snakemake

name: snakemake description: Practical Snakemake-on-SLURM knowledge — driver placement, rule-output conventions, monitoring, recovery from crashes. Use this skill whenever the user is working with Snakemake (Snakefile, snakemake CLI, snakemake-executor-plugin-slurm), debugging a pipeline that uses Snakemake to orchestrate cluster jobs, or asking how to monitor / restart / recover a Snakemake run on a SLURM cluster. Pairs with the sciencecluster skill (general SLURM operational knowledge); this one is the Snakemake-specific overlay.

Snakemake on SLURM — operational knowledge

Grounded in real-incident debugging on a UZH-sciencecluster-like setup (snakemake 9.x + snakemake-executor-plugin-slurm). Per-user config (account name, login alias, env paths) stays in private global config / per-project CLAUDE.md. Per-project Snakefile lives in the repo (e.g., <project>/snakemake/Snakefile); generic patterns and recovery procedures live here.

Short on purpose. Three always-true rules (driver placement, per-wildcard outputs, env-inheritance gotcha) plus the config you set once. Symptom-specific playbooks (recovery from crash, mtime cascades, slurm_extra error, Invalid qos, opaque squeue names) live in references/ and load on demand.

1. Driver placement: in sbatch, NOT on the login node

The Snakemake driver is a long-running Python program that keeps a Timer thread per in-flight tracked job. With jobs: 150 + default polling, the driver easily holds 100+ threads. Login nodes typically cap ulimit -u at a few hundred (UZH sciencecluster: 256). The driver crashes mid-run with RuntimeError: can't start new thread.

Fix: run the driver as its own SLURM job. Compute nodes have ulimits in the hundreds of thousands. A 2-CPU / 8 GB / 24 h slot is plenty for a 1000-job pipeline.

Real template: references/run_driver.sh — cd to the repo, conda-activate, unlock+--rerun-incomplete pre-flight, then exec snakemake. Submit via:

ssh <cluster> 'cd ~/git/<project> && sbatch <project>/snakemake/run_driver.sh'

Walltime caps are partition × QoS dependent — see references/qos_walltime.md if you hit Invalid qos specification or want to know what --time is allowed. (Short answer: lowprio is 1 day; standard + medium is 2 days; standard + long is 7 days. Drivers usually fit in 1 day and resume cleanly via .snakemake/ persistence.)

2. Rule outputs must be true per-wildcard files

Snakemake enforces: all output paths of a rule must contain the same wildcards. If a tool writes to a shared scratch location indexed by something OTHER than a rule wildcard (e.g., neuropythy writing to freesurfer/<sub>/mri/ regardless of which PRF model sourced it), you have two options:

1. Sentinel file (last resort). Write a small marker file at output: f"{shared_dir}/_done_{wildcards.model}.touch". Cheap to implement but Snakemake's existence check is then disconnected from real output files — manual deletion of the real output doesn't trigger rerun.

2. Per-wildcard archive (preferred). Have the upstream tool copy its output to a per-wildcard path after running, and use that copy as the rule output. neuropythy's register_retinotopy.py does this: derivatives/neuropythy/model{N}/sub-XX/{mri,surf}/inferred_*.mgz. Pass the wildcard through to the script (--model {wildcards.model}) so the per-model copy lands in the right place.

If a Snakemake agent or earlier dev built sentinel-based rules, audit the upstream tool — there's often a real per-model output already being produced that wasn't being used.

3. Env inheritance: Snakemake's submitter env is cleaner than yours

Hand-sbatch'd scripts inherit MODULEPATH, PATH, LD_LIBRARY_PATH from the login shell that submitted them. snakemake-executor-plugin-slurm submits with a much cleaner env, so env-dependent scripts that "work by hand" can break the moment Snakemake submits the same script.

Classic case: source /etc/profile.d/lmod.sh defines module but leaves MODULEPATH empty — module load <X> then fails with module(s) are unknown. Fix is source /etc/profile (whole chain) or shebang #!/bin/bash -l. See the sciencecluster skill's references/script_shell_setup.md for the full story.

When a rule running an existing sbatch script fails fast on the compute node, suspect this class first — diff env between a hand-sbatched run and a Snakemake-submitted run before touching rule resources or plugin config.

4. jobs: cap and polling rate — set once

jobs: caps concurrent SLURM jobs in flight. A few interacting factors:

• Cluster's per-user job ceiling. Above some N the cluster queues inside SLURM rather than running concurrently.
• NFS dogpile. Submitting a huge array burst (1000+ in seconds) triggers user env retrieval failed requeued held on some clusters. Cap at ~150 to avoid.
• Driver thread count. Each tracked job spawns Timer threads. At 150 jobs + default 10 s polling, login nodes with ulimit -u 256 crash. Compute-node drivers are fine to 500+.

Reasonable defaults for a sciencecluster-style cluster (in profile/config.yaml):

jobs: 150
seconds-between-status-checks: 30     # default 10 is fine on compute nodes
max-status-checks-per-second: 1
rerun-triggers: [input]                # avoid mtime-driven chain cascades

That last line matters; see references/rerun_triggers.md for why default rerun-triggers: [mtime, input, params, code] causes forward-cascade reruns of a serial chain.

Real profile config: references/profile_config.yaml.

Templates

Drop-in starting points under references/ — substitute <project>, <account>, <cluster> placeholders, tweak per-rule resources:

Don't copy blindly — read the comments. Resource specs in particular need to match each rule's actual cost (and the cluster's QoS caps).

Reference index

Load on demand — each is one symptom or one design decision.

• qos_walltime.md — Invalid qos specification; what --time is allowed where; why a 24h driver re-submit is safe
• driver_recovery.md — LockException vs IncompleteFilesException after scancel; --cleanup-metadata escape hatch
• orphaned_jobs.md — why "preserve the expensive in-flight jobs across a driver restart" silently causes duplicate dispatch + scratch racing + corrupt gzip intermediates; the right way to restart a driver mid-flight
• rule_output_changes.md — why changing a rule's output: path without backfilling the new sentinel triggers a full cohort re-dispatch (e.g. 14 × 5h fmripreps); the backfill-first pattern that prevents it
• rerun_triggers.md — why dropping mtime from rerun-triggers stops forward-cascade reruns
• monitoring.md — opaque UUID job names
  • Comment field; --summary, --rulegraph
• slurm_extra.md — plugin-owned flags vs first-class resource keys; the silent-inaction failure mode

See also

• sciencecluster skill — general SLURM operational knowledge (cuInit/flock, conda activation, NFS dogpile). Snakemake inherits these via the driver's sbatch submission; per-rule SLURM resources reuse the same conventions.
• Per-project Snakefile — <repo>/<project>/snakemake/ typically has Snakefile + profile/ + config.yaml + run_driver.sh + status.sh.