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Opened 4 years ago
Closed 4 years ago
#5010 closed defect (not a bug)
Simulation doesn't start
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | 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-4.19.0-14-amd64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
I amusing Isolde, everytime I start a simulation, it never starts moving the atoms and after some time chimerax hangs and has to be killed.
Fatal Python error: Aborted
Current thread 0x00007fd57149c740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 745 in rapid_access_shown
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 225 in build
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 687 in init
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in
File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 194 in _run_module_as_main
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
OpenGL version: 3.3.0 NVIDIA 418.181.07
OpenGL renderer: Quadro K4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T3610
OS: Debian GNU/Linux 10 buster
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v2 @ 3.70GHz
Cache Size: 10240 KB
Memory:
total used free shared buff/cache available
Mem: 7.7Gi 2.4Gi 2.1Gi 132Mi 3.2Gi 4.9Gi
Swap: 15Gi 810Mi 15Gi
Graphics:
02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK106GL [Quadro K4000] [10de:11fa] (rev a1)
Subsystem: NVIDIA Corporation GK106GL [Quadro K4000] [10de:097c]
Kernel driver in use: nvidia
Locale: ('en_GB', '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
Attachments (2)
Change History (12)
comment:1 by , 4 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Simulation doesn't start |
comment:2 by , 4 years ago
comment:3 by , 4 years ago
Second question: is this for a specific model, or *all* models? To test for the latter, try "isolde demo crystal_intro" and see if that will start.
comment:5 by , 4 years ago
The GPU you're running on is a mid-range model launched 9 years ago so I'm not entirely surprised it struggles... ISOLDE started around 6 years ago now, and my aim was to focus development on that year's generation of moderate-to-high end GPUs (i.e. the GTX 10-series) with the idea that their capabilities would be becoming reasonably mainstream by the time ISOLDE reached maturity.
The "High", "Medium" and "Quick" sim fidelity modes are a new addition - "High" is the original ISOLDE settings, whereas "Medium" and "Quick" are designed to support lower-end GPUs at the expense of some loss in simulation quality (at the "Quick" end the simulation is performed in vacuo, so you'll want to pay close attention to charged sidechains in particular and, if your resolution is lower than ~3A, make extensive use of secondary structure and/or reference model restraints). I've been thinking about adding some code to automatically pick the most suitable setting based on GPU capabilities - but the problem is that there are many different GPUs, and not all of them are that great at reporting their capabilities up-front. I'm really not keen to set the default mode to "quick" because that will degrade the quality of the end result for all those users who never try to adjust it. I'll try to set up some level of automatic assignment, but that may take some time - what's likely to happen far faster is that I'll be providing a facility to save preferences for settings like this so you won't have to remember to choose it for every session.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 06 August 2021 10:00
Cc: Tristan Croll <tic20@cam.ac.uk>; wim.burmeister@ibs.fr <wim.burmeister@ibs.fr>
Subject: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Changes (by Wim.Burmeister@…):
* Attachment "high-sim-fidelity-2021-08-06_10-09.png" added.
Added by email2trac
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:6 by , 4 years ago
Hello,
the computational platform is "CPU" and the only other proposition "Reference".
I could run it with "Medium" sim fidelity, but that is dead slow even for the simulation of the surrounding of one residue.
Wim
ps : A year ago I ran it on the same machine, now under Debian 10, (which was under Debian 9 at the time) and ISOLDE ran fine !
----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: "Wim Burmeister" <wim.burmeister@ibs.fr>, tic20@cam.ac.uk
Envoyé: Vendredi 6 Août 2021 13:24:59
Objet: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
The GPU you're running on is a mid-range model launched 9 years ago so I'm
not entirely surprised it struggles... ISOLDE started around 6 years ago
now, and my aim was to focus development on that year's generation of
moderate-to-high end GPUs (i.e. the GTX 10-series) with the idea that
their capabilities would be becoming reasonably mainstream by the time
ISOLDE reached maturity.
The "High", "Medium" and "Quick" sim fidelity modes are a new addition -
"High" is the original ISOLDE settings, whereas "Medium" and "Quick" are
designed to support lower-end GPUs at the expense of some loss in
simulation quality (at the "Quick" end the simulation is performed in
vacuo, so you'll want to pay close attention to charged sidechains in
particular and, if your resolution is lower than ~3A, make extensive use
of secondary structure and/or reference model restraints). I've been
thinking about adding some code to automatically pick the most suitable
setting based on GPU capabilities - but the problem is that there are many
different GPUs, and not all of them are that great at reporting their
capabilities up-front. I'm really not keen to set the default mode to
"quick" because that will degrade the quality of the end result for all
those users who never try to adjust it. I'll try to set up some level of
automatic assignment, but that may take some time - what's likely to
happen far faster is that I'll be providing a facility to save preferences
for settings like this so you won't have to remember to choose it for
every session.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 06 August 2021 10:00
Cc: Tristan Croll <tic20@cam.ac.uk>; wim.burmeister@ibs.fr
<wim.burmeister@ibs.fr>
Subject: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Changes (by Wim.Burmeister@…):
* Attachment "high-sim-fidelity-2021-08-06_10-09.png" added.
