Attendees

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

Agenda

• Next meeting: Who will develop mmCIF writer?
• 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
          \ file size        144K     1.6M     14M      54M
          \ save time         .12      1.3     9.5     30.5
      uncompressed pickle   0.039     0.21    1.30     6.85
          \ file size        652K      11M     96M     379M
          \ save time        0.04      .18     1.4     11.4
      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
           \ file size       143K     1.6M     14M      54M
           \ save time       0.13      1.4     9.7     31.8
      uncompressed msgpack  0.038     0.18    1.14     5.82
           \ file size       628K      10M     93M     366M
           \ save time       0.06      0.2     1.7     12.1
      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)