Attendees

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

On-site Genentech Hall N436A

Agenda

• Scooter presenting
• CentOS 7 support for SBGrid
• ChimeraX 1.4 release schedule
• NIAID contract
• Review Action Items listed below

Discussion Notes

• NIAID contract
  • Have not heard from MSC, but contract is supposed to start May 1.

• Poster printer
  • Technician will look at it today, try to fix it.
  • Money may be available to repair it from water damage due to fire a year ago.

• American Association for Cancer Research conference
  • Scooter gave Cytoscape cancer talk in New Orleans
  • About 150 people attended presentation

• Vizvault projector
  • Tom Ferrin still looking for a vendor

• PyQt license was renewed for 1 year

• New hardware
  • Zach is trying new Philips 4K display, works great
  • Mac Studio machine ordered for Eric
  • Need top order display for Eric
  • Department discourages using credit cards for purchases.
  • But only computer vendors through Bear Buy are Dell, B+H and CDWG with limited offerings.

• Stanford ChimeraX tutorial
  • TomG gave tutorial to Wah Chiu's cryoEM class of 8 students on-site

• New Cytoscape / Chimera app
  • New Cytoscape app to look at distance variation between atoms in MD trajectories published last month.
  • Interacts with Chimera, PyMol and VMD for structure display.

• ChimeraX 1.4 release for CentOS 7
  • SBGrid says half of 440 ChimeraX users in last 6 months on CentOS 7, used it 7800 times.
  • Greg is trying compiling Qt 6 on CentOS 7.
  • If compiling fails then ChimeraX 1.3 will be last release for CentOS 7.

• Wynton update from Scooter
  • BeeGFS parallel file system from ThinkParq
    • data stored on multiple servers
    • also has multiple metadata servers
    • serves 400 wynton nodes
    • 18 storage servers
    • will have 10 petabytes of storage soon.
    • 24 metadata servers (12 mirrored)
    • metadata servers can get out of sync requiring resync
    • ThinkParq provided patch to fix deadlock
  • BeeHive
    • future database that optimizes metadata access
    • helps scans of files system, like unix "find" or malware scans
  • Backups
    • IS3 (UC Information Security Standard) mandates backups for availability level 3
    • Wynton had storage failure last year
    • Backups are only for disaster recovery, only latest copy of files
    • Have $500K to work on a backup solution
  • Archival backups
    • Might use Rubrik service
    • Samba server pulls data
    • Users opt in
    • Needs single group that can access all files to be backed up
    • Users will have to pay
    • Scooter not fond of this plan
  • Upgrades
    • 13 new GPU nodes, 4 A40 gpus each, installed and soon to be available.
    • New AMD CPUs available with many cores
    • Two new storage servers, using 16 TB instead of 10 TB drives
    • Wynton averaging 300K jobs/day, about 30 per core per day.

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