ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg

June 12, 2023

Agenda

• Linux daily builds not working, failed to build !PyQt5!
• ChimeraX Protein Science paper outline
• Update Mac Intel build machine?

Zach: I think I fixed the build failures on Essex2. They ended up being that the Python 3.11 archive uses some header format that the old version of bsdtar on Mojave doesn’t know about, and that the Python 3.11 archive is universal2-only, so bundle builder was trying to build intel-arm binaries without the arm Xcode libraries available on the machine (they first appear in Xcode 12, compatible with 10.15 and up, but we run Xcode 11 on 10.14). We might consider updating Essex2 from 10.14 soon, at least to Catalina but preferably to Big Sur, since we’re soon to be 5(!) versions behind when Sonoma releases.

Eric: Essex2 is also the Chimera build machine

• Chimera 1.17.2 release (FFmpeg)?
• Update ChimeraX prereqs, PyQt 6.5.1, Python 3.11
• ChimeraX 1.7 roadmap
• 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

• Greg busy working on Wynton problems
  • Making new accounts broken, 50 users waiting to get new accounts.
  • Working on restoring 15 Tbytes, and millions of files where file names are known but directory structure was lost.

• mmCIF out of memory crash
  • Eric says 1 or 2 mmcif crash reports coming in every day.
  • Greg has valgrind giving the out of memory crash.
  • Tried not using memory mapping and not doing template fetches and valgrind still gets out of memory.
  • valgrind does not get out of memory opening pdb file.
  • next step is put in print statements and see how far it gets under valgrind.

• Trac login from Windows Chrome broken
  • Greg says ucsf web server scan says we are not offering TLS or SSL, believed to be false result.
  • Possibly Chrome login failure is related.
  • Scooter will need to look at this problem after he is back tomorrow.

• Mac Intel daily builds failed to start
  • PyOpenGL could not find OpenGL.framework, only on Intel, not ARM.
  • Daily build does start on macOS 10.14 build machine essex2.
  • Also starts using TomG's development build on new macOS 13.3
  • Seems to be related to building on old macOS 10.14.
  • Using development build ChimeraX launcher executable fixes problem.
  • Zach patched PyOpenGL to work around problem.

• Update Intel Mac build machine to macOS 10.15?
  • Chimera is also built on this machine, essex2.
  • Might run into difficulties building chimera on newer XCode.
  • Would want to try chimera build on 10.15 but don't have a test machine.
  • Decided to just keep the builds on 10.14 since it is working.
  • Zach said he made a bundle builder change when updating to python 3.11 because 10.14 machine did not know how to deal with Python universal build.

• Chimera 1.17.2 release
  • Chimera 1.17.1 was missing ffmpeg so no movies can be recorded.
  • Only one bug report so far. Why so few?
  • Error message does not give "report a bug" button, so probably users don't know how to report it.
  • Decided to make 1.17.2 release on all platforms.
  • Ubuntu gets ffmpeg from RPM dependency so probably already works.
  • Will just promote current daily build to 1.17.2.
  • Chimera will notify users of new release.
  • Don't plan on announcing new release.
  • Eric will update release notes.
  • Release planned or this Thursday.

• PyQt 6.5.1 update
  • yes we will update to PyQt 6.5.1
  • Also time to update all the other prereqs.
  • Greg suggests adding required hash values to requirements.txt file because some PyPi hacking has been in the news.

• Python 3.11.4
  • ChimeraX is at Python 3.11.2
  • A change in 3.11.4 breaks PyQt handling of enums.
  • Wait for python 3.11.5 to see how it gets resolved, or whether we will need to fix our PyQt enum usage.

• Python 3.11 speed up
  • addh took 23.0 seconds on ChimeraX 1.6 / Python 3.9 and 20.7 seconds on daily build with Python 3.11, 10% speed-up. Tom only tried it once, so needs more testing to verify.
  • mmcif read speeds vary fro 9-11 seconds in weekly benchmark so not clear if read speed changed. Not expected to change since mostly C++.

• Toolshed prevent bundle downgrades
  • Eric asks how to avoid users downgrading to the old addh bundle on Toolshed.
  • Greg says put in that ChimeraX core version must be older than date that had that addh version.

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Action Items

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