Add LightGBM OpenMP conflict fix script

fix_lightgbm_openmp.sh

@@ -0,0 +1,140 @@
+#!/usr/bin/env bash
+#
+# fix_lightgbm_openmp.sh
+# -----------------------------------------------------------------------------
+# Make the conda LightGBM dylib resolve its OpenMP runtime (libomp) from the
+# CURRENT conda environment instead of an external copy (e.g. Homebrew/MacPorts).
+#
+# Why: some `defaults`-channel LightGBM builds leak an absolute rpath such as
+# `/opt/homebrew/opt/libomp/lib` that ranks ABOVE the env's own libomp. If that
+# external libomp exists, LightGBM loads it while numpy/scikit-learn load the
+# env's libomp -> TWO OpenMP runtimes in one process. With OMP_WAIT_POLICY=active
+# both busy-wait and oversubscribe the cores, making many-tiny-fit workloads
+# (e.g. retrain-mode Shapley benchmarks) up to ~20x slower.
+#
+# This script removes any absolute LC_RPATH that points OUTSIDE the active conda
+# env AND actually contains a libomp*.dylib, then re-signs the binary ad-hoc.
+# It is idempotent (a clean dylib is left untouched) and macOS-only.
+#
+# Usage:
+#   conda activate <env>
+#   bash fix_lightgbm_openmp.sh           # apply the fix
+#   bash fix_lightgbm_openmp.sh --revert  # restore from the .bak backup
+# -----------------------------------------------------------------------------
+set -euo pipefail
+
+if [[ "$(uname -s)" != "Darwin" ]]; then
+    echo "This script only applies to macOS (dyld/rpath specific). Nothing to do."
+    exit 0
+fi
+
+for tool in otool install_name_tool codesign python; do
+    command -v "$tool" >/dev/null 2>&1 || { echo "ERROR: '$tool' not found in PATH." >&2; exit 1; }
+done
+
+: "${CONDA_PREFIX:?Activate the target conda environment first (CONDA_PREFIX is unset).}"
+
+# --- locate the compiled LightGBM dylib (handles both packaging layouts) ------
+LIB="$(python - <<'PY'
+import glob, os
+try:
+    import lightgbm
+except ImportError:
+    print(""); raise SystemExit
+roots = [os.path.join(os.path.dirname(lightgbm.__file__), "lib"),
+         os.path.join(os.environ.get("CONDA_PREFIX", ""), "lib")]
+hits = []
+for r in roots:
+    hits += glob.glob(os.path.join(r, "lib_lightgbm*.dylib"))
+    hits += glob.glob(os.path.join(r, "liblightgbm*.dylib"))
+print(hits[0] if hits else "")
+PY
+)"
+
+if [[ -z "$LIB" || ! -f "$LIB" ]]; then
+    echo "ERROR: could not locate the LightGBM dylib (is lightgbm importable in this env?)." >&2
+    exit 1
+fi
+echo "LightGBM dylib: $LIB"
+
+# --- revert mode --------------------------------------------------------------
+if [[ "${1:-}" == "--revert" ]]; then
+    if [[ -f "$LIB.bak" ]]; then
+        cp -p "$LIB.bak" "$LIB"
+        codesign --force --sign - "$LIB" >/dev/null 2>&1 || true
+        echo "Reverted from $LIB.bak and re-signed."
+    else
+        echo "No backup found at $LIB.bak; nothing to revert."
+    fi
+    exit 0
+fi
+
+# --- collect LC_RPATH entries -------------------------------------------------
+# (avoid `mapfile`: it is a bash 4+ builtin and macOS ships bash 3.2)
+RPATHS=()
+while IFS= read -r _rp; do
+    [ -n "$_rp" ] && RPATHS+=("$_rp")
+done < <(otool -l "$LIB" | awk '/^ *cmd LC_RPATH/{f=1;next} f&&/^ *path /{print $2; f=0}')
+
+echo "Current rpaths:"
+for p in "${RPATHS[@]}"; do echo "    $p"; done
+
+# --- decide which rpaths are offending ----------------------------------------
+# Offending = absolute path, NOT under $CONDA_PREFIX, and contains a libomp dylib.
+OFFENDING=()
+for p in "${RPATHS[@]}"; do
+    [[ "$p" == /* ]] || continue                 # skip @loader_path/@rpath/etc.
+    [[ "$p" == "$CONDA_PREFIX"/* ]] && continue   # keep env-internal paths
+    if compgen -G "$p/libomp*.dylib" >/dev/null 2>&1; then
+        OFFENDING+=("$p")
+    fi
+done
+
+if [[ ${#OFFENDING[@]} -eq 0 ]]; then
+    echo "No external OpenMP rpath found. The dylib is already clean -- nothing to do."
+    exit 0
+fi
+
+echo "Offending external OpenMP rpaths to remove:"
+for p in "${OFFENDING[@]}"; do echo "    $p"; done
+
+# --- backup, patch, re-sign ---------------------------------------------------
+if [[ ! -f "$LIB.bak" ]]; then
+    cp -p "$LIB" "$LIB.bak"
+    echo "Backup written: $LIB.bak"
+else
+    echo "Backup already exists: $LIB.bak (keeping it)"
+fi
+
+for p in "${OFFENDING[@]}"; do
+    install_name_tool -delete_rpath "$p" "$LIB"
+    echo "Deleted rpath: $p"
+done
+
+codesign --force --sign - "$LIB"
+echo "Re-signed (ad-hoc): $LIB"
+
+# --- verify -------------------------------------------------------------------
+echo "Rpaths after:"
+otool -l "$LIB" | awk '/^ *cmd LC_RPATH/{f=1;next} f&&/^ *path /{print "    "$2; f=0}'
+
+echo "Verifying loaded OpenMP runtimes (expect exactly one, inside the env)..."
+python - <<'PY'
+import ctypes, os, sys
+libc = ctypes.CDLL(None)
+libc._dyld_image_count.restype = ctypes.c_uint32
+libc._dyld_get_image_name.restype = ctypes.c_char_p
+libc._dyld_get_image_name.argtypes = [ctypes.c_uint32]
+import numpy as np, lightgbm as lgb
+lgb.LGBMRegressor(verbosity=-1).fit(np.random.rand(80, 4), np.random.rand(80))
+names = [libc._dyld_get_image_name(i).decode() for i in range(libc._dyld_image_count())]
+omp = sorted({n for n in names if any(k in n.lower() for k in ("libomp.dylib", "libgomp", "libiomp"))})
+print("  loaded OpenMP runtimes:")
+for n in omp:
+    print("   ", n)
+prefix = os.environ.get("CONDA_PREFIX", "")
+ok = len(omp) == 1 and omp[0].startswith(prefix)
+print("  RESULT:", "OK -- single env-internal runtime" if ok else "STILL MULTIPLE / external -- check above")
+sys.exit(0 if ok else 2)
+PY
+echo "Done."