Feature #3147

Task #2045: API design and language bindings

Feature #2994: Data flow topology in gmxapi 2020

gmxapi workflow checkpointing

Added by Eric Irrgang about 1 month ago. Updated about 1 month ago.



The simulation restartability from gmxapi 0.0.7 is specific to MD work and has outstanding issues from the old GitHub project. More importantly, it is based on assumptions about gmx::mdrun behavior and not generalizable to multi-operation work graphs. We need to develop the metadata and framework by which a gmxapi Context implementation can discover the state of complete or incomplete work from past invocations to avoid duplicating data or re-executing work. We also need to develop the interaction between high level and lower-level tools in order to establish a well-defined graph state when individual nodes are partially executed but recoverable.

Note that this feature interacts with #3146 and other issues.


- Establish reproducible/deterministic labeling of work graph invariants/immutables (defined work and data) and of filesystem artifacts.
- Extend deserialization of a work graph with initialized data sources.
- Design and implement lower level API bridge for library internal or operation-specific checkpointing facilities.
- Negotiate an achievable shared state.
- Make low-level checkpointing more pluggable. Allow deference of the library to gmxapi abstractions so that we can make bridges to different data/work management software or particular environments.
- More... Various issues and considerations from the gmxapi GitHub project should be migrated to the GROMACS issue tracking system.
- Prioritize and sequence the tasks and release targets.

Related issues

Related to GROMACS - Feature #3149: Python user interface for obtaining simulation artifacts as files.New


#2 Updated by Eric Irrgang about 1 month ago

  • Private changed from Yes to No

#3 Updated by Eric Irrgang about 1 month ago

  • Related to Feature #3149: Python user interface for obtaining simulation artifacts as files. added

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