Notes 09 03 2014

Important Dates:

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.

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]

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.

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.