Recurring Meeting of Cleveland Clinic - Stanford University

Date: September 17, 2014

Time: 4:00 PM EST

Means: Conference Call


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


  1. Update on upgrade.

  2. Progress on cloud computing interface.
  3. Open Knee(s) compatibility with FEBio version 2.0.
  4. Other.

Immediate Action Items:


  1. Update on upgrade.

    • decided to move to FusionForge during the upgrade process. This platform provides plugins to GitHub; has a Midas Platform like folder structure (particularly for documents). The latter feature can be used for data organization. The group will take a look at it collaboratively. Storage may still be problematic; the Stanford University team may need to think of implementation of quotas.

    • Completion of migration is estimated to be within the next 6 months.
  2. Progress on cloud computing interface.
    • Following migration and the upgrade, the group needs to make decisions for new features in regard to cloud computing capacity and interface. The cloud computing will be launched after migration. In the meanwhile, the team can utilize the staging server to as an example and start preparing the community for this feature.
    • Joy has started to evaluate how Galaxy implemented cloud computing interface. This example may particularly be useful to design the administration interface, i.e., to understand the workflow on how models are prepared for uploaded to the cloud for others to use.
  3. Open Knee(s) compatibility with FEBio version 2.0.
    • Open Knee(s) - Generation 1 now runs with FEBio version 2.0. The Cleveland Clinic team will prepare scripts for cloud based simulations using this version. FEBio version 2.0 needs to be installed on compute servers.
    • Compatibility constraints between models and solvers raise issues in user interface. This can be accommodated by providing simple guidelines with the model, e.g. indicating compatible FEBio versions. Potentially, incompatible solvers can be inactive at the software selection interface.
  4. Other.
    • It may be desirable to use multi-threading in FEBio. Henry wondered if this is set automatically. Number of cores to use is not automatically set by FEBio; FEBio uses the environment variable, OMP_NUM_THREADS to see how many cores should be used during solution process. This variable can be set in the Python script to run the simulations or it can be set at the wrapper which loads and executes all the scripts and the model to the desirable compute server.
    • Administration interface should enable descriptions for desirable servers and guidelines for expectations. Instructions for queuing to use high performance computing clusters may be helpful.
    • Joy requested to have conference calls every two months due to the workload of upgrade. The group concurred. For the next six months, the meetings will be during November, January, and March.

RecurringMeetings/2014-09-17 (last edited 2016-05-04 22:09:48 by localhost)