#!/bin/bash
#SBATCH --job-name=bubbleCoal-S1
#SBATCH --nodes=1
#SBATCH --ntasks=48
#SBATCH --cpus-per-task=1
#SBATCH --time=12:00:00
#SBATCH --partition=genoa
#SBATCH --mail-type=ALL
#SBATCH [email protected]
#SBATCH --output=slurm-stage1-%j.out
#SBATCH --error=slurm-stage1-%j.err
# ============================================================
# Bubble Coalescence - Stage 1 Serial Runner (Snellius)
# ============================================================
# This script runs Stage 1 (initialization) for all cases in parallel.
# Each case runs on 1 core (serial, no OpenMP/MPI).
# Up to 48 cases run simultaneously.
#
# Stage 1 generates restart files needed for Stage 2 (MPI simulation).
#
# AFTER RUNNING:
# Submit Stage 2 with: sbatch runSweepSnellius.sbatch
#
# SBATCH Parameters to Customize:
# --ntasks: Number of concurrent cases (currently 48)
# --time: Wall time for all Stage 1 runs (currently 12 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
# ============================================================
SCRIPT_DIR="\${SLURM_SUBMIT_DIR}"
SWEEP_FILE="\${SCRIPT_DIR}/sweep.params"
# Maximum concurrent jobs (matches SLURM allocation)
MAX_CONCURRENT=\${SLURM_NTASKS:-48}
# Stage 1 tmax - short run to generate restart file
STAGE1_TMAX="5e-2"
# ============================================================
# Print Job Information
# ============================================================
echo "============================================="
echo "Bubble Coalescence - Stage 1 (Serial)"
echo "============================================="
echo "Job started at: \$(date)"
echo "Running on node: \$(hostname)"
echo "Working directory: \$(pwd)"
echo "Job ID: \${SLURM_JOB_ID}"
echo "Max concurrent cases: \${MAX_CONCURRENT}"
echo "Partition: \${SLURM_JOB_PARTITION}"
echo ""
echo "Mode: Stage 1 only (serial initialization)"
echo " Generates restart files for Stage 2"
echo " Each case runs on 1 core (no OpenMP/MPI)"
echo ""
# ============================================================
# Load Required Modules (minimal for serial)
# ============================================================
echo "Loading modules..."
module purge
module load 2024
# No MPI needed for serial execution
echo "Modules loaded (serial mode - no MPI)"
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
# ============================================================
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
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 "\$SWEEP_FILE"
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
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=()
while IFS='=' read -r key value; do
[[ "\$key" =~ ^[[:space:]]*# ]] && continue
[[ -z "\$key" ]] && continue
if [[ "\$key" =~ ^[[:space:]]*SWEEP_([^=]+) ]]; then
var_name="\${BASH_REMATCH[1]}"
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..."
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=()
generate_combinations() {
local depth=\$1
shift
local current_values=("\$@")
if [ \$depth -eq \${#SWEEP_VARS[@]} ]; then
local case_file="\${TEMP_DIR}/case_\$(printf "%04d" \$CASE_NUM).params"
cp "\$BASE_CONFIG" "\$case_file"
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"
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
echo "Case \$CASE_NUM:"
for i in "\${!SWEEP_VARS[@]}"; do
echo " \${SWEEP_VARS[\$i]} = \${current_values[\$i]}"
done
echo ""
((CASE_NUM++)) || true
return
fi
local values="\${SWEEP_VALUES[\$depth]}"
IFS=',' read -ra value_array <<< "\$values"
for val in "\${value_array[@]}"; do
val=\$(echo "\$val" | xargs)
generate_combinations \$((depth + 1)) \${current_values[@]+"\${current_values[@]}"} "\$val"
done
}
generate_combinations 0
echo "Generated \$COMBINATION_COUNT parameter combinations"
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
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 ""
# ============================================================
# Prepare Status Tracking
# ============================================================
STATUS_DIR="\${TEMP_DIR}/status"
mkdir -p "\$STATUS_DIR"
# ============================================================
# Function to Run Single Case (Stage 1)
# ============================================================
run_stage1_case() {
local param_file=\$1
local status_dir=\$2
local script_dir=\$3
local stage1_tmax=\$4
# Source parameter parsing in subshell
source "\${script_dir}/src-local/parse_params.sh"
parse_param_file "\$param_file"
local CASE_NO=\$(get_param "CaseNo")
local OhOut=\$(get_param "OhOut" "1e-2")
local RhoIn=\$(get_param "RhoIn" "1e-3")
local Rr=\$(get_param "Rr" "1.0")
local MAXlevel=\$(get_param "MAXlevel" "10")
local zWall=\$(get_param "zWall" "0.01")
if [ -z "\$CASE_NO" ]; then
echo "FAILED" > "\${status_dir}/\${CASE_NO:-unknown}"
return 1
fi
local CASE_DIR="\${script_dir}/simulationCases/\${CASE_NO}"
local LOG_FILE="\${CASE_DIR}/stage1.log"
# Create case directory BEFORE redirecting to log file
mkdir -p "\$CASE_DIR"
# Use existing case.params if present (allows manual parameter edits for reruns)
# Otherwise, create from sweep-generated params
if [ ! -f "\$CASE_DIR/case.params" ]; then
cp "\$param_file" "\$CASE_DIR/case.params"
fi
# Re-parse from case.params (source of truth for this case)
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")
zWall=\$(get_param "zWall" "0.01")
{
echo "========================================="
echo "Case \$CASE_NO - Stage 1 (\$(date))"
echo "========================================="
echo "Parameters: OhOut=\$OhOut, RhoIn=\$RhoIn, Rr=\$Rr"
echo " MAXlevel=\$MAXlevel, tmax=\$stage1_tmax, zWall=\$zWall"
cd "\$CASE_DIR"
# Copy source file
local SRC_FILE_ORIG="\${script_dir}/simulationCases/coalescenceBubble.c"
if [ ! -f "\$SRC_FILE_ORIG" ]; then
echo "ERROR: Source file not found"
echo "FAILED" > "\${status_dir}/\${CASE_NO}"
return 1
fi
# Use existing source file if present (allows local code edits for reruns)
if [ ! -f "coalescenceBubble.c" ]; then
cp "\$SRC_FILE_ORIG" "coalescenceBubble.c"
fi
# Create symlink to DataFiles
if [ ! -e "DataFiles" ]; then
ln -s ../DataFiles DataFiles
fi
# Compile SERIAL (no OpenMP, no MPI)
echo "Compiling (serial)..."
