Opened 3 years ago

Closed 3 years ago

#8441 closed defect (fixed)

Incorrectly installed CUDA

Reported by: saverio.lemme@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-58-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
After upgrading from  VGA compatible controller: NVIDIA Corporation GK208B [GeForce GT 730] (rev a1) to VGA compatible controller: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] (rev a1) loading a molecule and moving the strucure around is very very slow.
The same is not true in pymol  and vmd.

Some information about th pc:

uname -a && cat /etc/*release 
Linux xxxx-X399-DESIGNARE-EX 5.15.0-58-generic #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.1 LTS"
PRETTY_NAME="Ubuntu 22.04.1 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.1 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy

cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module  525.78.01  Mon Dec 26 05:58:42 UTC 2022
GCC version:  

dpkg --get-selections | grep nvidia
libnvidia-compute-495:amd64		install
libnvidia-compute-510:amd64		install
libnvidia-ml-dev:amd64			install
linux-modules-nvidia-525-5.15.0-58-generic	install
linux-modules-nvidia-525-generic-hwe-22.04	install
linux-objects-nvidia-525-5.15.0-58-generic	install
linux-signatures-nvidia-5.15.0-58-generic	install
nvidia-cuda-dev:amd64			install
nvidia-cuda-gdb			install
nvidia-cuda-toolkit			install
nvidia-cuda-toolkit-doc			install
nvidia-kernel-common-525		install
nvidia-opencl-dev:amd64			install
nvidia-prime				deinstall
nvidia-profiler			install
nvidia-settings			deinstall
nvidia-visual-profiler			install

dpkg --get-selections | grep cuda
libcudart11.0:amd64			install
nvidia-cuda-dev:amd64			install
nvidia-cuda-gdb			install
nvidia-cuda-toolkit			install
nvidia-cuda-toolkit-doc			install


Thanks.

Saverio


Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7b3b format mmcif fromDatabase pdb

7b3b title:  
Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with
Remdesivir at position -3 (structure 1) [more info...]  
  
Chain information for 7b3b #1  
---  
Chain | Description | UniProt  
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2  
B | Non-structural protein 8 | R1AB_SARS2  
C | Non-structural protein 7 | R1AB_SARS2  
P | DNA/RNA (5'-R(P*CP*UP*AP*CP*GP*CP*G)-D(P*(RMP))-R(P*UP*G)-3') |  
T | RNA (5'-R(P*UP*GP*CP*AP*UP*CP*GP*CP*GP*UP*AP*G)-3') |  
  
Non-standard residues in 7b3b #1  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate (Remdesivir, bound form)  
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 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon2d
XDG_SESSION_DESKTOP=cinnamon2d
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: X399 DESIGNARE EX
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen Threadripper 1950X 16-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       2.7Gi        22Gi       197Mi       6.4Gi        27Gi
	Swap:           11Gi          0B        11Gi

Graphics:
	08:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK208B [GeForce GT 730] [10de:1287] (rev a1)	
	Subsystem: NVIDIA Corporation GK208B [GeForce GT 730] [10de:1287]	
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DevelExtras: 0.4.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyqtgraph: 0.13.1
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    Send2Trash: 1.8.0
    SEQCROW: 1.5.13
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (3)

in reply to:  1 ; comment:1 by saverio.lemme@…, 3 years ago 

Sorry ,
I have incorrectly installed  cuda.
Now it works fine.
Thanks.

Saverio
________________________________
Da: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Inviato: domenica 5 febbraio 2023 10:15
A: saverio lemme <saverio.lemme@alumni.uniroma2.eu>
Oggetto: [ChimeraX] #8441: ChimeraX bug report submission

#8441: ChimeraX bug report submission
-----------------------------+-----------------------------
 Reporter:  saverio.lemme@…  |                Type:  defect
   Status:  new              |            Priority:  normal
Component:  Unassigned       |          Blocked By:
 Blocking:                   |  Notify when closed:
-----------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-5.15.0-58-generic-x86_64-with-glibc2.35
 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
 Description
 After upgrading from  VGA compatible controller: NVIDIA Corporation GK208B
 [GeForce GT 730] (rev a1) to VGA compatible controller: NVIDIA Corporation
 TU102 [GeForce RTX 2080 Ti] (rev a1) loading a molecule and moving the
 strucure around is very very slow.
 The same is not true in pymol  and vmd.

 Some information about th pc:

 uname -a && cat /etc/*release
 Linux xxxx-X399-DESIGNARE-EX 5.15.0-58-generic #64-Ubuntu SMP Thu Jan 5
 11:43:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
 DISTRIB_ID=Ubuntu
 DISTRIB_RELEASE=22.04
 DISTRIB_CODENAME=jammy
 DISTRIB_DESCRIPTION="Ubuntu 22.04.1 LTS"
 PRETTY_NAME="Ubuntu 22.04.1 LTS"
 NAME="Ubuntu"
 VERSION_ID="22.04"
 VERSION="22.04.1 LTS (Jammy Jellyfish)"
 VERSION_CODENAME=jammy
 ID=ubuntu
 ID_LIKE=debian
 HOME_URL="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ubuntu.com%2F&data=05%7C01%7Csaverio.lemme%40alumni.uniroma2.eu%7C7929a2409dfb461923b208db0759955e%7C24c5be2ad76440c5997582d08ae47d0e%7C0%7C0%7C638111853610537773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=95juRigqjjFVI%2BNb90MbstKRDNxpyyWjZBYdptBoLn0%3D&reserved=0"
 SUPPORT_URL="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhelp.ubuntu.com%2F&data=05%7C01%7Csaverio.lemme%40alumni.uniroma2.eu%7C7929a2409dfb461923b208db0759955e%7C24c5be2ad76440c5997582d08ae47d0e%7C0%7C0%7C638111853610537773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2Fyio14kT4VfZGVYGHJt5WuZzvYWKIu0Xw%2F%2FxYk9lG1o%3D&reserved=0"
 BUG_REPORT_URL="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbugs.launchpad.net%2Fubuntu%2F&data=05%7C01%7Csaverio.lemme%40alumni.uniroma2.eu%7C7929a2409dfb461923b208db0759955e%7C24c5be2ad76440c5997582d08ae47d0e%7C0%7C0%7C638111853610537773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=6TnYSaTTmYFhOuXYFyVPNYHCqiWTaFBa2t93A3l97fw%3D&reserved=0"
 PRIVACY_POLICY_URL="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ubuntu.com%2Flegal%2Fterms-and-policies&data=05%7C01%7Csaverio.lemme%40alumni.uniroma2.eu%7C7929a2409dfb461923b208db0759955e%7C24c5be2ad76440c5997582d08ae47d0e%7C0%7C0%7C638111853610537773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=X5xUJfdQpPnKBpeze%2Fp4Q3CZhTRMtqoooxO7uD94gac%3D&reserved=0
 /privacy-policy"
 UBUNTU_CODENAME=jammy

 cat /proc/driver/nvidia/version
 NVRM version: NVIDIA UNIX x86_64 Kernel Module  525.78.01  Mon Dec 26
 05:58:42 UTC 2022
 GCC version:

 dpkg --get-selections | grep nvidia
 libnvidia-compute-495:amd64             install
 libnvidia-compute-510:amd64             install
 libnvidia-ml-dev:amd64                  install
 linux-modules-nvidia-525-5.15.0-58-generic      install
 linux-modules-nvidia-525-generic-hwe-22.04      install
 linux-objects-nvidia-525-5.15.0-58-generic      install
 linux-signatures-nvidia-5.15.0-58-generic       install
 nvidia-cuda-dev:amd64                   install
 nvidia-cuda-gdb                 install
 nvidia-cuda-toolkit                     install
 nvidia-cuda-toolkit-doc                 install
 nvidia-kernel-common-525                install
 nvidia-opencl-dev:amd64                 install
 nvidia-prime                            deinstall
 nvidia-profiler                 install
 nvidia-settings                 deinstall
 nvidia-visual-profiler                  install

 dpkg --get-selections | grep cuda
 libcudart11.0:amd64                     install
 nvidia-cuda-dev:amd64                   install
 nvidia-cuda-gdb                 install
 nvidia-cuda-toolkit                     install
 nvidia-cuda-toolkit-doc                 install


 Thanks.

 Saverio


 Log:
 UCSF ChimeraX version: 1.5 (2022-11-24)
 © 2016-2022 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open 7b3b format mmcif fromDatabase pdb

 7b3b title:
 Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with
 Remdesivir at position -3 (structure 1) [more info...]

