predict-runtime-breakdown

Testing & Quality

Produce a detailed phase-by-phase runtime breakdown of a single `prank predict` run (JVM boot, class-loading, Groovy config compile, model load, PDB parse, surface, feature extraction, prediction, output) on the current JRE. Use when asked where p2rank prediction time goes, to profile startup/runtime overhead, to find what to optimize, or to compare launchers/JVMs at sub-phase granularity.

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P2Rank predict runtime breakdown

Decompose where a single prank predict run spends wall-clock time. For typical single-file prediction most of the time is fixed overhead (JVM startup, Groovy config compile, model deserialization, JIT warmup), not pocket-finding, so a flat "it took N seconds" hides the real cost structure. This skill produces the per-phase table.

How to run

The reproducible tool is committed at misc/test-scripts/predict_breakdown.sh. It runs against the distro launchers, so build first:

./gradlew assemble
./misc/test-scripts/predict_breakdown.sh                         # small default protein, stock launcher
./misc/test-scripts/predict_breakdown.sh distro/test_data/2W83.pdb   # a specific (larger) protein
./misc/test-scripts/predict_breakdown.sh -l distro/prank_burst      # see the CDS + C1-JIT launcher
./misc/test-scripts/predict_breakdown.sh --deep                      # + classpath, class-load histogram, subsystem first-load, zstd/deserialize split, JIT/GC

It is also exposed as a mode of the main bench script, alongside --phases/--profile:

./misc/test-scripts/predict_bench.sh --breakdown                      # same, via predict_bench.sh
./misc/test-scripts/predict_bench.sh --breakdown -l distro/prank_burst distro/test_data/2W83.pdb

To compare JREs, switch the active JVM (e.g. via SDKMAN JAVA_HOME) and re-run; the script always reports the JRE it used in its header.

What the script does (and how to reproduce by hand if needed)

It combines five probes into one report:

Bare JVM boot -- /usr/bin/time java -version. Establishes the floor (~0.06 s); proves the "startup" phase is application class-loading, not the JVM itself.
JVM Create VM -- JAVA_OPTS="-Xlog:startuptime". The JVM-internal init cost, including module-system init (inflated by --add-modules jdk.incubator.vector).
Timestamped run -- a full per-line perl -MTime::HiRes timeline (the same technique as predict_bench.sh --phases, but unfiltered) whose milestone log lines give the phase boundaries.
Phase table -- deltas between those milestones, as seconds and % of total.
Class-load census -- JAVA_OPTS="-Xlog:class+load=info:file=...:uptime,tags", bucketed by phase window and tallied by top-level package. Shows that class loading dominates startup and the Groovy compiler dominates config parse.

Plus model-dir facts (du/find on distro/models/default) and the raw milestone timeline as evidence.

The phases (what each milestone means)

Phase	Milestone span	What dominates
A. startup	process start -> "loading default config"	JVM boot (~0.15 s) + application class-loading (Groovy runtime, Log4j2, BioJava/Arrow/Parquet, classpath `bin/lib/*` scan)
B. config parse	"loading default config" -> "predicting pockets for proteins"	the Groovy compiler (`org.codehaus.groovy` + `groovyjarjarantlr4`) compiling `default.groovy` at runtime
C. model load	"Loading model from directory" -> "effectively enabled features"	zstd-decompress of the ~22 MB `model.zst` + `ObjectInputStream` RF deserialize
D1. PDB parse	"loading protein" -> "structure atoms"	BioJava structure parsing
D2. surface	"structure atoms" -> "SAS points"	FasterMolecularSurface accessible-surface computation
D3. features	"SAS points" -> "PREDICTING POCKETS"	per-SAS-point feature vectors (kd-tree heavy)
E. prediction	"PREDICTING POCKETS" -> "pocket 1 -"	clustering + random-forest scoring of SAS points
F. output	"pocket 1 -" -> "predicting pockets finished"	writing CSV / points / visualization files, copying input

JIT warmup is not a separate phase; first-time-interpreted code is smeared across A/B/D.

How to present results

Show the phase table (seconds + share) and call out the largest targets. Typical finding on a small protein with stock distro/prank: roughly A ~27%, B ~22%, C ~25%, D ~17%, E ~1%, F ~5%, i.e. ~93% fixed overhead, ~7% actual prediction. The biggest single lever is A+B (class loading + runtime Groovy config compile), which is what AppCDS in distro/prank_burst attacks.

Caveats (state these)

Numbers are from ONE cold run and drift with machine load. The sub-phase proportions are the stable signal, not the absolute seconds. Re-run a few times before fine claims.
Phase boundaries are derived from log milestones, so this is a best-effort decomposition, not instrumentation inside the code. The script also prints the raw timeline for verification.
Use a small protein to make fixed overhead easiest to read; use a large one (e.g. 1AHP.pdb) to see phases C-F grow relative to startup.

misc/test-scripts/predict_bench.sh -- wall-time tables, --compare, --phases, --profile (JFR hot methods).
misc/test-scripts/predict_bench_jres.sh -- cross-JRE timing comparison.
documentation/dev/jvm-performance-tuning.md -- the prose analysis this skill automates.
misc/dev/benchmarks/2026-06-05-predict-runtime-breakdown.md -- captured findings, including the expanded sub-phase decomposition and the JIT/GC cross-cutting costs.