Merge pull request 'fix: 05_inference viser-kill + background-poll + offload_to_cpu from yaml' (#13) from fix/05-inference-viser-kill-offload into feature/auto-pipeline

- kill_stale_demo_py() before each segment to prevent GPU contention from orphan processes
- Remote script runs demo.py in background via nohup, polls for PLY file every 30s, kills viser server once PLY written — prevents indefinite SSH block on viser listener
- offload_to_cpu now read from thresholds.yaml[inference] (default false for 24GB VRAM)
- timeout reads inference_timeout_s from yaml (already 10800s)
- min_frames guard included (from fix/05-inference-min-frames-timeout)

Root cause: demo.py starts viser server after writing PLY; SSH timed out → orphan; two orphans competed for GPU with offload_to_cpu → pure CPU inference = 6h+ for 493 frames

pipeline/stages/05_inference.py

@@ -13,11 +13,12 @@ Workers:
 Auto: pick by lowest GPU memory usage (nvidia-smi via SSH).
 
 Flow:
-1. rsync frames .83 → worker /root/cosma-frames-tmp/ (or /home/floppyrj45/)
-2. SSH launch demo.py with windowed mode (window=64, overlap=16)
-3. Retrieve PLY + NPZ → .83 ~/cosma-pipeline/data/<mission>/ply/<AUV>/<segment>.{ply,npz}
-4. Cleanup worker temp dir
-5. Log to SQLite: duration, GPU peak mem, nb points in PLY
+1. Kill any stale demo.py on worker before starting
+2. rsync frames .83 → worker /root/cosma-frames-tmp/
+3. SSH launch demo.py in background; poll for PLY file; kill viser server once PLY done
+4. Retrieve PLY + NPZ → .83 ~/cosma-pipeline/data/<mission>/ply/<AUV>/<segment>.{ply,npz}
+5. Cleanup worker temp dir
+6. Log to SQLite: duration, GPU peak mem, nb points in PLY
 
 Usage:
     python3 05_inference.py --frames-dir ~/cosma-pipeline/data/20260505-Lepradet/frames/AUV210/GX019837 --worker auto --mission 20260505-Lepradet
@@ -83,6 +84,21 @@ def get_gpu_mem_used(worker_key: str) -> int:
         return 99999
 
 
+def kill_stale_demo_py(worker_key: str) -> None:
+    """Kill any lingering demo.py processes on worker before starting new inference."""
+    w = WORKERS[worker_key]
+    ssh_target = f"{w['user']}@{w['host']}"
+    try:
+        subprocess.run(
+            ["ssh", "-o", "StrictHostKeyChecking=no", "-o", "ConnectTimeout=10",
+             ssh_target, "pkill -9 -f demo.py 2>/dev/null; sleep 1; echo stale_killed"],
+            capture_output=True, text=True, timeout=15,
+        )
+        print(f"  [05] Stale demo.py killed on {worker_key}")
+    except Exception as e:
+        print(f"  [05] Warning: kill_stale failed on {worker_key}: {e}")
+
+
 def pick_worker() -> str:
     """Auto-select worker with lowest GPU memory usage."""
     best = None
@@ -140,6 +156,9 @@ def run_inference(frames_dir: Path, worker_key: str, mission_name: str,
         "status": "ok",
     }
 
+    # Step 0: kill any stale demo.py on worker
+    kill_stale_demo_py(worker_key)
+
     # Step 1: create remote temp dir + rsync frames
     print(f"  [05] rsync {frames_dir} → {ssh_target}:{worker_frames}...")
     subprocess.run(
@@ -165,6 +184,9 @@ def run_inference(frames_dir: Path, worker_key: str, mission_name: str,
     conf_thr = _INF_CFG.get("ply_conf_threshold", 1.5)
     kf_interval = _INF_CFG.get("keyframe_interval", 1)
     max_frames = _INF_CFG.get("max_frame_num", 1024)
+    use_offload = _INF_CFG.get("offload_to_cpu", False)
+    offload_flag = "--offload_to_cpu" if use_offload else "--no-offload_to_cpu"
+
     if inf_mode == "windowed":
         window_size = _INF_CFG.get("window_size", 64)
         overlap_size = _INF_CFG.get("overlap_size", 16)
@@ -179,39 +201,67 @@ def run_inference(frames_dir: Path, worker_key: str, mission_name: str,
             f"--keyframe_interval {kf_interval} "
             f"--max_frame_num {max_frames} "
         )
-    demo_cmd = (
-        f"cd {w['ai_dir']} && "
-        f"{w['venv']} demo.py "
-        f"--model_path {checkpoint} "
-        f"--image_folder {worker_frames} "
-        f"{mode_flags}"
-        f"--ply_conf_threshold {conf_thr} "
-        f"--save_ply {ply_remote} "
-        f"--save_poses {npz_remote} "
-        f"--use_sdpa "
-        f"--offload_to_cpu "
-        f"2>&1"
-    )
 
