Notes 09 03 2014

Important Dates:

• Next CDI Meeting: Friday, 5th 10 AM E

Antons

• Repex
  • CDI folks provided Antons with more realistic (larger + more complex) use-case which will drive Antons' development over the next couple of weeks.
  • Anton is currently working on the implementation of Schema-4 which is almost working. Schema{1,2,3} are working on Trestles and Stampede, but need more feedback from CDI folks to become stable.
  • TODO: Anton will create a testing protocol (analogous to the RP one) for CDI folks and group members by Thursday. Shantenu and Ole will review and then present at Friday's CDI meeting.
• EnsembleMD Toolkit
  • Antons added a pattern as well as example invocation to the repository:
    • https://github.com/radical-cybertools/radical.ensemblemd/blob/nouveauapi/src/radical/ensemblemd/patterns/replica_exchange_pattern.py
    • https://github.com/radical-cybertools/radical.ensemblemd/blob/nouveauapi/examples/replica_exchange_2.py
    • TODO: Ole will review this and integrate it with the code base / tests.

Vivek

• Extasy: Gromacs / LSDMap

  • Works on Stampede.
  • Jordan is testing but feedback is still somewhat limited.
  • TODO: Vivek will create a testing protocol similar to the one we are creating for RepEx. Ole and Shantenu will review and next week we will pass this on to the relevant people.
  • TODO: Vivek will focus his work on making Gromacs/LSDMap work on Archer as this is required for the upcoming Extasy release.
  • Two use-cases have been identified: MSMA (Multiple-Simulations, Multiple-Analysis) and MSSA (Multiple-Simulation, Single analysis). Current API seems to support this.
    • https://drive.google.com/drive/u/0/#folders/0BwTDDNO3et-hZ0x5d3R3bkdjV1k
    • Execution pattern needs to support cases where num_cus == num_cores and num_cus < num_cores.
    • TODO Ole will add that to the use-case proof-of-concepts.

• Extasy: Amber / Coco

  • Works on Stampede, tested by Iain, Charlie and Ardita.
  • Some issues with Coco input files -- needs to be resolved with Ardita.
    • TODO: Vivek solve input file min0 issue with Ardita.
  • TODO: Vivek will focus his work on making Amber/CODO work on Archer as this is required for the upcoming Extasy release. Iain's efforts to get SciPy et al. onto Archer should make this straight forward

• EnsembleMD Toolkit

  • Discussed examples, APIs. Two things Vivek needs feedback on:
    • TODO: Ole provide Vivek with "kernel concatenation* example. [DONE]
    • TODO: Ole provide Vivek with input output file handling example. [DONE]

Ole

• HT-BAC

  • No new developments since UCL visit.
  • Creating document capturing the 'whole pipeline' HT-BAC scenario in more detail (based on discussions wit Jacob)

• EnsembleMD Toolkit

  • Updated API and created minimally working examples for
    • Pipeline
    • Simulation analysis
  • Updated documentation and unit-tests, added use-cases:
    • http://radicalensemblemd.readthedocs.org/en/latest/usecases.html
  • TODO Ole: Create release plan for 0.1, October 1st, 2014.

EnsembleMD Toolkit Meeting

• Attendees: Vivek, Antons, Andre, Shantenu (sort of), Ole
• We agreed to slightly change the format of the EnsembleMD Toolkit meeting. Since Ole, Antons and Vivek catch up on technical details right before the meeting, we decided to provide just a quick "executive overview" and shorten the meeting to 30 minutes (up to 1h only if required). Periodically, we will have hands-On sessions and tutorials.
• TODO: Shantenu Review API / examples and give feedback by Wednesday.