usage-prof.md

prof — usage

Parse and align profiler output (denet, Snakemake bench files) with logger events for per-phase resource attribution.

Status: not yet implemented. This page will cover the Python submodule (obkit.prof) and the R prefix group (prof_*) once the API stabilises.

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Concept

A sampling profiler such as denet records CPU / RSS / IO at a fixed cadence. The logger records sparse phase anchors (align start, align end, …). prof joins the two on timestamp, attributing profiler samples to the phase active at each sample time.

denet samples:       ~~.~..~~..~~..~~..~~..~~..
logger events:  |start "align"                    |end "align"
                └──────────── attributed ──────────┘

The result is a per-phase resource summary without any instrumentation inside the profiler or changes to the workflow rule.

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Planned API surface

Python (obkit.prof)

from obkit.prof import load_events, load_denet, attribute

R (prof_*)

library(obkit)

prof_load_events(log_file)
prof_load_denet(denet_file)
prof_attribute(events, samples)