Recurring Meeting of Cleveland Clinic - Stanford University

Date: March 19, 2014

Time: 4:00 PM EST

Means: Conference Call

Attendees:

1. Ahmet Erdemir (Cleveland Clinic)
2. Craig Bennetts (Cleveland Clinic)
3. Joy Ku (Stanford University)
4. Henry Kwong (Stanford University)

Agenda:

1. Progress on mockup interface development for the compute gateway.
2. Update on XSEDE application.
3. Update on data management tool.

4. SimTk site bugs & features.

5. Decide action items for next meeting.
6. Other.

Immediate Action Items:

• Stanford University (Joy & Henry)

  • Implement security patches to current prototype.
  • Develop results retrieval interface.

• Cleveland Clinic (Ahmet & Craig)

  • Follow up on numerical reproducibility of FEBio simulations.

Notes:

1. Progress on mockup interface development for the compute gateway.
   • The prototype for underlying infrastructure and remote execution is fully functional on staging servers. The prototype sends e-mails associated with job request, start, and execution (3 e-mails). The system is able to run FEBio with and without modification to the model files (depending on the staging server).
   • Use of g-mail for user notification is problematic with staging servers.
   • Model modification script provided by the Cleveland Clinic team appears to require Python version 2.7. Current servers utilize the latest Centos Linux which defaults to Python version 2.6. Henry notes that workaround is possible. The team needs to choose the Python version, possibly version 2.7 for now.
   • Retrieval of model results and administration of model provision are the next steps. There are few security holes that needs to be patched before this.
   • Once all job administration, submission, and retrieval features are implemented, the Cleveland Clinic team will likely provide Open Knee - Generation 1 for cloud computing.
   • Henry asked if the Cleveland Clinic team is using 32 bit or 64 bit systems. The Cleveland Clinic team commonly utilizes 64 bit Linux machines.
2. Update on XSEDE application.
   • XSEDE has quarterly deadlines for applications. Next submission window is March 15 - April 15 for a July 1 start of allocation. The following submission window is June 15 - July 15 for an October 1 start of allocation. Currently, the team does not need XSEDE resources to prototype. The allocation may be useful to iron out any issues that may be relevant to establishing a gateway. Nonetheless, the team agrees that XSEDE resources (potentially including some portion of FTE) should be used as effective as possible.
   • The team will wait until a full cloud computing prototype is ready. The issue related to XSEDE application will be revisited in 3 months to potentially meet the June deadline. In the meanwhile, the Cleveland Clinic team will accumulate information on potential computational cost of running knee joint models.
   • Ahmet wondered if virtual machines work on XSEDE platforms. This may facilitate launching of servers.
3. Update on data management tool.

   • For the next generation of SimTk, a data management tool is a possibility but not a priority. There is a need from several groups utilizing SimTk. Discussions will continue.

   • The Cleveland Clinic team will launch a local Midas Platform for their in-house data management needs, which will also support Open Knee(s). When and if SimTk provides such tools, they will port the data management activities related to Open Knee(s) there.

4. SimTk site bugs & features.

   • The focus of Stanford group is shifting to the new SimTk site. The teams will continue communicating about bugs and features. Unless a bug is critical and urgent, it will not be prioritized.

5. Decide action items for next meeting.
   • See Immediate Action Items above.
6. Other.
   • Henry raised a concern about FEBio running exactly the same way all the time. He observed differences in output file sizes, even when the model file remained the same. He will provide some information about this mismatch. The Cleveland Clinic team will check this to see if it is an expected behaviour.
   • Stanford team met with representatives from Amazon Inc. The meeting provided helpful information to communicate with AWS.

   • Work on next generation of SimTk is in progress. There may be 6 months before anything happens to accommodate preparation of specifications and development time.