From c90ea82e0d3143034401781e4156d4f87fb089db Mon Sep 17 00:00:00 2001
From: Abhyuday Sharda <117782573+ab6361@users.noreply.github.com>
Date: Tue, 3 Feb 2026 14:31:33 -0500
Subject: [PATCH] Add files via upload

---
 SCRIPTS/setup.sh | 266 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 266 insertions(+)
 create mode 100644 SCRIPTS/setup.sh

diff --git a/SCRIPTS/setup.sh b/SCRIPTS/setup.sh
new file mode 100644
index 00000000..00025787
--- /dev/null
+++ b/SCRIPTS/setup.sh
@@ -0,0 +1,266 @@
+#!/usr/bin/env bash
+# Preflight checks for externals_xem2_XEM batch submission.
+# For this to work, externals directory should be in /group/$USER/
+# Usage: bash SCRIPTS/preflight.sh [target_tag]
+set -u
+
+# sets repo_root to the absolute path of the parent directory of the script’s location
+repo_root="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+scripts_dir="$repo_root/SCRIPTS"
+
+# Key paths used by the workflow.
+run_extern="$repo_root/run_extern"
+externals_bin="$repo_root/externals_all"
+make_grid="$repo_root/make_grid.f"
+make_inputs="$scripts_dir/make_xem2_input_files.sh"
+make_scripts="$scripts_dir/make_xem2_scripts.sh"
+do_submit="$scripts_dir/do_farmsubmission.sh"
+template_part1="$repo_root/INP/xem2_inp_part1.template"
+hcswif_json="$repo_root/hcswif/json"
+farm_out="/farm_out/${USER}/externals_xem2_XEM_OUT"
+
+# Optional target tag (e.g., 12carbon22_hms) for target-specific checks.
+target="${1-}"
+
+# Buckets for errors (fail) and warnings (soft issues).
+fails=()
+warns=()
+
+# Record helpers to keep output consistent.
+# += appends a new element. "$1" is the first argument passed to the function.	Quotes preserve spaces (critical!)
+add_fail() { fails+=("$1"); }
+add_warn() { warns+=("$1"); }
+
+# Customize hardcoded user paths (replacing "gaskelld/GIT/").
+fix_user="${USER-}"
+if [[ -z "$fix_user" ]]; then
+  add_warn "USER not set; skipping hardcoded path fixups"
+else
+  fix_files=(
+    "$scripts_dir/make_xem2_scripts.sh"
+    "$scripts_dir/do_farmsubmission.sh"
+    "$scripts_dir/do_src_farmsubmission.sh"
+    "$repo_root/hcswif/hcswif.py"
+    "$repo_root/run_extern"
+  )
+  for fix_file in "${fix_files[@]}"; do
+    if [[ -f "$fix_file" ]]; then
+      python - <<'PY' "$fix_file" "$fix_user"
+import sys
+path = sys.argv[1]
+user = sys.argv[2]
+needle = "gaskelld/GIT/"
+repl = f"{user}/"
+with open(path, "r") as f:
+    data = f.read()
+if needle in data:
+    data = data.replace(needle, repl)
+    with open(path, "w") as f:
+        f.write(data)
+PY
+    fi
+  done
+fi
+
+# Simple existence check for critical files.
+check_file() {
+  local path="$1"
+  local label="$2"
+  if [[ ! -e "$path" ]]; then
+    add_fail "${label} missing: ${path}"
+  fi
+}
+
+# Executable bit check for runnable files.
+check_exec() {
+  local path="$1"
+  local label="$2"
+  if [[ -e "$path" && ! -x "$path" ]]; then
+    add_warn "${label} not executable: ${path}"
+  fi
+}
+
+# Directory existence + writability checks for output locations.
+check_dir_writable() {
+  local path="$1"
+  local label="$2"
+  if [[ ! -d "$path" ]]; then
+    # Try to create missing directories when possible.
+    if mkdir -p "$path" 2>/dev/null; then
+      add_warn "${label} created: ${path}"
+    else
+      add_warn "${label} missing: ${path}"
+      return
+    fi
+  fi
+  if [[ ! -w "$path" ]]; then
+    add_warn "${label} not writable: ${path}"
+  fi
+}
+
+# Basic path checks for expected files.
