ChimeraX Developer Meeting

Attendance: Piet, Greg, Tom, Eric, Zach

December 2, 2024

Agenda

• ChimeraX 1.9 release candidates, branch and tickets
• 1.9 release planned for December 9, 2024
• What to do about Mac external display crashes
• Should developer tutorial section on commands talk more about keywords
• GitHub Actions builds
• Clean-up ChimeraX 1.9 roadmap wiki page
• Work in progress reports
• Make Chimera end-of-life bug report and registration changes.
• Back up the Chimera build machine to a solid state drive, Windows 7.

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Discussion

• UCSF VPN
  • Elaine still getting kicked off UCSF VPN periodically with network access control message.
  • Eric not using UCSF VPN but sometimes needs it for timesheet or Windows ChimeraX gui bugs.
  • Tom not using UCSF VPN much, not kicked off yet.

• Plato OS updates
  • Wynton Rocky updates done by Josh via a Wynton-Rocky repo.
  • Updates from official rocky repo copied to a wynton-test repo and tested on test cluster, then moved to wynton-rocky repo.
  • Greg looking at how plato updates would be done independent of Wynton.

• SPOKE
  • Greg and Eric discussed steps taken to fix broken SPOKE devel site, required pcs restart.
  • Person on spoke project who had sudo access to pcs restart is no longer part of spoke.
  • Updates to Neo4j available but Greg was told there is a problem to address if updates are made, but does not have details of the problem.

• Qt 6.8.1
  • New Qt released, but PyQt 6.8 not yet available.
  • Will switch ChimeraX daily to pyqt 6.8 when available.

• ChimeraX 1.9
  • Eric working on two bugs. Missing segment labels broken in morph. French language KVFinder entry field will not accept "." or ",".
  • Tom wants to add bug reporter check for specific crashes that will then show explanation of crash but still allow users to report.
  • Zach has a few obscure segmentation bugs to fix for 1.9 release.
  • Greg and Zach will remilestone or close 1.9 tickets by Friday for planned release on Monday.

• Linux daily builds failing
  • Github daily builds failed for Linux, not able to reach plato.
  • Greg thinks that is probably the UCSF or plato DNS server not responding.
  • Greg suggests trying tracepath -n after failure to see if plato is reachable.
  • Zach says he could revert daily builds from github to RBVI machines if plato can't be reached reliably.

• Email on NAS
  • Greg created /nas/home/ferrin/{gregc,pett,meng,goddard,zjp...} shadow directories for handling email and tried moving his ~/mail to NAS with a symbolic link from beegfs ~/mail to NAS.
  • If /wynton/home unmounted then mail would continue to work using symbolic link on NAS from /wynton/home to /nas/home.

• Scenes
  • Piet made atomic model scene code use take_snapshot()

• ScholAR
  • Piet says Lars at USC said he may simplify API token system for uploading figures.

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Action Items