New scripting method to efficiently run the solver over a wide parameter range on the cluster.
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Karthik
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4d10f6e515
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8bc8ab71d6
71
Dipolar-Gas-Simulator/+Scripts/run_hybrid_worker.m
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71
Dipolar-Gas-Simulator/+Scripts/run_hybrid_worker.m
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function run_hybrid_worker(batchParams, batchIdx)
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% Set up local cluster for parallel pool
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cluster = parcluster('local');
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nprocs = str2double(getenv('SLURM_CPUS_PER_TASK'));
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if isnan(nprocs), nprocs = feature('numcores'); end
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tmpdir = fullfile(getenv('TMPDIR'), sprintf('matlab_job_%d', batchIdx));
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if ~exist(tmpdir, 'dir'); mkdir(tmpdir); end
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cluster.JobStorageLocation = tmpdir;
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pool = parpool(cluster, nprocs);
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nJobs = size(batchParams, 1);
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parfor k = 1:nJobs
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% Unpack parameter tuple
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a_s = batchParams(k, 1);
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theta_deg = batchParams(k, 2);
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phi_deg = batchParams(k, 3);
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N_atoms = batchParams(k, 4);
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theta_rad = deg2rad(theta_deg);
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phi_rad = deg2rad(phi_deg);
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% Create unique save directory
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jobName = sprintf('aS_%03d_theta_%03d_phi_%03d_N_%d', a_s, theta_deg, phi_deg, N_atoms);
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saveDir = fullfile('./Results/Data_3D/GradientDescent', jobName);
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if ~exist(saveDir, 'dir')
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mkdir(saveDir);
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end
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% Options for this run
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OptionsStruct = struct;
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OptionsStruct.NumberOfAtoms = N_atoms;
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OptionsStruct.DipolarPolarAngle = theta_rad;
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OptionsStruct.DipolarAzimuthAngle = phi_rad;
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OptionsStruct.ScatteringLength = a_s;
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OptionsStruct.TrapFrequencies = [50, 20, 150];
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OptionsStruct.TrapPotentialType = 'Harmonic';
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OptionsStruct.NumberOfGridPoints = [128, 256, 128];
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OptionsStruct.Dimensions = [30, 50, 30];
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OptionsStruct.UseApproximationForLHY = true;
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OptionsStruct.IncludeDDICutOff = true;
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OptionsStruct.CutoffType = 'Cylindrical';
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OptionsStruct.SimulationMode = 'EnergyMinimization';
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OptionsStruct.GradientDescentMethod = 'NonLinearCGD';
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OptionsStruct.MaxIterationsForGD = 15000;
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OptionsStruct.NoiseScaleFactor = 0.010;
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OptionsStruct.PlotLive = false;
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OptionsStruct.JobNumber = 0;
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OptionsStruct.RunOnGPU = true;
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OptionsStruct.SaveData = true;
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OptionsStruct.SaveDirectory = saveDir;
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options = Helper.convertstruct2cell(OptionsStruct);
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sim = Simulator.DipolarGas(options{:});
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pot = Simulator.Potentials(options{:});
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sim.Potential = pot.trap();
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NumberOfOutputs = 5;
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[~, ~, ~, ~, ~, stats] = Helper.runWithProfiling(@() sim.run(), NumberOfOutputs, saveDir);
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fprintf('Batch %d | Job %d: a_s = %d, theta = %d°, phi = %d°, N = %d | Time = %.2f s\n', ...
