PD-sep matrix results: C2/C3/C4 figures + empirical mechanism refined

Captures 5 runs from the experiment matrix (combined-ca x3 seeds,
pdsep-4p4d seed1, pdsep-6p2d seed1) on traces/w600_r0.0015_st30.jsonl
with cuda graphs enabled. The headline:

  combined-ca:  TTFT p50 0.91s   success 99.5%
  pdsep-4p4d:   TTFT p50 62.8s   success 52%   (69x worse, half dropped)
  pdsep-6p2d:   TTFT p50 51.1s   success 68%   (56x worse, third dropped)

C2 (fig_c2): headline bars per config with error bars.
C3 (fig_c3): per-instance KV utilization time-series. Both PD-sep
  splits hit the memory wall, but the side differs by P:D ratio --
  4P+4D pins the P-side, 6P+2D pins both sides (D-side back-pressures
  P-side).
C4 (fig_c4): TTFT stacked breakdown. 99% of PD-sep TTFT is P-side
  prefill compute; D-side wait + first token is <=1.2s. The bottleneck
  is P-side prefill queueing, not D-side decode wait as the original
  analytical model assumed.

system_analysis.md gains a Layer 5b that reconciles the analytical
KV-wall model (which considered D-side only) with the empirical
finding that the wall hits whichever side has fewer GPUs, and
co-saturates both at extreme splits via D-side back-pressure.

plot_pd_matrix.py ingests outputs/pd_matrix/* into all four figures.
bench.sh gained AGENTIC_STEP_LOG_DIR hooks for future runs (set during
this work but not used by the current matrix's data).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

analysis/pd_sep_paper_section/scripts/bench_pd_matrix.sh

@@ -41,6 +41,7 @@ WITH_RR=false
 WITH_EAGER=false
 DRY_RUN=false
 TAG_PREFIX="pd_matrix"
+ONLY=""             # comma-separated list of tags to run (subset of the matrix)
 
 while [[ $# -gt 0 ]]; do
     case "$1" in
@@ -50,6 +51,7 @@ while [[ $# -gt 0 ]]; do
         --with-rr) WITH_RR=true; shift ;;
         --with-eager) WITH_EAGER=true; shift ;;
         --tag-prefix) TAG_PREFIX="$2"; shift 2 ;;
+        --only) ONLY="$2"; shift 2 ;;
         --dry-run) DRY_RUN=true; shift ;;
         -h|--help)
             sed -n '2,30p' "$0"; exit 0 ;;
@@ -57,6 +59,20 @@ while [[ $# -gt 0 ]]; do
     esac
 done
 
+# Build set of allowed tags from --only (if provided).
+declare -A ALLOWED
+if [ -n "$ONLY" ]; then
+    IFS=',' read -ra _tags <<< "$ONLY"
+    for t in "${_tags[@]}"; do
+        ALLOWED["$(echo "$t" | xargs)"]=1
+    done
+fi
+is_allowed() {
+    # if ONLY not set, everything is allowed
+    [ -z "$ONLY" ] && return 0
+    [ -n "${ALLOWED[$1]:-}" ]
+}
+
 if [ ! -f "$TRACE" ]; then
     echo "[ERROR] trace not found: $TRACE"
     exit 1
@@ -141,13 +157,17 @@ for c in "${CONFIGS[@]}"; do
     for m in "${MODES[@]}"; do
         mode_name="${m%%|*}"; mode_args="${m##*|}"
         for s in $(seq 1 $SEEDS); do
+            tag_name="${cfg_name}_${mode_name}_seed${s}"
+            if ! is_allowed "$tag_name"; then
+                continue
+            fi
             if run_one "$cfg_name" "$cfg_args" "$mode_name" "$mode_args" "$s"; then
                 N_DONE=$((N_DONE + 1))
             else
                 N_FAIL=$((N_FAIL + 1))
             fi
             ELAPSED=$(( $(date +%s) - START_TS ))
-            echo "[progress] $N_DONE done, $N_FAIL failed, $((N_TOTAL - N_DONE - N_FAIL)) remaining, ${ELAPSED}s elapsed"
+            echo "[progress] $N_DONE done, $N_FAIL failed, ${ELAPSED}s elapsed"
         done
     done
 done