+check_file "$run_extern" "run_extern"
+check_file "$externals_bin" "externals_all"
+check_file "$make_grid" "make_grid.f"
+check_file "$make_inputs" "make_xem2_input_files.sh"
+check_file "$make_scripts" "make_xem2_scripts.sh"
+check_file "$do_submit" "do_farmsubmission.sh"
+check_file "$template_part1" "xem2_inp_part1.template"
+
+# Executable bit sanity.
+check_exec "$run_extern" "run_extern"
+check_exec "$externals_bin" "externals_all"
+
+# Ensure output locations exist and are writable.
+check_dir_writable "$repo_root/runout" "runout dir"
+check_dir_writable "$hcswif_json" "hcswif/json"
+check_dir_writable "$farm_out" "farm_out"
+check_dir_writable "$repo_root/RUNPLAN" "RUNPLAN dir"
+check_dir_writable "$repo_root/OUT" "out dir"
+
+# Extract angle settings and runplan filename from make_grid.f.
+grid_vals="$(python - <<'PY'
+import re
+vals = {"thetamin": None, "thetamax": None, "thetastep": None}
+runplan_line = None
+try:
+    with open("make_grid.f", "r") as f:
+        for line in f:
+            if line.lstrip().startswith("c"):
+                continue
+            if runplan_line is None and "RUNPLAN/" in line and "part1" in line:
+                runplan_line = line.strip()
+            m = re.search(r"\b(thetamin|thetamax|thetastep)\s*=\s*([0-9.+-]+)", line)
+            if m:
+                vals[m.group(1)] = m.group(2)
+except FileNotFoundError:
+    pass
+print("thetamin=" + (vals["thetamin"] or ""))
+print("thetamax=" + (vals["thetamax"] or ""))
+print("thetastep=" + (vals["thetastep"] or ""))
+print("runplan=" + (runplan_line or ""))
+PY
+)"
+
+# Unpack angle values for later consistency checks.
+thetamin="$(printf "%s\n" "$grid_vals" | awk -F= '/^thetamin=/{print $2}')"
+thetamax="$(printf "%s\n" "$grid_vals" | awk -F= '/^thetamax=/{print $2}')"
+thetastep="$(printf "%s\n" "$grid_vals" | awk -F= '/^thetastep=/{print $2}')"
+runplan_line="$(printf "%s\n" "$grid_vals" | awk -F= '/^runplan=/{print $2}')"
+
+# Compute how many angle settings you should have, based on the angle range and step size defined in make_grid.f
+expected_angles=""
+if [[ -n "$thetamin" && -n "$thetamax" && -n "$thetastep" ]]; then
+  expected_angles="$(python - <<PY
+import math
+tmin=float("$thetamin")
+tmax=float("$thetamax")
+tstep=float("$thetastep")
+n=int((tmax - tmin)/tstep) + 1
+print(n)
+PY
+)"
+fi
+
+# Parse make_xem2_input_files.sh or make_xem2_scripts.sh for min_angle and number of loop iterations.
+parse_csh_vals() {
+  local path="$1"
+  python - <<'PY' "$path"
+import re,sys
+min_angle = None
+count = None
+with open(sys.argv[1], "r") as f:
+    for line in f:
+        if line.strip().startswith("#"):
+            continue
+        m = re.search(r"set\s+min_angle\s*=\s*([0-9.+-]+)", line)
+        if m:
+            min_angle = m.group(1)
+        m = re.search(r"while\s*\\(\\$i\\s*<=\\s*([0-9]+)\\)", line)
+        if m:
+            count = m.group(1)
+            break
+print("min_angle=" + (min_angle or ""))
+print("count=" + (count or ""))
+PY
+}
+
+# Compare input file generator angles with make_grid.f.
