#!/bin/bash
#SBATCH --job-name=bubbleCoalescence
#SBATCH --nodes=1
#SBATCH --ntasks=48
#SBATCH --cpus-per-task=1
#SBATCH --time=100:00:00
#SBATCH --partition=genoa
#SBATCH --mail-type=ALL
#SBATCH [email protected]
#SBATCH --output=slurm-%j.out
#SBATCH --error=slurm-%j.err
# ============================================================
# Bubble Coalescence - HPC Parameter Sweep Runner (Snellius)
# ============================================================
# This script runs Stage 2 (MPI simulation) on Snellius 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. Edit sweep.params to set parameter ranges and case numbers
# 3. Adjust SBATCH parameters above (especially --ntasks, --time)
# 4. Submit with: sbatch runSweepSnellius.sbatch
#
# SBATCH Parameters to Customize:
# --ntasks: Number of MPI tasks per case (currently 48)
# --time: Wall time for entire sweep (currently 100 hours)
# --partition: Compute partition (currently genoa)
# --mail-user: Email for job notifications
# ============================================================
set -e # Exit on error (but we'll handle case failures gracefully)
# ============================================================
# 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"
# ============================================================
# Print Job Information
# ============================================================
echo "============================================="
echo "Bubble Coalescence - 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: \${SLURM_NTASKS}"
echo "Partition: \${SLURM_JOB_PARTITION}"
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 2024
module load OpenMPI/5.0.3-GCC-13.3.0
echo "Modules loaded successfully"
echo ""
# ============================================================
# Setup Basilisk Environment
# ============================================================
echo "Setting up Basilisk environment..."
# Source version configuration
if [ -f "\${SCRIPT_DIR}/src-local/basilisk_version.sh" ]; then
source "\${SCRIPT_DIR}/src-local/basilisk_version.sh"
else
echo "ERROR: src-local/basilisk_version.sh not found" >&2
exit 1
fi
echo "Installing Basilisk (ref: \${BASILISK_REF})..."
install_basilisk --hard
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" >&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
# HPC note: Don't use /tmp - use local work directory instead
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[@]+"\${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 (\${SLURM_NTASKS} 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")
OhOut=\$(get_param "OhOut" "1e-2")
RhoIn=\$(get_param "RhoIn" "1e-3")
Rr=\$(get_param "Rr" "1.0")
MAXlevel=\$(get_param "MAXlevel" "10")
tmax=\$(get_param "tmax" "40.0")
zWall=\$(get_param "zWall" "0.01")
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: OhOut=\$OhOut, RhoIn=\$RhoIn, Rr=\$Rr"
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"
# Use existing case.params if present (allows manual parameter edits)
if [ ! -f "\$CASE_DIR/case.params" ]; then
cp "\$param_file" "\$CASE_DIR/case.params"
else
echo "Using existing case.params (manual edits preserved)"
fi
# Re-parse from case.params (source of truth)
parse_param_file "\$CASE_DIR/case.params"
OhOut=\$(get_param "OhOut" "1e-2")
RhoIn=\$(get_param "RhoIn" "1e-3")
Rr=\$(get_param "Rr" "1.0")
MAXlevel=\$(get_param "MAXlevel" "10")
tmax=\$(get_param "tmax" "40.0")
zWall=\$(get_param "zWall" "0.01")
# Copy source file to case directory if needed
SRC_FILE_ORIG="\${SCRIPT_DIR}/simulationCases/coalescenceBubble.c"
SRC_FILE_LOCAL="\$CASE_DIR/coalescenceBubble.c"
if [ ! -f "\$SRC_FILE_ORIG" ]; then
echo "ERROR: Source file \$SRC_FILE_ORIG not found" >&2
((FAILED_CASES++)) || true
cd "\$SCRIPT_DIR"
continue
fi
# Use existing source file if present (allows local code edits for reruns)
if [ ! -f "\$SRC_FILE_LOCAL" ]; then
cp "\$SRC_FILE_ORIG" "\$SRC_FILE_LOCAL"
else
echo "Using existing coalescenceBubble.c (local edits preserved)"
fi
# Create symlink to DataFiles if needed
if [ ! -e "DataFiles" ]; then
ln -s ../DataFiles DataFiles
fi
# ============================================================
# Stage 2: Full Simulation with MPI
# ============================================================
echo ""
echo "Running 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 \
coalescenceBubble.c -o coalescenceBubble -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 srun
echo "Running full simulation with \${SLURM_NTASKS} MPI tasks..."
echo "Command: srun -n \${SLURM_NTASKS} ./coalescenceBubble \$OhOut \$RhoIn \$Rr \$MAXlevel \$tmax \$zWall"
echo ""
if srun -n \${SLURM_NTASKS} ./coalescenceBubble \$OhOut \$RhoIn \$Rr \$MAXlevel \$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
