Toolkit Release 0.2

Projected release date: 01-16-2015

Objectives

Maturing of existing codebases and example fragments. Consistent documentation.

Patterns

Pipeline

Primarily responsible: Ole

Task	Assigned	Status
Implement proper parallel execution	Ole	DONE
Rudimentary unit-test template	Ole	DONE
Finalize examples [1] [2]	Ole	DONE
Finalize documentation [3] [4] [5]	Ole	DONE
Finalize and document HT-BAC Use-Case [6]	Ole	DONE
Basic Performance Characterization	Ole	Framework in place.

• [1] https://github.com/radical-cybertools/radical.ensemblemd/blob/master/examples/bag_of_ensembles.py
• [2] https://github.com/radical-cybertools/radical.ensemblemd/blob/master/examples/pipeline.py
• [3] http://radicalensemblemd.readthedocs.org/en/latest/_generated_example_pipeline.html
• [4] http://radicalensemblemd.readthedocs.org/en/latest/_generated_example_bag_of_ensembles.html
• [5] http://radicalensemblemd.readthedocs.org/en/latest/library.html#pipleline-pattern-api
• [6] https://github.com/radical-cybertools/radical.ensemblemd/tree/master/usecases/ucl_htbac

Simulation-Analysis-Loop

Primarily responsible: Vivek

Task	Assigned	Status
Implement remaining data deps.	Ole	DONE
Rudimentary unit-test template	Ole	DONE
CI Integration	Ole	DONE
Finalize examples [1] [2] [3]	Ole	DONE
Finalize documentation [4]	Ole	DONE
Finalize and document LSDMap/GROMACS use-case [5]	Vivek	DONE
Create / implement / document CoCo/Amber use-case [6]	Vivek	DONE
Basic Performance Characterization	Ole	Framework in place

• [1] https://github.com/radical-cybertools/radical.ensemblemd/blob/master/examples/simulation_analysis_loop.py
• [2] https://github.com/radical-cybertools/radical.ensemblemd/blob/master/examples/multiple_simulations_multiple_analysis.py
• [3] https://github.com/radical-cybertools/radical.ensemblemd/blob/master/examples/multiple_simulations_single_analysis.py
• [4] http://radicalensemblemd.readthedocs.org/en/latest/library.html#simulationanalysisloop-pattern-api
• [5] https://github.com/radical-cybertools/radical.ensemblemd/tree/master/usecases/extasy_gromacs_lsdmap
• [6] https://github.com/radical-cybertools/radical.ensemblemd/tree/master/usecases/extasy_coco_amber

All-Pairs

Primarily responsible: Giannis

Task	Assigned	Status
Rudimentary unit-test template	Ole	DONE
CI Integration	Ole	WIP
Implement All-Pairs backend	Giannis	Done
Finalize / document 'generic' example	Giannis	Done
Document API	Giannis	Done
Create and document science use-case	Giannis	WIP
Basic Performance Characterization	Ole	Framework in place

Replica-Exchange

Primarily responsible: Antons

Task	Assigned	Status
Rudimentary unit-test template	Ole	DONE
CI Integration	Ole	DONE
Finalize examples [1] [2]	Antons	?
Finalize documentation [3] [4] [5]	Antons	?
Create and document working CDI use-case [6]	Antons	?
Basic Performance Characterization	Ole	Framework in place

Documentation

Primarily responsible: Ole

Task	Assigned	Status
Overal grooming	Ole	WIP
Tutorial / getting started guide [1]	Ole	WIP

• [1] http://radicalensemblemd.readthedocs.org/en/latest/getstarted.html

Dissemination / Integration

Primarily responsible: Shantenu

Task	Assigned	Status
Present / demo CoCo/Amber example to ExTASY folks	Shantenu/Ole/Vivek	?
Present / demo Gromacs/LSDMAP example to ExTASY folks	Shantenu/Ole/Vivek	?
Present / demo RepEx example to CDI folks	Shantenu/Ole/Antons	?