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.