if ! qcc -I../../src-local -Wall -O2 -disable-dimensions \
coalescenceBubble.c -o coalescenceBubble -lm 2>&1; then
echo "ERROR: Compilation failed"
echo "FAILED" > "\${status_dir}/\${CASE_NO}"
return 1
fi
echo "Compilation successful"
# Run Stage 1 with small tmax
echo "Running Stage 1 (tmax=\$stage1_tmax)..."
if ./coalescenceBubble \$OhOut \$RhoIn \$Rr \$MAXlevel \$stage1_tmax \$zWall; then
echo "Stage 1 completed"
# Verify restart file was created
if [ -f "restart" ]; then
echo "Restart file created successfully"
echo "SUCCESS" > "\${status_dir}/\${CASE_NO}"
else
echo "WARNING: restart file not found after Stage 1"
echo "FAILED" > "\${status_dir}/\${CASE_NO}"
return 1
fi
else
echo "ERROR: Stage 1 failed"
echo "FAILED" > "\${status_dir}/\${CASE_NO}"
return 1
fi
echo "Case \$CASE_NO Stage 1 complete"
} > "\$LOG_FILE" 2>&1
return 0
}
export -f run_stage1_case
# ============================================================
# Run All Cases in Parallel (Stage 1)
# ============================================================
echo "============================================="
echo "Running \$COMBINATION_COUNT Cases (Stage 1)"
echo "============================================="
echo "Max concurrent: \${MAX_CONCURRENT}"
echo "Each case: serial execution, tmax=\${STAGE1_TMAX}"
echo ""
RUNNING_JOBS=0
PIDS=()
for param_file in "\${CASE_FILES[@]}"; do
# Wait if we've hit the concurrency limit
while [ \$RUNNING_JOBS -ge \$MAX_CONCURRENT ]; do
# Wait for any background job to finish
wait -n 2>/dev/null || true
((RUNNING_JOBS--)) || true
done
# Launch case in background
run_stage1_case "\$param_file" "\$STATUS_DIR" "\$SCRIPT_DIR" "\$STAGE1_TMAX" &
PIDS+=(\$!)
((RUNNING_JOBS++)) || true
# Extract case number for logging
parse_param_file "\$param_file"
CASE_NO=\$(get_param "CaseNo")
echo "Launched case \$CASE_NO (PID: \${PIDS[-1]}, running: \$RUNNING_JOBS)"
done
echo ""
echo "All cases launched, waiting for completion..."
echo ""
# Wait for all remaining jobs
wait
# ============================================================
# Collect Results
# ============================================================
SUCCESSFUL_CASES=0
FAILED_CASES=0
for status_file in "\${STATUS_DIR}"/*; do
if [ -f "\$status_file" ]; then
status=\$(cat "\$status_file")
case_no=\$(basename "\$status_file")
if [ "\$status" = "SUCCESS" ]; then
((SUCCESSFUL_CASES++)) || true
else
((FAILED_CASES++)) || true
echo "FAILED: Case \$case_no"
fi
fi
done
# ============================================================
# Final Summary
# ============================================================
echo ""
echo "============================================="
echo "Stage 1 Complete"
echo "============================================="
echo "Job completed at: \$(date)"
echo "Total cases: \$COMBINATION_COUNT"
echo "Successful: \$SUCCESSFUL_CASES"
echo "Failed: \$FAILED_CASES"
echo ""
echo "Restart files location: simulationCases/*/restart"
echo ""
if [ \$SUCCESSFUL_CASES -gt 0 ]; then
echo "Next step: Submit Stage 2 with:"
echo " sbatch runSweepSnellius.sbatch"
fi
echo "============================================="
if [ \$FAILED_CASES -gt 0 ]; then
echo "WARNING: \$FAILED_CASES case(s) failed. Check logs in simulationCases/*/stage1.log" >&2
exit 1
fi
exit 0