Added by email2trac
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 5 comment:7 by , 4 years ago
Hello,
the computational platform is "CPU" and the only other proposition "Reference".
I could run it with "Medium" sim fidelity, but that is dead slow even for the simulation of the surrounding of one residue.
Wim
----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: "Wim Burmeister" <wim.burmeister@ibs.fr>, tic20@cam.ac.uk
Envoyé: Vendredi 6 Août 2021 13:24:59
Objet: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
The GPU you're running on is a mid-range model launched 9 years ago so I'm
not entirely surprised it struggles... ISOLDE started around 6 years ago
now, and my aim was to focus development on that year's generation of
moderate-to-high end GPUs (i.e. the GTX 10-series) with the idea that
their capabilities would be becoming reasonably mainstream by the time
ISOLDE reached maturity.
The "High", "Medium" and "Quick" sim fidelity modes are a new addition -
"High" is the original ISOLDE settings, whereas "Medium" and "Quick" are
designed to support lower-end GPUs at the expense of some loss in
simulation quality (at the "Quick" end the simulation is performed in
vacuo, so you'll want to pay close attention to charged sidechains in
particular and, if your resolution is lower than ~3A, make extensive use
of secondary structure and/or reference model restraints). I've been
thinking about adding some code to automatically pick the most suitable
setting based on GPU capabilities - but the problem is that there are many
different GPUs, and not all of them are that great at reporting their
capabilities up-front. I'm really not keen to set the default mode to
"quick" because that will degrade the quality of the end result for all
those users who never try to adjust it. I'll try to set up some level of
automatic assignment, but that may take some time - what's likely to
happen far faster is that I'll be providing a facility to save preferences
for settings like this so you won't have to remember to choose it for
every session.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 06 August 2021 10:00
Cc: Tristan Croll <tic20@cam.ac.uk>; wim.burmeister@ibs.fr
<wim.burmeister@ibs.fr>
Subject: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Changes (by Wim.Burmeister@…):
* Attachment "high-sim-fidelity-2021-08-06_10-09.png" added.
Added by email2trac
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 6 comment:8 by , 4 years ago
Hmm... in that case the most likely culprit is to do with your GPU driver installation. Do you have the official Nvidia drivers installed (not the third-party Nouveau ones)?
Apart from that, the following might help:
Go to Tools/General/Shell, then in the Python window that appears:
from simtk.openmm import Platform
Platform.getPluginLoadFailures()
... which will give OpenMM's explanation for *why* the OpenCL and CUDA platforms failed to load.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 06 August 2021 14:18
To: wim.burmeister@ibs.fr <wim.burmeister@ibs.fr>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Comment (by wim.burmeister@…):
{{{
Hello,
the computational platform is "CPU" and the only other proposition
"Reference".
I could run it with "Medium" sim fidelity, but that is dead slow even for
the simulation of the surrounding of one residue.
Wim
ps : A year ago I ran it on the same machine, now under Debian 10, (which
was under Debian 9 at the time) and ISOLDE ran fine !
----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: "Wim Burmeister" <wim.burmeister@ibs.fr>, tic20@cam.ac.uk
Envoyé: Vendredi 6 Août 2021 13:24:59
Objet: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
The GPU you're running on is a mid-range model launched 9 years ago so
I'm
not entirely surprised it struggles... ISOLDE started around 6 years ago
now, and my aim was to focus development on that year's generation of
moderate-to-high end GPUs (i.e. the GTX 10-series) with the idea that
their capabilities would be becoming reasonably mainstream by the time
ISOLDE reached maturity.