+if [[ -e "$make_inputs" ]]; then
+  input_vals="$(parse_csh_vals "$make_inputs")"
+  input_min="$(printf "%s\n" "$input_vals" | awk -F= '/^min_angle=/{print $2}')"
+  input_cnt="$(printf "%s\n" "$input_vals" | awk -F= '/^count=/{print $2}')"
+  if [[ -n "$thetamin" && -n "$input_min" && "$thetamin" != "$input_min" ]]; then
+    add_warn "make_xem2_input_files.sh min_angle (${input_min}) != make_grid.f thetamin (${thetamin})"
+  fi
+  if [[ -n "$expected_angles" && -n "$input_cnt" && "$expected_angles" != "$input_cnt" ]]; then
+    add_warn "make_xem2_input_files.sh loop count (${input_cnt}) != expected angles (${expected_angles})"
+  fi
+fi
+
+# Compare make_xem2_scripts.sh generator angles with make_grid.f.
+if [[ -e "$make_scripts" ]]; then
+  script_vals="$(parse_csh_vals "$make_scripts")"
+  script_min="$(printf "%s\n" "$script_vals" | awk -F= '/^min_angle=/{print $2}')"
+  script_cnt="$(printf "%s\n" "$script_vals" | awk -F= '/^count=/{print $2}')"
+  if [[ -n "$thetamin" && -n "$script_min" && "$thetamin" != "$script_min" ]]; then
+    add_warn "make_xem2_scripts.sh min_angle (${script_min}) != make_grid.f thetamin (${thetamin})"
+  fi
+  if [[ -n "$expected_angles" && -n "$script_cnt" && "$expected_angles" != "$script_cnt" ]]; then
+    add_warn "make_xem2_scripts.sh loop count (${script_cnt}) != expected angles (${expected_angles})"
+  fi
+fi
+
+# Ensure submission time respects the 1-day production limit.
+if [[ -e "$do_submit" ]]; then
+  time_val="$(awk '/--time[[:space:]]+[0-9]+/ {for(i=1;i<=NF;i++) if($i=="--time") print $(i+1)}' "$do_submit" | head -n1)"
+  if [[ -n "$time_val" && "$time_val" -gt 86400 ]]; then
+    add_warn "do_farmsubmission.sh --time (${time_val}) exceeds 86400 seconds"
+  fi
+fi
+
+# Target-specific checks: ensure script count matches expected angle count/bin size.
+if [[ -n "$target" ]]; then
+  scripts_glob=( "$repo_root/hcswif/FARM_SCRIPTS"/*_"${target}"_part1*.sh )
+  if [[ ${#scripts_glob[@]} -eq 1 && ! -e "${scripts_glob[0]}" ]]; then
+    add_warn "no FARM_SCRIPTS for target ${target}"
+  else
+    script_count="${#scripts_glob[@]}"
+    if [[ -n "$expected_angles" && "$script_count" -ne "$expected_angles" ]]; then
+      add_warn "script count (${script_count}) != expected angles (${expected_angles}) for target ${target}"
+    fi
+    first_script="${scripts_glob[0]}"
+    if [[ -e "$first_script" ]]; then
+      run_path="$(awk 'NR==2{print $1}' "$first_script")"
+      if [[ -n "$run_path" && "$run_path" != "$repo_root/run_extern" ]]; then
+        add_warn "FARM_SCRIPTS run_extern path differs: ${run_path}"
+      fi
+    fi
+  fi
+fi
+
+# Final report.
+if [[ ${#fails[@]} -eq 0 && ${#warns[@]} -eq 0 ]]; then
+  echo "Preflight OK: no issues found."
+  exit 0
+fi
+
+if [[ ${#fails[@]} -gt 0 ]]; then
+  echo "Preflight errors:"
+  for f in "${fails[@]}"; do
+    echo "  - ${f}"
+  done
+fi
+
+if [[ ${#warns[@]} -gt 0 ]]; then
+  echo "Preflight warnings:"
+  for w in "${warns[@]}"; do
+    echo "  - ${w}"
+  done
+fi
+
+# Non-zero exit on errors.
+if [[ ${#fails[@]} -gt 0 ]]; then
+  exit 2
+fi
+exit 0
\ No newline at end of file