-    print(f"  [05] Launching inference on {host}...")
+    inf_timeout = int(_INF_CFG.get("inference_timeout_s", 10800))
+
+    # Remote script: launch demo.py in background, poll for PLY, kill viser when done
+    # This avoids the SSH blocking on the viser server that starts after inference
+    remote_script = f"""#!/bin/bash
+set -e
+PLY={ply_remote}
+LOG=/tmp/cosma_demo_{segment}.log
+# Launch demo.py in background
+nohup {w['venv']} {w['ai_dir']}/demo.py \\
+  --model_path {checkpoint} \\
+  --image_folder {worker_frames} \\
+  {mode_flags}--ply_conf_threshold {conf_thr} \\
+  --save_ply  \\
+  --save_poses {npz_remote} \\
+  --use_sdpa {offload_flag} \\
+  >  2>&1 &
+DEMO_PID=
+echo "demo.py PID=" >&2
+# Poll for PLY file (check every 30s)
+WAITED=0
+while [  -lt {inf_timeout} ]; do
+  if [ -f "" ] && [ $(wc -c < "") -gt 100 ]; then
+    sleep 10  # let write finish
+    echo "PLY_DONE size=$(wc -c < )" >&2
+    kill  2>/dev/null || true
+    exit 0
+  fi
+  # Check if process died with error
+  if ! kill -0  2>/dev/null; then
+    echo "Process died early" >&2
+    exit 1
+  fi
+  sleep 30
+  WAITED=30
+done
+echo "TIMEOUT after {inf_timeout}s" >&2
+kill -9  2>/dev/null || true
+exit 2
+"""
+
+    print(f"  [05] Launching inference on {host} (background+poll, timeout={inf_timeout}s)...")
     t0 = time.time()
     r = subprocess.run(
-        ["ssh", "-o", "StrictHostKeyChecking=no", ssh_target, demo_cmd],
-        capture_output=True, text=True, timeout=7200,  # 2h max
+        ["ssh", "-o", "StrictHostKeyChecking=no", ssh_target,
+         "bash -s"],
+        input=remote_script,
+        capture_output=True, text=True, timeout=inf_timeout + 60,
     )
     elapsed = time.time() - t0
     metrics["inference_s"] = round(elapsed, 1)
 
     if r.returncode != 0:
         metrics["status"] = "error"
-        metrics["error"] = r.stdout[-500:] + r.stderr[-200:]
+        metrics["error"] = (r.stdout + r.stderr)[-500:]
         print(f"  [05] inference error: {metrics['error'][-200:]}")
         return metrics
 
-    print(f"  [05] Inference done in {elapsed:.1f}s")
+    print(f"  [05] Inference done in {elapsed:.1f}s (returncode={r.returncode})")
 
-    # Step 3: GPU peak mem from nvidia-smi log (best-effort parse)
-    gpu_mem_line = [l for l in r.stdout.split("\n") if "MiB" in l]
     metrics["gpu_peak_mb"] = get_gpu_mem_used(worker_key)
 
     # Step 4: rsync PLY + NPZ back
@@ -242,17 +292,14 @@ def run_inference(frames_dir: Path, worker_key: str, mission_name: str,
 
 def process_frames_dir(frames_dir: Path, worker_key: str, mission_name: str) -> list[dict]:
     """Process a directory of frames (single segment or AUV tree)."""
-    # Detect if frames_dir contains frame_*.jpg directly or subdirs
     direct_frames = list(frames_dir.glob("frame_*.jpg"))
 
     if direct_frames:
-        # Single segment
         parts = frames_dir.parts
         auv_id = frames_dir.parent.name if len(parts) >= 2 else "UNKNOWN"
         segment = frames_dir.name
         return [run_inference(frames_dir, worker_key, mission_name, auv_id, segment)]
 
-    # Tree: frames_dir/<AUV>/<segment>/frame_*.jpg
     all_metrics = []
     for auv_dir in sorted(frames_dir.iterdir()):
         if not auv_dir.is_dir():
@@ -265,6 +312,19 @@ def process_frames_dir(frames_dir: Path, worker_key: str, mission_name: str) ->
             if not frames:
                 continue
             print(f"\n[05] === {auv_id}/{seg_dir.name}: {len(frames)} frames ===")
+            # Guard: min frames required for model (RoPE/attention)
+            min_frames = int(_INF_CFG.get("min_frames_for_inference", 32))
+            if len(frames) < min_frames:
+                print(f"  [05] SKIP {auv_id}/{seg_dir.name}: {len(frames)} frames < {min_frames} min")
+                init_db()
+                with get_conn() as conn_mf:
+                    mr = conn_mf.execute("SELECT id FROM missions WHERE name=?", (mission_name,)).fetchone()
+                    if mr:
+                        upsert_job(conn_mf, mr["id"], auv_id, seg_dir.name, "05_inference",
+                                   status="skipped",
+                                   error_msg=f"frames_too_few={len(frames)}<{min_frames}")
+                continue
+
             m = run_inference(seg_dir, worker_key, mission_name, auv_id, seg_dir.name)
             all_metrics.append(m)
 
@@ -291,12 +351,9 @@ def process_frames_dir(frames_dir: Path, worker_key: str, mission_name: str) ->
 
 def main():
     ap = argparse.ArgumentParser(description="Stage 05 — lingbot-map inference")
-    ap.add_argument("--frames-dir", type=Path, required=True,
-                    help="Frames dir (single segment or AUV tree)")
-    ap.add_argument("--worker", type=str, default="auto",
-                    choices=["auto", ".84", ".87"])
-    ap.add_argument("--mission", type=str, required=True,
-                    help="Mission name (e.g. 20260505-Lepradet)")
+    ap.add_argument("--frames-dir", type=Path, required=True)
+    ap.add_argument("--worker", type=str, default="auto", choices=["auto", ".84", ".87"])
+    ap.add_argument("--mission", type=str, required=True)
     args = ap.parse_args()
 
     worker = args.worker