Fix pickup_to_init big-endian I/O and NaN/Inf handling

- Read pickup as big-endian (>f8) matching MITgcm's useSingleCPUIO output
- Write init files as big-endian (>f4) matching readBinaryPrec=32
- Replace NaN/Inf with zero after float64→float32 cast to prevent
  INI_THETA crash from overflow at land points
- Add --start=N flag to repeat_year_chain.sh for resuming from a given run

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: fluidnumericsJoe

simulations/glorysv12-curvilinear/workflows/repeat_year_chain.sh

@@ -20,13 +20,16 @@ SCRIPT_DIR=$(dirname "$(readlink -f "$0")")
 SIMULATION_DIR=$(dirname "$SCRIPT_DIR")
 
 N_RUNS=50
+START_RUN=1
 EXPERIMENT="repeat-year-50"
 DRY_RUN=false
 
-if [[ "${1:-}" == "--dry-run" ]]; then
-    DRY_RUN=true
-    echo "[DRY RUN] Will print sbatch commands without submitting."
-fi
+for arg in "$@"; do
+    case "$arg" in
+        --dry-run) DRY_RUN=true; echo "[DRY RUN] Will print sbatch commands without submitting." ;;
+        --start=*) START_RUN="${arg#--start=}" ;;
+    esac
+done
 
 EXPERIMENT_DIR="${SIMULATION_DIR}/${EXPERIMENT}"
 mkdir -p "${EXPERIMENT_DIR}"
@@ -38,7 +41,7 @@ echo "======================================="
 
 PREV_JOB_ID=""
 
-for i in $(seq 1 $N_RUNS); do
+for i in $(seq $START_RUN $N_RUNS); do
     RUN_NUM=$(printf "%03d" $i)
     PREV_RUN_NUM=""
     if [[ $i -gt 1 ]]; then

spectre_utils/pickup_to_init.py

@@ -35,7 +35,7 @@ def parse_pickup_meta(meta_path: Path) -> dict:
 
     # Extract precision
     prec_match = re.search(r"dataprec\s*=\s*\[\s*'(\w+)'\s*\]", text)
-    dtype = np.float64 if prec_match and "64" in prec_match.group(1) else np.float32
+    dtype = np.dtype(">f8") if prec_match and "64" in prec_match.group(1) else np.dtype(">f4")
 
     # Extract number of records
     nrec_match = re.search(r"nrecords\s*=\s*\[\s*(\d+)\s*\]", text)
@@ -123,7 +123,9 @@ def pickup_to_init(pickup_prefix: str, output_dir: str, nx: int, ny: int, nr: in
             init_path = out / init_name
             if init_path.is_symlink() or init_path.exists():
                 init_path.unlink()
-            data.astype(np.float32).tofile(init_path)
+            data32 = data.astype(">f4")
+            data32[~np.isfinite(data32)] = 0.0
+            data32.tofile(init_path)
             size_mb = init_path.stat().st_size / 1e6
             print(f"  Wrote {init_path} ({size_mb:.1f} MB)")