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This lesson is in the pre-alpha phase, which means that it is in early development, but has not yet been taught.
HPC Workflow Management with Snakemake
- The amdahl code is a model of a parallel application
- The execution speed depends on the degree of parallelism
- Snakemake is an indirect way of running executables
- Snakemake has a notion of system state, and can be fooled.
- Snakemake rule files can be mapped to task graphs
- Tasks are executed as required in dependency order
- Where possible, tasks may run concurrently.
- Snakemake rule files can submit cluster jobs.
- There are a lot of options.
- Snakemake profiles encapsulate cluster complexity.
- Retaining operational flexibliity is also important.
- A relatively compact snakemake file collects interesting data.