run_all: auto-resume crashed jobs; spheroid colour scale 50 Pa

experiments/evaluate.py

@@ -8,7 +8,7 @@ Evaluate released checkpoints, baselines and trained ablation runs on every spli
 
 Metrics are computed PER IMAGE (mean and SD are then taken across images):
     mse, ms_ssim, pixel_r (Pearson), rme (per-image WFM-RME), mean_gt / mean_pred (heatmap units),
-    mean_gt_Pa / mean_pred_Pa (x colour-scale limit of the set, 500 Pa single cells, 200 Pa spheroids),
+    mean_gt_Pa / mean_pred_Pa (x colour-scale limit of the set, 500 Pa single cells, 50 Pa spheroids),
     gt_frac_saturated (pixels >= 0.98 of the colour limit), inference time.
 Outputs (experiments/results/eval/ by default; existing rows of other models are kept):
     per_image.csv, summary.csv
@@ -116,7 +116,7 @@ def evaluate_one(name, spec, manifest, dataset_root, device, mw, norm, substrate
             for i in range(y.size(0)):
                 r = rows_meta[k]; k += 1
                 t, q = y[i:i + 1], p[i:i + 1]
-                yt = float(r.get("ythreshold_Pa") or (200 if "spheroid" in manifest else 500))
+                yt = float(r.get("ythreshold_Pa") or (50 if "spheroid" in manifest else 500))
                 out.append({"model": name, "manifest": manifest, "substrate_mode": substrate_mode if use_settings else "n/a",
                             "sample_dir": r["sample_dir"], "set": r.get("set", ""), "condition": r.get("condition", ""),
                             "mse": mw.compute_mse(t, q), "ms_ssim": mw.compute_ms_ssim(t, q),

experiments/layout.py

@@ -62,8 +62,8 @@ LEGACY_SETS = {
     "Y27632_SET_I": ("single_cell/Drugs/Fibros_Y27632_SET_I_for_Kaveh", "external", "fibro_Y27632_setI", dict(FIBRO_6KPA, condition="Y-27632")),
     "U2OS/test": ("single_cell/u2os/test", "external", "u2os_6kPa", dict(cell_type="U2OS", coating="collagen I", young_Pa=6000, tfm_pixelsize=6.1538, ythreshold_Pa=500, condition="U2OS")),
     "Drugs/all": ("single_cell/Drugs/all", "union", None, {}),
-    "spheroid/train": ("spheroid/train", "published", "spheroid_train", dict(cell_type="LS174T spheroid", coating="collagen I", ythreshold_Pa=200, condition="spheroid")),
-    "spheroid/test": ("spheroid/test", "published", "spheroid_val", dict(cell_type="LS174T spheroid", coating="collagen I", ythreshold_Pa=200, condition="spheroid")),
+    "spheroid/train": ("spheroid/train", "published", "spheroid_train", dict(cell_type="LS174T spheroid", coating="collagen I", ythreshold_Pa=50, condition="spheroid")),
+    "spheroid/test": ("spheroid/test", "published", "spheroid_val", dict(cell_type="LS174T spheroid", coating="collagen I", ythreshold_Pa=50, condition="spheroid")),
 }
 
 # Published repository dataset (S2F/dataset), relative paths

experiments/run_all.py

@@ -41,9 +41,12 @@ def finished(variant, seed):
     return len(json.load(open(h))) >= get_config(variant)["epochs"]
 
 
-def gpu_queue(queue, gpus, num_workers, extra=()):
-    """Run training jobs in parallel, one per GPU (each job sees only its GPU as cuda:0)."""
-    running, failed = {}, []
+def gpu_queue(queue, gpus, num_workers, extra=(), max_retries=2):
+    """Run training jobs in parallel, one per GPU (each job sees only its GPU as cuda:0).
+    A job that crashes (e.g. Windows access violation 3221225477) is re-queued and resumes from its last
+    epoch checkpoint, up to `max_retries` times. Python is started with -X faulthandler so that a native
+    crash writes the stack trace into train.log."""
+    running, failed, tries = {}, [], {}
     queue = list(queue)
     while queue or running:
         for gpu in gpus:
@@ -53,18 +56,25 @@ def gpu_queue(queue, gpus, num_workers, extra=()):
                 os.makedirs(run_dir, exist_ok=True)
                 log = open(os.path.join(run_dir, "train.log"), "a")
                 env = dict(os.environ, CUDA_DEVICE_ORDER="PCI_BUS_ID", CUDA_VISIBLE_DEVICES=gpu, PYTHONUNBUFFERED="1")  # same numbering as nvidia-smi
-                cmd = [sys.executable, "-m", "experiments.train", "--variant", v, "--seed", seed, "--resume",
-                       "--num-workers", num_workers] + list(extra)
+                cmd = [sys.executable, "-X", "faulthandler", "-m", "experiments.train", "--variant", v, "--seed", seed,
+                       "--resume", "--num-workers", num_workers] + list(extra)
                 running[gpu] = (subprocess.Popen(cmd, cwd=S2F_ROOT, env=env, stdout=log, stderr=subprocess.STDOUT), v, seed, log)
                 print(f"[{time.strftime('%H:%M')}] GPU {gpu}: started {v} seed {seed}  (log {run_dir}/train.log)", flush=True)
         time.sleep(10 if extra else 30)
         for gpu, (proc, v, seed, log) in list(running.items()):
             if proc.poll() is not None:
                 log.close(); del running[gpu]
-                status = "finished" if proc.returncode == 0 else f"FAILED (exit {proc.returncode}, see train.log)"
-                if proc.returncode:
+                if proc.returncode == 0:
+                    print(f"[{time.strftime('%H:%M')}] GPU {gpu}: {v} seed {seed} finished", flush=True)
+                    continue
+                tries[(v, seed)] = tries.get((v, seed), 0) + 1
+                if tries[(v, seed)] <= max_retries:
+                    queue.insert(0, (v, seed))
+                    print(f"[{time.strftime('%H:%M')}] GPU {gpu}: {v} seed {seed} crashed (exit {proc.returncode}); "
+                          f"resuming from last checkpoint (retry {tries[(v, seed)]}/{max_retries})", flush=True)
+                else:
                     failed.append((v, seed))
-                print(f"[{time.strftime('%H:%M')}] GPU {gpu}: {v} seed {seed} {status}", flush=True)
+                    print(f"[{time.strftime('%H:%M')}] GPU {gpu}: {v} seed {seed} FAILED (exit {proc.returncode}, see train.log)", flush=True)
     if failed:
         print(f"failed jobs: {failed}")
 

experiments/splits/spheroid_train.csv

@@ -1,130 +1,130 @@
-sample_dir,split,set,condition,cell_type,coating,young_Pa,tfm_pixelsize,ythreshold_Pa,legacy_folder,legacy_substrate_code,substrate_legacy,substrate_nominal,bf_md5
-spheroid/train/01,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,01,01,,,c699004cc17c8ac555042e4c0d9bf192
-spheroid/train/02,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,02,02,,,8ee92b7d32698b1ee627fdd393460757
-spheroid/train/03,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,03,03,,,5df176b3398b1884f9095362de187401
-spheroid/train/04,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,04,04,,,9f376bc46814b997bc735a76fe702305
-spheroid/train/06,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,06,06,,,059ea10495a9f1bfe7263004340715ba
-spheroid/train/07,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,07,07,,,9fbe6fdb7d3c85ef620c8b585a08c329
-spheroid/train/08,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,08,08,,,39ffe78fd1385d2a40aade3262bf5a2f
-spheroid/train/09,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,09,09,,,b47dc557d1ccf18e370b55d90bf06168
-spheroid/train/10,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,10,10,,,ffb90f1b0802f2f78ec932ee26293c52
-spheroid/train/11,train,spheroid/train,spheroid,LS174T spheroid,collagen I,,,200,11,11,,,aed7afe58ed837013a6a5c9ec1117752
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