The "High", "Medium" and "Quick" sim fidelity modes are a new addition -
"High" is the original ISOLDE settings, whereas "Medium" and "Quick" are
designed to support lower-end GPUs at the expense of some loss in
simulation quality (at the "Quick" end the simulation is performed in
vacuo, so you'll want to pay close attention to charged sidechains in
particular and, if your resolution is lower than ~3A, make extensive use
of secondary structure and/or reference model restraints). I've been
thinking about adding some code to automatically pick the most suitable
setting based on GPU capabilities - but the problem is that there are
many
different GPUs, and not all of them are that great at reporting their
capabilities up-front. I'm really not keen to set the default mode to
"quick" because that will degrade the quality of the end result for all
those users who never try to adjust it. I'll try to set up some level of
automatic assignment, but that may take some time - what's likely to
happen far faster is that I'll be providing a facility to save
preferences
for settings like this so you won't have to remember to choose it for
every session.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 06 August 2021 10:00
Cc: Tristan Croll <tic20@cam.ac.uk>; wim.burmeister@ibs.fr
<wim.burmeister@ibs.fr>
Subject: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Changes (by Wim.Burmeister@…):
* Attachment "high-sim-fidelity-2021-08-06_10-09.png" added.
Added by email2trac
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ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
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Ticket URL:
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}}}
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Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 7 comment:9 by , 4 years ago
Hello,
thank you very much !
Apparently in the upgrade process, the cuda libraries got lost.
I reinstalled them with apt-get install nvidia-cuda-toolkit from the debian buster repository
and chimerax is now working fine indicating "OpenCL" as computational platform!
Wim
----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: "Wim Burmeister" <wim.burmeister@ibs.fr>, "tic20" <tic20@cam.ac.uk>
Envoyé: Vendredi 6 Août 2021 15:28:41
Objet: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
Hmm... in that case the most likely culprit is to do with your GPU driver
installation. Do you have the official Nvidia drivers installed (not the
third-party Nouveau ones)?
Apart from that, the following might help:
Go to Tools/General/Shell, then in the Python window that appears:
from simtk.openmm import Platform
Platform.getPluginLoadFailures()
... which will give OpenMM's explanation for *why* the OpenCL and CUDA
platforms failed to load.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 06 August 2021 14:18
To: wim.burmeister@ibs.fr <wim.burmeister@ibs.fr>; Tristan Croll
<tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Comment (by wim.burmeister@…):
{{{
Hello,
the computational platform is "CPU" and the only other proposition
"Reference".
I could run it with "Medium" sim fidelity, but that is dead slow even for
the simulation of the surrounding of one residue.
Wim
ps : A year ago I ran it on the same machine, now under Debian 10, (which
was under Debian 9 at the time) and ISOLDE ran fine !
----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: "Wim Burmeister" <wim.burmeister@ibs.fr>, tic20@cam.ac.uk
Envoyé: Vendredi 6 Août 2021 13:24:59
Objet: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
The GPU you're running on is a mid-range model launched 9 years ago so
I'm
not entirely surprised it struggles... ISOLDE started around 6 years ago
now, and my aim was to focus development on that year's generation of
moderate-to-high end GPUs (i.e. the GTX 10-series) with the idea that
their capabilities would be becoming reasonably mainstream by the time
ISOLDE reached maturity.
The "High", "Medium" and "Quick" sim fidelity modes are a new addition -
"High" is the original ISOLDE settings, whereas "Medium" and "Quick" are
designed to support lower-end GPUs at the expense of some loss in
simulation quality (at the "Quick" end the simulation is performed in
vacuo, so you'll want to pay close attention to charged sidechains in
particular and, if your resolution is lower than ~3A, make extensive use
of secondary structure and/or reference model restraints). I've been
thinking about adding some code to automatically pick the most suitable
setting based on GPU capabilities - but the problem is that there are
many
different GPUs, and not all of them are that great at reporting their
capabilities up-front. I'm really not keen to set the default mode to
"quick" because that will degrade the quality of the end result for all
those users who never try to adjust it. I'll try to set up some level of
automatic assignment, but that may take some time - what's likely to
happen far faster is that I'll be providing a facility to save
preferences
for settings like this so you won't have to remember to choose it for
every session.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 06 August 2021 10:00
Cc: Tristan Croll <tic20@cam.ac.uk>; wim.burmeister@ibs.fr
<wim.burmeister@ibs.fr>
Subject: Re: [ChimeraX] #5010: Simulation doesn't start
#5010: Simulation doesn't start
---------------------------------------+---------------------------
Reporter: wim.burmeister@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+---------------------------
Changes (by Wim.Burmeister@…):
* Attachment "high-sim-fidelity-2021-08-06_10-09.png" added.
Added by email2trac
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
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Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
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Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
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Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5010#comment:8>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 8 comment:10 by , 4 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
Great to hear it! I'll go ahead and close this ticket as "not a bug" - but I will work on improving ISOLDE's communication in situations like this.
Note:
See TracTickets
for help on using tickets.
Hmm... that's a new one for me. To start with the debugging, could you set the "Experience Level" drop-down at the bottom right of the ISOLDE screen to "advanced", then on the "Sim settings" tab tell me what it says under "Computational platform" (and also what other options are available in that drop-down menu?