#!/bin/bash
#SBATCH --job-name=burstingBubble
#SBATCH -N 1
#SBATCH -n 128
#SBATCH -c 1
#SBATCH --mem=240G
#SBATCH --time=3-00:00:00
#SBATCH --gres=tmp:100G
#SBATCH -p multi
#SBATCH --mail-type=END,FAIL
#SBATCH [email protected]
#SBATCH --output=slurm-%j.out
#SBATCH --error=slurm-%j.err
# ============================================================
# Bursting Bubble - HPC Parameter Sweep Runner (Hamilton)
# ============================================================
# This script runs Stage 2 (MPI simulation) on Durham University's Hamilton HPC.
#
# PREREQUISITE: Restart files must already exist for each case.
# Run Stage 1 locally before submitting:
# ./runParameterSweep.sh --stage1-only sweep.params
#
# BEFORE RUNNING:
# 1. Run Stage 1 locally to generate restart files for all cases
# 2. Clone repo to /nobackup/\$USER/ (NOT home directory)
# 3. Install Basilisk locally (creates basilisk/ and .project_config):
# curl -sL https://raw.githubusercontent.com/comphy-lab/basilisk-C/main/reset_install_basilisk-ref-locked.sh | bash -s -- --ref=v2026-01-13
# 4. Edit sweep.params to set parameter ranges and case numbers
# 5. Update --mail-user above with your Durham email
# 6. Submit with: sbatch runSweepHamilton.sbatch
#
# SBATCH Parameters (Hamilton-specific):
# -n 128: Number of MPI tasks (whole node = 128 cores)
# --mem=240G: Memory per node (max 250G on standard nodes)
# --time=3-00:00:00: Max wall time (3 days for multi partition)
# --gres=tmp:100G: Temporary disk space (\$TMPDIR)
# -p multi: Partition for whole-node jobs
# ============================================================
set -e # Exit on error (but we'll handle case failures gracefully)
set -o pipefail
# ============================================================
# Configuration
# ============================================================
# Use SLURM_SUBMIT_DIR (directory where sbatch was called) as the project root
SCRIPT_DIR="\${SLURM_SUBMIT_DIR}"
SWEEP_FILE="\${SCRIPT_DIR}/sweep.params"
# Source file to compile inside each case directory
SOURCE_FILE_NAME="burstingBubble.c"
EXECUTABLE_NAME="\${SOURCE_FILE_NAME%.c}"
# Number of MPI tasks for Stage 2
MPI_TASKS=\${SLURM_NTASKS:-128}
# ============================================================
# Validate Working Directory
# ============================================================
if [[ ! "\$SCRIPT_DIR" =~ ^/nobackup/ ]]; then
echo "WARNING: Running from \$SCRIPT_DIR"
echo " Consider using /nobackup/\$USER/ for better performance"
echo " Home directory has only 10GB quota and is slower"
echo ""
fi
# ============================================================
# Print Job Information
# ============================================================
echo "============================================="
echo "Bursting Bubble - HPC Parameter Sweep"
echo "============================================="
echo "Job started at: \$(date)"
echo "Running on node: \$(hostname)"
echo "Working directory: \$(pwd)"
echo "Job ID: \${SLURM_JOB_ID}"
echo "Number of MPI tasks: \${MPI_TASKS}"
echo "Partition: \${SLURM_JOB_PARTITION}"
echo "Memory allocated: \${SLURM_MEM_PER_NODE}MB"
echo ""
echo "Mode: Stage 2 only (MPI simulation)"
echo " Restart files must exist for each case"
echo ""
# ============================================================
# Load Required Modules
# ============================================================
echo "Loading modules..."
module purge
module load gcc
module load openmpi
echo "Modules loaded successfully"
echo ""
# ============================================================
# Setup Basilisk Environment
# ============================================================
echo "Setting up Basilisk environment..."
echo "Ensuring Basilisk is installed locally (ref v2026-01-13)..."
