Make batch_runner checkpoint incremental and atomic

batch_runner.py

@@ -29,6 +29,7 @@ from typing import List, Dict, Any, Optional, Tuple
 from datetime import datetime
 from multiprocessing import Pool, Lock
 import traceback
+import tempfile
 
 from rich.progress import Progress, SpinnerColumn, BarColumn, TextColumn, TimeRemainingColumn, MofNCompleteColumn
 from rich.console import Console
@@ -650,13 +651,32 @@ class BatchRunner:
         """
         checkpoint_data["last_updated"] = datetime.now().isoformat()
 
+        def _atomic_write():
+            """Write checkpoint atomically (temp file + replace) to avoid corruption on crash."""
+            self.checkpoint_file.parent.mkdir(parents=True, exist_ok=True)
+            fd, tmp_path = tempfile.mkstemp(
+                dir=str(self.checkpoint_file.parent),
+                prefix='.checkpoint_',
+                suffix='.tmp',
+            )
+            try:
+                with os.fdopen(fd, 'w', encoding='utf-8') as f:
+                    json.dump(checkpoint_data, f, indent=2, ensure_ascii=False)
+                    f.flush()
+                    os.fsync(f.fileno())
+                os.replace(tmp_path, self.checkpoint_file)
+            except BaseException:
+                try:
+                    os.unlink(tmp_path)
+                except OSError:
+                    pass
+                raise
+
         if lock:
             with lock:
-                with open(self.checkpoint_file, 'w', encoding='utf-8') as f:
+                _atomic_write()
-                    json.dump(checkpoint_data, f, indent=2, ensure_ascii=False)
         else:
-            with open(self.checkpoint_file, 'w', encoding='utf-8') as f:
+            _atomic_write()
-                json.dump(checkpoint_data, f, indent=2, ensure_ascii=False)
     
     def _scan_completed_prompts_by_content(self) -> set:
         """
@@ -781,13 +801,15 @@ class BatchRunner:
             print(f"   New batches created:       {len(batches_to_process)}")
             print("=" * 70 + "\n")
         
-        # Initialize checkpoint data (needed for saving at the end)
+        # Load existing checkpoint (so resume doesn't clobber prior progress)
-        checkpoint_data = {
+        checkpoint_data = self._load_checkpoint()
-            "run_name": self.run_name,
+        if checkpoint_data.get("run_name") != self.run_name:
-            "completed_prompts": [],
+            checkpoint_data = {
-            "batch_stats": {},
+                "run_name": self.run_name,
-            "last_updated": None
+                "completed_prompts": [],
-        }
+                "batch_stats": {},
+                "last_updated": None
+            }
         
         # Prepare configuration for workers
         config = {
@@ -809,7 +831,7 @@ class BatchRunner:
         }
         
         # For backward compatibility, still track by index (but this is secondary to content matching)
-        completed_prompts_set = set()
+        completed_prompts_set = set(checkpoint_data.get("completed_prompts", []))
         
         # Aggregate statistics across all batches
         total_tool_stats = {}
@@ -818,6 +840,9 @@ class BatchRunner:
         
         print(f"\n🔧 Initializing {self.num_workers} worker processes...")
         
+        # Checkpoint writes happen in the parent process; keep a lock for safety.
+        checkpoint_lock = Lock()
+
         # Process batches in parallel
         with Pool(processes=self.num_workers) as pool:
             # Create tasks for each batch
@@ -863,6 +888,25 @@ class BatchRunner:
                     for result in pool.imap_unordered(_process_batch_worker, tasks):
                         results.append(result)
                         progress.update(task, advance=1)
+
+                        # Incremental checkpoint update (so resume works after crash)
+                        try:
+                            batch_num = result.get('batch_num')
+                            completed = result.get('completed_prompts', []) or []
+                            completed_prompts_set.update(completed)
+
+                            if isinstance(batch_num, int):
+                                checkpoint_data.setdefault('batch_stats', {})[str(batch_num)] = {
+                                    'processed': result.get('processed', 0),
+                                    'skipped': result.get('skipped', 0),
+                                    'discarded_no_reasoning': result.get('discarded_no_reasoning', 0),
+                                }
+
+                            checkpoint_data['completed_prompts'] = sorted(completed_prompts_set)
+                            self._save_checkpoint(checkpoint_data, lock=checkpoint_lock)
+                        except Exception as ckpt_err:
+                            # Don't fail the run if checkpoint write fails
+                            print(f"⚠️  Warning: Failed to save incremental checkpoint: {ckpt_err}")
                 finally:
                     root_logger.setLevel(original_level)
         
@@ -891,9 +935,12 @@ class BatchRunner:
             for key in total_reasoning_stats:
                 total_reasoning_stats[key] += batch_result.get("reasoning_stats", {}).get(key, 0)
         
-        # Save final checkpoint
+        # Save final checkpoint (best-effort; incremental writes already happened)
-        checkpoint_data["completed_prompts"] = all_completed_prompts
+        try:
-        self._save_checkpoint(checkpoint_data)
+            checkpoint_data["completed_prompts"] = all_completed_prompts
+            self._save_checkpoint(checkpoint_data, lock=checkpoint_lock)
+        except Exception as ckpt_err:
+            print(f"⚠️  Warning: Failed to save final checkpoint: {ckpt_err}")
         
         # Calculate success rates
         for tool_name in total_tool_stats: