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Opened 3 years ago
Closed 3 years ago
#8809 closed defect (nonchimerax)
Slow performance
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Performance | 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-5.15.0-69-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6rc202304050652 (2023-04-05 06:52:02 UTC)
Description
when I open a big protein ,chimerax often display"chimerax is not responding",and the display is very slowly.the GPU we purchaged is new.coot and pymol software have not such problem.(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6rc202304050652 (2023-04-05)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/user/Desktop/6g90.pdb format pdb
6g90.pdb title:
Prespliceosome structure provides insight INTO spliceosome assembly and
regulation (map A2) [more info...]
Chain information for 6g90.pdb #1
---
Chain | Description | UniProt
1 | U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA |
2 | U2 snRNA |
A | U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein
A,U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A,U1
small nuclear ribonucleoprotein A | RU1A_YEAST 1-118 149-298
B | U1 small nuclear ribonucleoprotein 70 kda homolog,U1 small nuclear
ribonucleoprotein 70 kda homolog,U1 small nuclear ribonucleoprotein 70 kda
homolog | RU17_YEAST 1-57 89-300
C | U1C | RU1C_YEAST 1-231
D | pre-MRNA-processing factor 39 | PRP39_YEAST 1-629
E | U1 small nuclear ribonucleoprotein component PRP42 | PRP42_YEAST 1-544
F | protein NAM8 | NAM8_YEAST 1-523
G | 56 kda U1 small nuclear ribonucleoprotein component | SNU56_YEAST 1-492
H | protein LUC7,protein LUC7,protein LUC7 | LUC7_YEAST 1-261
I | yeast UBC4 pre-MRNA (mutant) |
J | U1 small nuclear ribonucleoprotein component SNU71 | SNU71_YEAST 1-620
O | U2 snrnp component HSH155 | SF3B1_YEAST 1-971
P | pre-MRNA-splicing factor RSE1 | RSE1_YEAST 1-1361
Q | cold sensitive U2 snRNA suppressor 1 | CUS1_YEAST 1-435
R | protein HSH49 | HSH49_YEAST 1-213
S | regulator OF DRUG sensitivity 3 | RDS3_YEAST 1-107
T | pre-MRNA-splicing factor PRP9 | PRP9_YEAST 1-530
U | pre-MRNA-splicing factor PRP11,pre-MRNA-splicing factor PRP11,pre-MRNA-
splicing factor PRP11 | PRP11_YEAST 1-114 137-266
V | pre-MRNA-splicing factor PRP21 | PRP21_YEAST 1-280
W | U2 small nuclear ribonucleoprotein A' | RU2A_YEAST 1-238
X | unknown |
Y | U2 snrnp B'' | MSL1_YEAST 1-111
Z | splicing factor 3B subunit | YSF3_YEAST 1-85
b s | small nuclear ribonucleoprotein-associated protein B | RSMB_YEAST 1-196
d v | small nuclear ribonucleoprotein Sm D3 | SMD3_YEAST 1-101
e w | small nuclear ribonucleoprotein E | RUXE_YEAST 1-94
f x | small nuclear ribonucleoprotein F | RUXF_YEAST 1-86
g y | small nuclear ribonucleoprotein G | RUXG_YEAST 1-77
h t | small nuclear ribonucleoprotein Sm D1 | SMD1_YEAST 1-146
i u | small nuclear ribonucleoprotein Sm D2 | SMD2_YEAST 1-110
Non-standard residues in 6g90.pdb #1
---
PSU — pseudouridine-5'-monophosphate
ZN — zinc ion
OpenGL version: 4.5 (Core Profile) Mesa 22.2.5
OpenGL renderer: llvmpipe (LLVM 15.0.6, 256 bits)
OpenGL vendor: Mesa/X.org
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Precision 5820 Tower X-Series
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 Intel(R) Core(TM) i9-10920X CPU @ 3.50GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 5.8Gi 216Gi 375Mi 28Gi 243Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
17:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A5000] [10de:2231] (rev a1)
Subsystem: NVIDIA Corporation GA102GL [RTX A5000] [10de:147e]
Kernel driver in use: nouveau
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202304050652
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.1.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (3)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Performance |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Slow performance |
comment:2 by , 3 years ago
ChimeraX is not using the Nvidia driver for your RTX A5000. Instead it is using Mesa software rendering. This probably is because the Nvidia driver is not installed or the installation of the driver is broken. The fix is to install the Nvidia driver.
Here is the graphics driver ChimeraX reports it is using in your bug report.
OpenGL version: 4.5 (Core Profile) Mesa 22.2.5
OpenGL renderer: llvmpipe (LLVM 15.0.6, 256 bits)
OpenGL vendor: Mesa/X.org
You can use the ChimeraX command "graphics driver" and it will report in the Log panel what driver is being used.
comment:3 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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Reported by Xiaopan Gao
Mesa driver