ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg

July 31, 2023

Agenda

• Should ChimeraX 1.7 use Qt 6.5 which requires macOS 11? Ticket #9421
• Toolshed website spinning progress never goes away.
• Mac dual display crash
• mmCIF out of memory
• Update ChimeraX prereqs, PyQt 6.5.1
• ChimeraX Protein Science paper progress
• Release initial ChimeraX library on PyPi or Conda
• Chimera/ChimeraX notarization scripts need updating, Apple deprecated altool command Fall 2023 ​#7234
• ChimeraX Ideas milestone clean-up.
• Install Splunk on plato to monitor web services.
• Back up the Chimera build machine to a solid state drive, Windows 7?
• Toolshed bundle requirement checking
• Discuss possible OpenMM and VR improvements for Tristan and Altos to pursue

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Discussion

• Modeller jobs get killed
  • There is a worker pool of 10 or 20 workers.
  • If job goes over 3 hours it gets killed by a monitoring process.
  • There is no useful error logged. User just sees "job failed", and they are likely to try again.
  • Eric suggests maybe a 6 hour limit is better.
  • Do not yet have sessions save in-process modeller jobs.
  • Saving a session should warn that modeller jobs was not saved.

• Warning about Modeller and AlphaFold will be lost at quit
  • Might want to interrupt quit and warn when computation will be lost.
  • Had this capability in Chimera.

• Automatic install of ChimeraX daily on Mac not working
  • rsyncs dmg, mounts, and then cp fails, can find ChimeraX_daily.app in dmg.
  • Eric and Tom looked and it worked when steps run by hand.

• PyPi ChimeraX library
  • Zach applied for an RBVI PyPi account. Waiting for approval.

• Web service log viewer
  • Current plan is to use Grafana.
  • Splunk resisted being containerized with singularity despite significant efforts by Zach.
  • Grafana is the viewer and there are two other programs that go with it to parse logs and manage a database.
  • Discussed whether Grafana should be containerized. Greg thinks no, because we don't update our containers because of the extra work of updating that way.

• Backups for old Chimera build machines
  • Still plan to get a small SSD drive to make a copy of Windows 7 Chimera build machine disk.
  • Tom put a backup drive on essex2, the old Mac 10.14 build machine.

• PDB new connectivity info
  • New mmCIF fields for N and C atoms of amino acids to help with connectivity.

• mmCIF reading crashes
  • Still get 3-5 crash reports per week, all on Windows ChimeraX 1.6
  • Not sure if it is fixed in ChimeraX daily, no crash reports, but there were very few in older daily builds.

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Action Items

• Present github continuous integration tutorial. Zach
• Beta releases on Toolshed - make ticket for this. Greg