from their surroundings, and mask their
maps to their immediate vicinity. The selection covered by the map(s) will be
expanded to include all residues approaching within surroundDistance of the
given selection. Any residues approaching within contextDistance of the result
will be displayed, but not covered by the map(s). If hideSurrounds is True,
all other atoms will be hidden. If focus is True, the view will be reset to
cover the visible atoms. To revert to the default viewing mode, use "clipper
spotlight".  

> clipper spotlight

> isolde start

> set selectionWidth 4

Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 90,90,92, pixel
0.347,0.347,0.326, shown at level 0.956, step 1, values float32  
Done loading forcefield  

> isolde restrain ligands #1

> addh

Summary of feedback from adding hydrogens to 1a0m #1.2  
---  
warning | Not adding hydrogens to /A ARG 7 CB because it is missing heavy-atom
bond partners  
notes | Termini for 1a0m (#1.2) chain A determined from SEQRES records  
Termini for 1a0m (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLY 1, /B GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A NH2 17, /B NH2 17  
Chain-final residues that are not actual C termini:  
107 hydrogen bonds  
271 hydrogens added  
  

> cview :/A ARG 7 CB

> view :/A ARG 7 CB; cofr center showpivot true

Expected an objects specifier or a view name or a keyword  

> cview /A ARG 7 CB

> view /A ARG 7 CB; cofr center showpivot true

Expected an integer >= 1 or a keyword  

> cview /A: ARG 7 CB

> view /A: ARG 7 CB; cofr center showpivot true

Expected a keyword  

> cview /A: ARG 7 CB

> view /A: ARG 7 CB; cofr center showpivot true

Expected a keyword  

> cview /A: ARG 7 CB

> view /A: ARG 7 CB; cofr center showpivot true

Expected a keyword  

> cview /A: ARG 7 CB

> view /A: ARG 7 CB; cofr center showpivot true

Expected a keyword  

> cview /A: ARG 7 CB

> view /A: ARG 7 CB; cofr center showpivot true

Expected a keyword  

> view /A ARG 7 CB

Expected an integer >= 1 or a keyword  

> view /A ARG 7 CB

Expected an integer >= 1 or a keyword  

> cview /A: ARG7

No objects specified.  

> cview /A: ARG 7

> select clear

[Repeated 3 time(s)]

> hide HC

[Repeated 1 time(s)]

> delete selection

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete select

Missing or invalid "atoms" argument: invalid atoms specifier  

> select delete

Expected an objects specifier or a keyword  

> select delete

Expected an objects specifier or a keyword  

> delete selection

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> select #1

544 atoms, 509 bonds, 76 residues, 26 models selected  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Fetching CCD ARG_LL from http://ligand-
expo.rcsb.org/reports/A/ARG_LL/ARG_LL.cif  

> select clear

> delete selAtoms

> select clear

> delete selAtoms

[Repeated 2 time(s)]

> select #1

540 atoms, 505 bonds, 1 pseudobond, 75 residues, 31 models selected  
Traceback (most recent call last):  
File "/home/dennis/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/dennis/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim  
sm.start_sim()  
File "/home/dennis/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/home/dennis/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File "/home/dennis/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error uploading array TabulatedFunction:
clEnqueueWriteBuffer (-4)  
  
openmm.OpenMMException: Error uploading array TabulatedFunction:
clEnqueueWriteBuffer (-4)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: GeForce GTX 550 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 4 Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           7.8G        4.6G        680M        160M        2.5G        2.6G
	Swap:          975M        5.2M        970M

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GF116 [GeForce GTX 550 Ti] [10de:1244] (rev a1)	
	Subsystem: CardExpert Technology GF116 [GeForce GTX 550 Ti] [10b0:0401]	
	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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → OpenMMException: Error uploading array TabulatedFunction

comment:2 by Tristan Croll, 3 years ago

Resolution: → duplicate
Status: assigned → closed

Ancient low-end GPU ran out of memory. Keeping related ticket #6998 open because successfully starting a simulation on the same GPU caused a segmentation fault - something it would obviously be a good idea to prevent.

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