Running a Parallel Application on the Cluster
- The amdahl code is a model of a parallel application
- The execution speed depends on the degree of parallelism
Introduction to Snakemake
- Snakemake is an indirect way of running executables
- Snakemake has a notion of system state, and can be fooled.
More Complicated Snakefiles
- Snakemake rule files can be mapped to task graphs
- Tasks are executed as required in dependency order
- Where possible, tasks may run concurrently.
Snakemake and the Cluster
- Snakemake rule files can submit cluster jobs.
- There are a lot of options.
Snakemake Profiles
- Snakemake profiles encapsulate cluster complexity.
- Retaining operational flexibliity is also important.
Amdahl Parallel Runs
- A relatively compact snakemake file collects interesting data.