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Opened 6 years ago
Last modified 6 years ago
#2624 assigned defect
Waking from sleep takes 20 or more seconds.
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | 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-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 0.91 (2019-11-22) Description I've seen a half-dozen or so instances now on Mac and Linux where after bringing the machine back from sleep ChimeraX is unresponsive (everything is drawn, but nothing responds to mouse or keyboard) for upwards of 20 seconds. In one instance on the Mac this persisted long enough that I eventually killed the process (after around 3 minutes waiting). When it *does* start responding, everything seems normal again. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-11-22) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open demo_6r9i_refine_2.pdb Summary of feedback from opening demo_6r9i_refine_2.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-11-27 Time 12:13:48 GMT +0000 (1574856828.89 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/demo/6r9i/reflections.mtz 48 messages similar to the above omitted Chain information for demo_6r9i_refine_2.pdb #1 --- Chain | Description A | No description available > open ../reflections.mtz structureModel #1 Summary of feedback from opening ../reflections.mtz --- warning | WARNING: multiple experimental reflection datasets found: (HKL_base) FOBS, SIGFOBS, (HKL_base) in.I_sigI.I, in.I_sigI.sigI Automatically choosing "(HKL_base) in.I_sigI.I, in.I_sigI.sigI". note | Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Opened crystallographic dataset from ../reflections.mtz Found experimental reflection data: (HKL_base) in.I_sigI.I, in.I_sigI.sigI Rwork: 0.2590; Rfree: 0.2952 Generated maps: Reflection Data (LIVE) 2mFo-DFc (LIVE) mFo-DFc (LIVE) 2mFo-DFc_sharp_29 Any unwanted maps may be safely closed via the Model panel. Chain information for demo_6r9i_refine_2.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > isolde start > set selectionWidth 4 Done loading forcefield > addh Summary of feedback from adding hydrogens to demo_6r9i_refine_2.pdb #1.1 --- notes | No usable SEQRES records for demo_6r9i_refine_2.pdb (#1.1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A SER 462 Chain-initial residues that are not actual N termini: /A ASN 493, /A ASN 585, /A SER 611, /A GLY 692, /A THR 719, /A GLU 891, /A ILE 932 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A PRO 1110, /A SER 486, /A LYS 580, /A ILE 601, /A ASN 687, /A CYS 713, /A GLY 883, /A GLU 922 538 hydrogen bonds Adding 'H' to /A ASN 493 Adding 'H' to /A ASN 585 Adding 'H' to /A SER 611 Adding 'H' to /A GLY 692 Adding 'H' to /A THR 719 2 messages similar to the above omitted /A PRO 1110 is not terminus, removing H atom from 'C' /A SER 486 is not terminus, removing H atom from 'C' /A LYS 580 is not terminus, removing H atom from 'C' /A ILE 601 is not terminus, removing H atom from 'C' /A ASN 687 is not terminus, removing H atom from 'C' 3 messages similar to the above omitted 4879 hydrogens added > hide HC > select #1 9803 atoms, 9902 bonds, 14 pseudobonds, 25 models selected QWidget::repaint: Recursive repaint detected Searching for templates for ligands: > select clear Updating bulk solvent parameters... Searching for templates for ligands: > select clear Updating bulk solvent parameters... > select up 14 atoms, 14 bonds, 1 model selected > select up 82 atoms, 84 bonds, 1 model selected Searching for templates for ligands: Updating bulk solvent parameters... > select up 17 atoms, 17 bonds, 1 model selected > select up 198 atoms, 200 bonds, 1 model selected > select up 212 atoms, 213 bonds, 1 model selected > select up 396 atoms, 401 bonds, 1 model selected Searching for templates for ligands: Updating bulk solvent parameters... Searching for templates for ligands: > select clear Updating bulk solvent parameters... > select up 14 atoms, 13 bonds, 1 model selected > select up 117 atoms, 117 bonds, 1 model selected Searching for templates for ligands: Updating bulk solvent parameters... > select up 191 atoms, 191 bonds, 1 model selected > select up 9803 atoms, 9902 bonds, 1 model selected > select down 191 atoms, 191 bonds, 1 model selected Searching for templates for ligands: Updating bulk solvent parameters... > select up 15 atoms, 14 bonds, 1 model selected > select up 183 atoms, 184 bonds, 1 model selected Searching for templates for ligands: > select clear > select up 15 atoms, 14 bonds, 1 model selected > select up 183 atoms, 184 bonds, 1 model selected Updating bulk solvent parameters... Searching for templates for ligands: > select clear > select up 21 atoms, 21 bonds, 1 model selected > select up 183 atoms, 184 bonds, 1 model selected Updating bulk solvent parameters... > select up 14 atoms, 13 bonds, 1 model selected > select up 345 atoms, 347 bonds, 1 model selected Searching for templates for ligands: Updating bulk solvent parameters... Searching for templates for ligands: Updating bulk solvent parameters... Searching for templates for ligands: Updating bulk solvent parameters... Searching for templates for ligands: Updating bulk solvent parameters... OpenGL version: 3.3.0 NVIDIA 418.87.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (4)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem waking from sleep (event loop stuck?) |
comment:2 by , 6 years ago
follow-up: 3 comment:3 by , 6 years ago
I’m afraid I haven’t yet found any pattern - it’s quite intermittent, but I can rule a few things out. Doesn’t seem time-related - I left a model open in ISOLDE over the weekend and it resumed without trouble, but on Friday I got a ~20-second hang after returning from lunch. It is ChimeraX-specific - everything else on the system was still fine. I didn’t have any simulations running (or paused) in either case. If I find a way to reliably reproduce it I’ll let you know.
comment:4 by , 6 years ago
| Summary: | Problem waking from sleep (event loop stuck?) → Waking from sleep takes 20 or more seconds. |
|---|
Since ChimeraX eventually recovers it seems like something is queued up and takes a long time to clear that queue. We will need either a clue about what is getting queued up, or a reproducible test case.
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During those 20 or more seconds is the ChimeraX process using the CPU? I wonder if Qt has somehow queued up an enormous number of events and is trying to process them all. If you use the "roll" command and then sleep, when it awakes and seems hung, is the graphics rotating? Or does it only start rotating after the 20 second frozen time?
How long do you have to sleep the laptop for this to happen? Does it happen 1 in 5 times, or how frequently? We don't have any Linux laptop to test this on, so it is better if you tell us details for the Mac laptop.