cd "\$SCRIPT_DIR"
if ! command -v curl >/dev/null 2>&1; then
echo "ERROR: curl not found (required to install Basilisk)" >&2
exit 1
fi
curl -sL https://raw.githubusercontent.com/comphy-lab/basilisk-C/main/reset_install_basilisk-ref-locked.sh | bash -s -- --ref=v2026-01-13
if [ -f "\${SCRIPT_DIR}/.project_config" ]; then
source "\${SCRIPT_DIR}/.project_config"
echo "Basilisk environment loaded from .project_config"
echo "BASILISK: \$BASILISK"
else
echo "ERROR: .project_config not found after Basilisk install" >&2
echo " Basilisk install likely failed; see slurm output for details" >&2
exit 1
fi
echo ""
# ============================================================
# Validate Environment
# ============================================================
# Source parameter parsing library
if [ -f "\${SCRIPT_DIR}/src-local/parse_params.sh" ]; then
source "\${SCRIPT_DIR}/src-local/parse_params.sh"
else
echo "ERROR: src-local/parse_params.sh not found" >&2
exit 1
fi
# Check sweep file exists
if [ ! -f "\$SWEEP_FILE" ]; then
echo "ERROR: Sweep file not found: \$SWEEP_FILE" >&2
exit 1
fi
echo "Sweep file: \$SWEEP_FILE"
echo ""
# ============================================================
# Parse Sweep Configuration
# ============================================================
echo "Parsing sweep configuration..."
# Source the sweep file to get variables
source "\$SWEEP_FILE"
# Validate required variables
if [ -z "\$BASE_CONFIG" ]; then
echo "ERROR: BASE_CONFIG not defined in sweep file" >&2
exit 1
fi
if [ -z "\$CASE_START" ] || [ -z "\$CASE_END" ]; then
echo "ERROR: CASE_START and CASE_END must be defined in sweep file" >&2
exit 1
fi
# Validate CaseNo range
if [ "\$CASE_START" -lt 1000 ] || [ "\$CASE_START" -gt 9999 ]; then
echo "ERROR: CASE_START must be 4-digit (1000-9999), got: \$CASE_START" >&2
exit 1
fi
if [ "\$CASE_END" -lt "\$CASE_START" ] || [ "\$CASE_END" -gt 9999 ]; then
echo "ERROR: CASE_END must be >= CASE_START and <= 9999, got: \$CASE_END" >&2
exit 1
fi
if [ ! -f "\$BASE_CONFIG" ]; then
echo "ERROR: Base configuration file not found: \$BASE_CONFIG" >&2
exit 1
fi
echo "Base configuration: \$BASE_CONFIG"
echo "Case number range: \$CASE_START to \$CASE_END"
echo ""
# ============================================================
# Extract Sweep Variables
# ============================================================
SWEEP_VARS=()
SWEEP_VALUES=()
# Read sweep file and extract SWEEP_* variables
while IFS='=' read -r key value; do
# Skip comments and empty lines
[[ "\$key" =~ ^[[:space:]]*# ]] && continue
[[ -z "\$key" ]] && continue
# Match SWEEP_* variables
if [[ "\$key" =~ ^[[:space:]]*SWEEP_([^=]+) ]]; then
var_name="\${BASH_REMATCH[1]}"
# Remove inline comments and whitespace
value=\$(echo "\$value" | sed 's/#.*//' | xargs)
SWEEP_VARS+=("\$var_name")
SWEEP_VALUES+=("\$value")
fi
done < "\$SWEEP_FILE"
if [ \${#SWEEP_VARS[@]} -eq 0 ]; then
echo "ERROR: No SWEEP_* variables found in \$SWEEP_FILE" >&2
exit 1
fi
echo "Sweep variables:"
for i in "\${!SWEEP_VARS[@]}"; do
echo " \${SWEEP_VARS[\$i]} = \${SWEEP_VALUES[\$i]}"
done
echo ""
# ============================================================
# Generate Parameter Combinations
# ============================================================
echo "Generating parameter combinations..."
