From a2dc78c87e15cc17cf17f33a12fea1e2ba78c994 Mon Sep 17 00:00:00 2001 From: Adam Wright <668955+adamjohnwright@users.noreply.github.com> Date: Fri, 9 Oct 2026 14:25:09 -0400 Subject: [PATCH] run_arm.sh: --max-edges option (default 40000); variant-node TP53 exceeds it (specs/046) Co-Authored-By: Claude Opus 5.5 (1M context) --- scripts/run_arm.sh | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scripts/run_arm.sh b/scripts/run_arm.sh index e006d8b..8942fce 100755 --- a/scripts/run_arm.sh +++ b/scripts/run_arm.sh @@ -4,6 +4,8 @@ # scripts/run_arm.sh NAME [--server K=V]... [--bench K=V]... [--port N] [--limit N] # # --limit N benchmark only the first N pathways (a smoke test, not an arm) +# --max-edges N skip pathways larger than N edges (default 40000; variant-node +# catalogs need more: TP53 exceeds it, specs/046) # --catalog ID run against builds/ID instead of `current` (a variant build) # # --server K=V a DS_* override for the SOLVER (set in the API container) @@ -41,13 +43,14 @@ die() { echo "run_arm: $*" >&2; exit 1; } [ $# -ge 1 ] || die "usage: scripts/run_arm.sh NAME [--server K=V]... [--bench K=V]... [--port N]" NAME=$1; shift [[ "$NAME" =~ ^[A-Za-z0-9._-]+$ ]] || die "NAME must be [A-Za-z0-9._-]+" -SERVER=(); BENCH=(); PORT=8090; LIMIT=(); CATALOG_ID="" +SERVER=(); BENCH=(); PORT=8090; LIMIT=(); CATALOG_ID=""; MAX_EDGES=40000 while [ $# -gt 0 ]; do case "$1" in --server) [[ "${2:-}" == DS_*=* ]] || die "--server needs DS_NAME=value"; SERVER+=("$2"); shift 2 ;; --bench) [[ "${2:-}" == *=* ]] || die "--bench needs NAME=value"; BENCH+=("$2"); shift 2 ;; --port) PORT=$2; shift 2 ;; --limit) LIMIT=(--limit "$2"); shift 2 ;; + --max-edges) [[ "${2:-}" =~ ^[0-9]+$ ]] || die "--max-edges needs a number"; MAX_EDGES=$2; shift 2 ;; --catalog) [ -n "${2:-}" ] || die "--catalog needs a build id"; CATALOG_ID=$2; shift 2 ;; *) die "unknown argument $1" ;; esac @@ -136,7 +139,7 @@ mkdir -p "$OUT" STARTED=$(date -Is); status=0 for gt in curator experimental; do env "${BENCH[@]}" DELTASIGNAL_BASE="http://localhost:$PORT" DS_CATALOG_ROOT="$BUILD" \ - "$PY" "$WT/bench/benchmark_vs_mpbiopath.py" --max-edges 40000 "${LIMIT[@]}" --ground-truth "$gt" \ + "$PY" "$WT/bench/benchmark_vs_mpbiopath.py" --max-edges "$MAX_EDGES" "${LIMIT[@]}" --ground-truth "$gt" \ --report "$OUT/${gt}_report.tsv" --dump-cases "$OUT/${gt}_cases.tsv" > "$OUT/$gt.log" 2>&1 \ || { echo "run_arm: $gt benchmark failed; see $OUT/$gt.log" >&2; status=1; break; } done