 Chain information for 7b3b #1
 ---
 Chain | Description | UniProt
 A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2
 B | Non-structural protein 8 | R1AB_SARS2
 C | Non-structural protein 7 | R1AB_SARS2
 P | DNA/RNA (5'-R(P*CP*UP*AP*CP*GP*CP*G)-D(P*(RMP))-R(P*UP*G)-3') |
 T | RNA (5'-R(P*UP*GP*CP*AP*UP*CP*GP*CP*GP*UP*AP*G)-3') |

 Non-standard residues in 7b3b #1
 ---
 F86 —
 [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
 dihydrogen phosphate (Remdesivir, bound form)
 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 6.3.1, Qt 6.3.1
 Qt runtime version: 6.3.2
 Qt platform: xcb

 XDG_SESSION_TYPE=x11
 DESKTOP_SESSION=cinnamon2d
 XDG_SESSION_DESKTOP=cinnamon2d
 XDG_CURRENT_DESKTOP=X-Cinnamon
 DISPLAY=:1
 Manufacturer: Gigabyte Technology Co., Ltd.
 Model: X399 DESIGNARE EX
 OS: Ubuntu 22.04 Jammy Jellyfish
 Architecture: 64bit ELF
 Virtual Machine: none
 CPU: 32 AMD Ryzen Threadripper 1950X 16-Core Processor
 Cache Size: 512 KB
 Memory:
                        total        used        free      shared
 buff/cache   available
         Mem:            31Gi       2.7Gi        22Gi       197Mi
 6.4Gi        27Gi
         Swap:           11Gi          0B        11Gi

 Graphics:
         08:00.0 VGA compatible controller [0300]: NVIDIA Corporation
 GK208B [GeForce GT 730] [10de:1287] (rev a1)
         Subsystem: NVIDIA Corporation GK208B [GeForce GT 730] [10de:1287]
         Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia

 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     asttokens: 2.1.0
     Babel: 2.11.0
     backcall: 0.2.0
     blockdiag: 3.0.0
     build: 0.8.0
     certifi: 2022.9.24
     cftime: 1.6.2
     charset-normalizer: 2.1.1
     ChimeraX-AddCharge: 1.4
     ChimeraX-AddH: 2.2.1
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2.1
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.6
     ChimeraX-AlphaFold: 1.0
     ChimeraX-AltlocExplorer: 1.0.3
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.41.5
     ChimeraX-AtomicLibrary: 8.0.3
     ChimeraX-AtomSearch: 2.0.1
     ChimeraX-AxesPlanes: 2.3
     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: 2.7.1
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.2
     ChimeraX-ButtonPanel: 1.0.1
     ChimeraX-CageBuilder: 1.0.1
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.3.1
     ChimeraX-ChangeChains: 1.0.2
     ChimeraX-CheckWaters: 1.3
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.2.4
     ChimeraX-ColorActions: 1.0.3
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.5.2
     ChimeraX-CommandLine: 1.2.4
     ChimeraX-ConnectStructure: 2.0.1
     ChimeraX-Contacts: 1.0.1
     ChimeraX-Core: 1.5
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3.2
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0.1
     ChimeraX-DataFormats: 1.2.2
     ChimeraX-DevelExtras: 0.4.2
     ChimeraX-Dicom: 1.1
     ChimeraX-DistMonitor: 1.3
     ChimeraX-DockPrep: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0.1
     ChimeraX-FunctionKey: 1.0.1
     ChimeraX-Geometry: 1.2
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 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: 1.1.2
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0.1
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.1.1
     ChimeraX-Markers: 1.0.1
     ChimeraX-Mask: 1.0.1
     ChimeraX-MatchMaker: 2.0.9
     ChimeraX-MDcrds: 2.6
     ChimeraX-MedicalToolbar: 1.0.2
     ChimeraX-Meeting: 1.0.1
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.8
     ChimeraX-MMTF: 2.2
     ChimeraX-Modeller: 1.5.6
     ChimeraX-ModelPanel: 1.3.6
     ChimeraX-ModelSeries: 1.0.1
     ChimeraX-Mol2: 2.0
     ChimeraX-Mole: 1.0
     ChimeraX-Morph: 1.0.1
     ChimeraX-MouseModes: 1.1.1
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0.3
     ChimeraX-OpenCommand: 1.9.1
     ChimeraX-PDB: 2.6.8
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBImages: 1.1
     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-RenumberResidues: 1.1
     ChimeraX-ResidueFit: 1.0.1
     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: 1.5.1
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.7.2
     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-StarMap: 1.1.70
     ChimeraX-StdCommands: 1.10
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-StructMeasure: 1.1
     ChimeraX-Struts: 1.0.1
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0.1
     ChimeraX-SwapRes: 2.1.3
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1.2
     ChimeraX-ToolshedUtils: 1.2.1
     ChimeraX-Tug: 1.0.1
     ChimeraX-UI: 1.24.3
     ChimeraX-uniprot: 2.2.1
     ChimeraX-UnitCell: 1.0.1
     ChimeraX-ViewDockX: 1.1.4
     ChimeraX-VIPERdb: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0.1
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0.1
     ChimeraX-WebServices: 1.1.0
     ChimeraX-Zone: 1.0.1
     colorama: 0.4.5
     cxservices: 1.2
     cycler: 0.11.0
     Cython: 0.29.32
     debugpy: 1.6.4
     decorator: 5.1.1
     distro: 1.7.0
     docutils: 0.19
     entrypoints: 0.4
     executing: 1.2.0
     filelock: 3.7.1
     fonttools: 4.38.0
     funcparserlib: 1.0.1
     grako: 3.16.5
     h5py: 3.7.0
     html2text: 2020.1.16
     idna: 3.4
     ihm: 0.33
     imagecodecs: 2022.7.31
     imagesize: 1.4.1
     importlib-metadata: 5.1.0
     ipykernel: 6.15.3
     ipython: 8.4.0
     ipython-genutils: 0.2.0
     jedi: 0.18.1
     Jinja2: 3.1.2
     jupyter-client: 7.3.4
     jupyter-core: 5.1.0
     kiwisolver: 1.4.4
     line-profiler: 3.5.1
     lxml: 4.9.1
     lz4: 4.0.2
     MarkupSafe: 2.1.1
     matplotlib: 3.5.2
     matplotlib-inline: 0.1.6
     MolecularDynamicsViewer: 1.4
     msgpack: 1.0.4
     nest-asyncio: 1.5.6
     netCDF4: 1.6.0
     networkx: 2.8.5
     numexpr: 2.8.4
     numpy: 1.23.1
     openvr: 1.23.701
     packaging: 21.3
     ParmEd: 3.4.3
     parso: 0.8.3
     pep517: 0.13.0
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 9.2.0
     pip: 22.2.2
     pkginfo: 1.8.3
     platformdirs: 2.5.4
     prompt-toolkit: 3.0.33
     psutil: 5.9.1
     ptyprocess: 0.7.0
     pure-eval: 0.2.2
     pycollada: 0.7.2
     pydicom: 2.3.0
     Pygments: 2.12.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 3.0.9
     PyQt6-commercial: 6.3.1
     PyQt6-Qt6: 6.3.2
     PyQt6-sip: 13.4.0
     PyQt6-WebEngine-commercial: 6.3.1
     PyQt6-WebEngine-Qt6: 6.3.2
     pyqtgraph: 0.13.1
     python-dateutil: 2.8.2
     pytz: 2022.6
     pyzmq: 24.0.1
     qtconsole: 5.3.1
     QtPy: 2.3.0
     RandomWords: 0.4.0
     requests: 2.28.1
     scipy: 1.9.0
     Send2Trash: 1.8.0
     SEQCROW: 1.5.13
     setuptools: 65.1.1
     sfftk-rw: 0.7.2
     six: 1.16.0
     snowballstemmer: 2.2.0
     sortedcontainers: 2.4.0
     Sphinx: 5.1.1
     sphinx-autodoc-typehints: 1.19.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 3.0.0
     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
     stack-data: 0.6.2
     tables: 3.7.0
     tifffile: 2022.7.31
     tinyarray: 1.2.4
     tomli: 2.0.1
     tornado: 6.2
     traitlets: 5.3.0
     urllib3: 1.26.13
     wcwidth: 0.2.5
     webcolors: 1.12
     wheel: 0.37.1
     wheel-filename: 1.4.1
     zipp: 3.11.0

 }}}

--
Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8441&data=05%7C01%7Csaverio.lemme%40alumni.uniroma2.eu%7C7929a2409dfb461923b208db0759955e%7C24c5be2ad76440c5997582d08ae47d0e%7C0%7C0%7C638111853610537773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=R7BIYYQ5aeqfjjxUTOnLIpaZSLrk9B%2BzrShQA0%2BU51I%3D&reserved=0>
ChimeraX <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7Csaverio.lemme%40alumni.uniroma2.eu%7C7929a2409dfb461923b208db0759955e%7C24c5be2ad76440c5997582d08ae47d0e%7C0%7C0%7C638111853610537773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lHLbrmyZQI3n1Yuk39e%2B4OM4kyvlaD6ZUURyxY%2FQTks%3D&reserved=0>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 3 years ago

Cc: Eric Pettersen added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Incorrectly installed CUDA

comment:3 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: assigned → closed

Hi Saverio,

Glad you were able to get it working.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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