# Create temporary directory for generated parameter files
# Use work directory, not /tmp (node-local on Hamilton)
TEMP_DIR="\${SCRIPT_DIR}/.sweep_tmp_\$\$"
mkdir -p "\$TEMP_DIR" || {
echo "ERROR: Failed to create temp directory: \$TEMP_DIR" >&2
exit 1
}
trap "rm -rf \$TEMP_DIR" EXIT
CASE_NUM=\$CASE_START
COMBINATION_COUNT=0
CASE_FILES=()
# Recursive function to generate all combinations
generate_combinations() {
local depth=\$1
shift
local current_values=("\$@")
if [ \$depth -eq \${#SWEEP_VARS[@]} ]; then
# Base case: all variables assigned, create parameter file
local case_file="\${TEMP_DIR}/case_\$(printf "%04d" \$CASE_NUM).params"
# Copy base config
cp "\$BASE_CONFIG" "\$case_file"
# Override CaseNo
if grep -q "^CaseNo=" "\$case_file"; then
sed -i'.bak' "s|^CaseNo=.*|CaseNo=\${CASE_NUM}|" "\$case_file"
else
echo "CaseNo=\${CASE_NUM}" >> "\$case_file"
fi
rm -f "\${case_file}.bak"
# Override with sweep values
for i in "\${!SWEEP_VARS[@]}"; do
local var="\${SWEEP_VARS[\$i]}"
local val="\${current_values[\$i]}"
if grep -q "^\${var}=" "\$case_file"; then
sed -i'.bak' "s|^\${var}=.*|\${var}=\${val}|" "\$case_file"
else
echo "\${var}=\${val}" >> "\$case_file"
fi
rm -f "\${case_file}.bak"
done
CASE_FILES+=("\$case_file")
((COMBINATION_COUNT++)) || true
# Print summary
echo "Case \$CASE_NUM:"
for i in "\${!SWEEP_VARS[@]}"; do
echo " \${SWEEP_VARS[\$i]} = \${current_values[\$i]}"
done
echo ""
((CASE_NUM++)) || true
return
fi
# Recursive case: iterate through values for current variable
local values="\${SWEEP_VALUES[\$depth]}"
IFS=',' read -ra value_array <<< "\$values"
for val in "\${value_array[@]}"; do
val=\$(echo "\$val" | xargs) # Trim whitespace
generate_combinations \$((depth + 1)) "\${current_values[@]}" "\$val"
done
}
# Start recursion
generate_combinations 0
echo "Generated \$COMBINATION_COUNT parameter combinations"
# Check if number of combinations matches the range
EXPECTED_COUNT=\$((CASE_END - CASE_START + 1))
if [ \$COMBINATION_COUNT -ne \$EXPECTED_COUNT ]; then
echo "WARNING: Generated \$COMBINATION_COUNT combinations, but CASE_END suggests \$EXPECTED_COUNT" >&2
echo " Consider adjusting CASE_END in sweep file" >&2
fi
if [ \$COMBINATION_COUNT -gt \$EXPECTED_COUNT ]; then
echo "ERROR: Too many combinations (\$COMBINATION_COUNT) for range \$CASE_START-\$CASE_END" >&2
exit 1
fi
echo ""
# ============================================================
# Run Simulations (Stage 2 Only - MPI)
# ============================================================
echo "============================================="
echo "Running \$COMBINATION_COUNT Simulations"
echo "============================================="
echo "Stage 2 only: MPI simulation (\${MPI_TASKS} tasks)"
echo "Requires existing restart files in each case directory"
echo ""
# Counters for tracking
SUCCESSFUL_CASES=0
FAILED_CASES=0
SKIPPED_CASES=0
for param_file in "\${CASE_FILES[@]}"; do
# Parse parameter file to get values
parse_param_file "\$param_file"
CASE_NO=\$(get_param "CaseNo")
MAXlevel=\$(get_param "MAXlevel" "10")
Oh=\$(get_param "Oh" "1e-2")
Bond=\$(get_param "Bond" "1e-3")
tmax=\$(get_param "tmax" "1.0")
zWall=\$(get_param "zWall" "0.025")
if [ -z "\$CASE_NO" ]; then
echo "ERROR: CaseNo not found in \$param_file" >&2
((FAILED_CASES++)) || true
