Attendees

• Conrad, Elaine, Eric, Greg, TomG, TomF

Agenda

• Review action items from 6/22 meeting
• ChimeraX paper
• Changing Windows build machine
• Yet another new bundle building change
• Sessions: msgpack vs pickle
• Chimera 1 fetching vs SSL certificate on Windows 7
• For next meeting: ChimeraX on Github

Discussion

• ChimeraX paper
• Changing Windows build machine
  • Move daily builds from vive (VR machine) to snow (Greg's Core i3 desktop)
• Yet another new bundle building change
  • Use blastprotein and rest_server for template bundle_info.xml and new Makefile
  • Edit bundle_info.xml using data from old Makefile and setup.py.in
  • New Makefile should work as is, i.e., it is the same for all bundles
  • Delete setup.cfg and setup.py.in when done
• Sessions: msgpack vs pickle

                             3xf5     1tr4    5ijn     3j3q
      number of atoms        3687    68540  594304  2440800
      file size (MB)          0.7      6.6      80      254
  
      compressed pickle     0.041     0.25    1.67     8.24
      uncompressed pickle   0.039     0.21    1.30     6.85
      for compressed files:
        deserialize data    12.2%    33.4%   56.0%    52.1%
        resolve reference   15.1%    17.6%    1.6%     0.1%
        restore data        13.2%    34.1%   40.4%    47.4%
  
      compressed msgpack    0.040     0.22    1.49     7.17
      uncompressed msgpack  0.038     0.18    1.14     5.82
      for compressed files:
        deserialize data     6.2%    28.3%   48.1%    42.7%
        resolve references  14.8%    17.2%    1.7%     0.1%
        restore data        13.8%    33.3%   47.4%    56.5%
  
      msgpack % faster       2.5%      14%     12%      15%
  

• Chimera 1 fetching vs SSL certificate on Windows 7
  • Works in 1.10 (Greg yes, TomG maybe)
  • Fails on 1.11.2, unable to verify certificate

Action Items

• Greg will create table of performance comparing msgpack vs pickle, for 4 sizes: 1,000, 10,000, 100,000 and 1 million atom range
• All: Go through tickets and assign alpha2 milestone to important defect tickets
• All will convert owned bundles to new layout
• Conrad will continue working on ribbon tickets
• Conrad will investigate implementing the "like" operator
  • e.g., to specify polymer in atomspec
• Scooter will investigate making tickets public (possibly marking some tickets private)