Attendees

• Zach, Eric, Elaine, Greg, TomG, Scooter, TomF

On-site Genentech Hall N436A

Agenda

• Eric Phenix R24 grant progress
• Create ChimeraX 1.4 roadmap
• NIAID contract
• Review Action Items listed below

Discussion Notes

• Scooter and Elaine move to N453
  • Department asked Scooter and Elaine to move to N453.
  • Will happen in coming weeks.

• Phenix R24
  • Eric gave overview of Phenix and R24 proposal ChimeraX tasks
  • Showed demo of ChimeraX phenix douse command.
  • Discussion of whether Phenix REST server of subprocess call should be used to run Phenix methods.
  • Many disadvantages of REST, starting server, determining when it is ready, polling it, shutting it down.
  • Does not seem like Phenix has persistent state that would make REST attractive.
  • One advantage of REST would be having Phenix running on a different machine (cluster). Rare case.
  • Scooter discussed DASK for parallelizing Python numpy/pandas jobs on a cluster like wynton, or on local cores.

• Slow downloads of ChimeraX
  • Elaine and TomG have 15-30 minute ChimeraX download times this week from home.
  • Both using sonic.net, but have fast connection to other sites.
  • Tom Ferrin and Scooter (comcast) had fast download times this week.
  • Greg (sonic) and Zach (comcast) have not tried yet.
  • Scooter notes entire UCSF Mission Bay campus has only 10 Gbit/sec internet connection.

• Wynton BeeGFS problem
  • Last week multiple day downtime was caused by BeeGFS file system bug, metadata server deadlock.
  • Caused by a single job from Schoichet lab using BeeGFS for scratch.
  • This job has been changed to use local disk scratch like all other jobs.
  • Giving BeeGFS vendor test case so they can patch it.

• New Wynton GPUs
  • 13 new Wynton GPU nodes just received, 4 A40 GPUs each (48 GB each).
  • Brings Wynton GPUs from about 150 to 200.
  • Nvidia announced new H100 GPU with 80 GB. Also RTX 4000 series expected in September 2022.

Action Items

• Move toolshed to it's own IP address and it's own Apache instance -- Greg/Scooter
• Set up toolshed test instance (UCSF only) -- Greg/Scooter
• Clean up VirtualHosts on our web servers -- Greg/Scooter
• Move webservices to https only and extensively test chimera to make sure it works
• Create self-signed certificate for webservices-test -- ongoing, Greg has run into a weird error
• Document new vpn setup on Linux -- Scooter
• Set up 2-factor authentication for hal2 vpn -- Scooter
• Audit followup -- Scooter