continue
fi
CASE_DIR="\${SCRIPT_DIR}/simulationCases/\${CASE_NO}"
echo "========================================="
echo "Case \$CASE_NO (\$(date))"
echo "========================================="
echo "Parameters: Oh=\$Oh, Bond=\$Bond"
echo " MAXlevel=\$MAXlevel, tmax=\$tmax, zWall=\$zWall"
# Check if case directory exists
if [ ! -d "\$CASE_DIR" ]; then
echo "ERROR: Case directory not found: \$CASE_DIR" >&2
echo " Run Stage 1 locally first" >&2
((SKIPPED_CASES++)) || true
continue
fi
# Change to case directory
cd "\$CASE_DIR"
# Check for restart file (CRITICAL)
if [ ! -f "restart" ]; then
echo "ERROR: restart file not found for case \$CASE_NO" >&2
echo " Run Stage 1 locally first:" >&2
echo " ./runSimulation.sh --stage1 <params_file>" >&2
((SKIPPED_CASES++)) || true
cd "\$SCRIPT_DIR"
continue
fi
echo "Found restart file"
# Copy source file to case directory if needed
SRC_FILE_ORIG="\${SCRIPT_DIR}/simulationCases/\${SOURCE_FILE_NAME}"
SRC_FILE_LOCAL="\$CASE_DIR/\$SOURCE_FILE_NAME"
if [ ! -f "\$SRC_FILE_ORIG" ]; then
echo "ERROR: Source file \$SRC_FILE_ORIG not found" >&2
((FAILED_CASES++)) || true
cd "\$SCRIPT_DIR"
continue
fi
cp "\$SRC_FILE_ORIG" "\$SRC_FILE_LOCAL"
# Create symlink to DataFiles if needed
if [ ! -e "DataFiles" ]; then
ln -s ../DataFiles DataFiles
fi
# ============================================================
# Stage 2: Full Simulation with MPI
# ============================================================
echo ""
echo "Stage 2: Full simulation (MPI)..."
# Compile with MPI
if CC99='mpicc -std=c99 -D_GNU_SOURCE=1' qcc -I../../src-local \
-Wall -O2 -D_MPI=1 -disable-dimensions \
"\$SOURCE_FILE_NAME" -o "\$EXECUTABLE_NAME" -lm 2>&1; then
echo "MPI compilation successful"
else
echo "ERROR: MPI compilation failed for case \$CASE_NO" >&2
((FAILED_CASES++)) || true
cd "\$SCRIPT_DIR"
continue
fi
# Run simulation with mpirun (Hamilton uses mpirun, not srun)
echo "Running full simulation with \${MPI_TASKS} MPI tasks..."
echo "Command: mpirun -np \${MPI_TASKS} ./\$EXECUTABLE_NAME \$MAXlevel \$Oh \$Bond \$tmax \$zWall"
echo ""
if mpirun -np \${MPI_TASKS} ./\$EXECUTABLE_NAME \$MAXlevel \$Oh \$Bond \$tmax \$zWall; then
echo ""
echo "Case \$CASE_NO completed successfully"
((SUCCESSFUL_CASES++)) || true
else
EXIT_CODE=\$?
echo ""
echo "ERROR: Case \$CASE_NO failed with exit code \$EXIT_CODE" >&2
((FAILED_CASES++)) || true
fi
# Return to root directory
cd "\$SCRIPT_DIR"
echo ""
done
# ============================================================
# Final Summary
# ============================================================
echo "============================================="
echo "Parameter Sweep Complete"
echo "============================================="
echo "Job completed at: \$(date)"
echo "Total cases: \$COMBINATION_COUNT"
echo "Successful: \$SUCCESSFUL_CASES"
echo "Failed: \$FAILED_CASES"
echo "Skipped (no restart file): \$SKIPPED_CASES"
echo "Output location: simulationCases/"
echo "============================================="
echo ""
# Exit with error if any cases failed or were skipped
if [ \$FAILED_CASES -gt 0 ] || [ \$SKIPPED_CASES -gt 0 ]; then
echo "WARNING: \$FAILED_CASES case(s) failed, \$SKIPPED_CASES case(s) skipped." >&2
echo " Check logs for details." >&2
exit 1
fi
exit 0
