V2 CN: CYTO-042 results (precision up, mosaic calls halved); pi_run reports process memory without page cache

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

scripts/pi_run.sh

@@ -21,10 +21,13 @@ else
 fi
 pid=$!
 peak=0
+anon_peak=0  # process memory without page cache (memory.peak counts cached file pages, e.g. a FASTA being read)
 tripped=0
 while kill -0 "$pid" 2>/dev/null; do
   if [[ -r $cg/memory.peak ]]; then
     peak=$(( $(cat "$cg/memory.peak") / 1024 ))
+    anon=$(awk '$1 == "anon" {print int($2 / 1024)}' "$cg/memory.stat" 2>/dev/null || echo 0)
+    (( anon > anon_peak )) && anon_peak=$anon
   else
     rss=$(ps -o rss= -g "$pid" 2>/dev/null | awk '{s+=$1} END {print s+0}'); (( rss > peak )) && peak=$rss
   fi
@@ -41,5 +44,7 @@ wait "$pid"; rc=$?
 (( tripped )) && rc=137
 (( rc == 137 && ! tripped )) && [[ $mode == cgroup* ]] \
   && echo "pi_run: the job was killed (SIGKILL); most likely it exceeded MemoryMax=$MEM" >&2
-echo "pi_run: exit $rc, peak memory $((peak / 1024)) MiB ($mode, guard ${MIN_FREE_MB} MiB free)" >&2
+anon_note=""
+(( anon_peak > 0 )) && anon_note=", process $((anon_peak / 1024)) MiB without page cache"
+echo "pi_run: exit $rc, peak memory $((peak / 1024)) MiB$anon_note ($mode, guard ${MIN_FREE_MB} MiB free)" >&2
 exit $rc