Job Grouping#

The graph of jobs that Snakemake determines before execution can be partitioned into groups. Such groups will be executed together in cluster or cloud mode, as a so-called group job, i.e., all jobs of a particular group will be submitted at once, to the same computing node. When executing locally, group definitions are ignored.

Groups can be defined along with the workflow definition via the group keyword, see Defining groups for execution. This way, queueing and execution time can be saved, in particular by attaching short-running downstream jobs to long running upstream jobs.

From Snakemake 7.11 on, Snakemake will request resources for groups by summing across jobs that can be run in parallel, and taking the max of jobs run in series. The only exception is runtime, where the max will be taken over parallel jobs, and the sum over series. If resource contraints are provided (via --resources or --cores), parallel job layers that exceed the constraints will be stacked in series. For example, if 6 instances of somerule are being run, each instance requires 1000MB of memory and 30 min runtime, and only 3000MB are available, Snakemake will request 3000MB and 60 min runtime, enough to run 3 instances of somerule, then another 3 instances of somerule in series.

Often, the ideal group will be dependent on the specifics of the underlying computing platform. Hence, it is possible to assign groups via the command line. For example, with

snakemake --groups somerule=group0 someotherrule=group0

we assign the two rules somerule and someotherrule to the same group group0.

By default, groups do not span disconnected parts of the DAG. This means that, for example, jobs of somerule and someotherrule only end in the same group if they are directly connected. It is, however, possible to configure the number of connected DAG components that are spanned by a group via the flag --group-components. This makes it possible to define batches of jobs of the same kind that shall be executed within one group. For instance:

snakemake --groups somerule=group0 --group-components group0=5

means that given n jobs spawned from rule somerule, Snakemake will create n / 5 groups which each execute 5 jobs of somerule together. For example, with 10 jobs from somerule you would end up with 2 groups of 5 jobs that are submitted as one piece each.