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batchIdx, k, a_s, theta_deg, phi_deg, N_atoms, stats.runtime);
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end
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delete(pool);
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end
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35
Dipolar-Gas-Simulator/+Scripts/run_hybrid_worker_wrapper.m
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35
Dipolar-Gas-Simulator/+Scripts/run_hybrid_worker_wrapper.m
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function run_hybrid_worker_wrapper(batchIdx)
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a_s_list = parse_environmental_variable('SCATTERING_LENGTH_RANGE', 85); % Scattering length
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theta_list = parse_environmental_variable('POLAR_ANGLE_RANGE', 0); % Polar angle
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phi_list = parse_environmental_variable('AZIMUTHAL_ANGLE_RANGE', 0); % Azimuthal angle
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N_atoms_list = parse_environmental_variable('NUM_ATOMS_LIST', 90000); % Atom number
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chunkSize = str2double(getenv('CHUNK_SIZE'));
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% Create full parameter grid (extendable)
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[A, T, P, N] = ndgrid(a_s_list, theta_list, phi_list, N_atoms_list);
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paramGrid = [A(:), T(:), P(:), N(:)];
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totalJobs = size(paramGrid, 1);
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totalBatches = ceil(totalJobs / chunkSize);
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if batchIdx > totalBatches
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error('Batch index %d exceeds total batches (%d)', batchIdx, totalBatches);
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end
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firstIdx = (batchIdx - 1) * chunkSize + 1;
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lastIdx = min(batchIdx * chunkSize, totalJobs);
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% Call worker with this batch of parameters
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batchParams = paramGrid(firstIdx:lastIdx, :);
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Scripts.run_hybrid_worker(batchParams, batchIdx);
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end
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function vals = parse_environmental_variable(varName, default)
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str = getenv(varName);
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if isempty(str)
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vals = default;
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elseif startsWith(str, '[')
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vals = str2num(str); %#ok<ST2NM>
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else
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vals = eval(str); % Trust only controlled environments
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end
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end
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@ -3,29 +3,24 @@ OptionsStruct = struct;
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OptionsStruct.NumberOfAtoms = 90000;
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OptionsStruct.DipolarPolarAngle = deg2rad(0);
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OptionsStruct.DipolarAzimuthAngle = 0;
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OptionsStruct.ScatteringLength = 95;
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OptionsStruct.ScatteringLength = 85;
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OptionsStruct.TrapFrequencies = [50, 20, 150];
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OptionsStruct.TrapPotentialType = 'Harmonic';
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OptionsStruct.NumberOfGridPoints = [64, 128, 64];
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OptionsStruct.Dimensions = [30, 30, 30];
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OptionsStruct.NumberOfGridPoints = [128, 256, 128];
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OptionsStruct.Dimensions = [30, 50, 30];
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OptionsStruct.UseApproximationForLHY = true;
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OptionsStruct.IncludeDDICutOff = true;
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OptionsStruct.CutoffType = 'Cylindrical';
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OptionsStruct.SimulationMode = 'EnergyMinimization'; % 'ImaginaryTimeEvolution' | 'RealTimeEvolution' | 'EnergyMinimization'
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OptionsStruct.GradientDescentMethod = 'NonLinearCGD'; % 'HeavyBall' | 'NonLinearCGD'
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OptionsStruct.MaxIterationsForGD = 1E5;
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OptionsStruct.TimeStepSize = 1E-3; % in s
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OptionsStruct.MinimumTimeStepSize = 1E-6; % in s
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OptionsStruct.TimeCutOff = 2E6; % in s
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OptionsStruct.EnergyTolerance = 5E-10;
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OptionsStruct.ResidualTolerance = 1E-08;
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OptionsStruct.MaxIterationsForGD = 15000;
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OptionsStruct.NoiseScaleFactor = 0.010;
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OptionsStruct.PlotLive = true;
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OptionsStruct.PlotLive = false;
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OptionsStruct.JobNumber = 0;
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OptionsStruct.RunOnGPU = false;
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OptionsStruct.RunOnGPU = true;
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OptionsStruct.SaveData = true;
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OptionsStruct.SaveDirectory = './Results/Data_3D/GradientDescent'; % './Results/Data_3D/AnisotropicTrap/Tilted0'
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options = Helper.convertstruct2cell(OptionsStruct);
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65
Dipolar-Gas-Simulator/submit_jobs.sh
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65
Dipolar-Gas-Simulator/submit_jobs.sh
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# Define scan ranges (encoded as strings)
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SCATTERING_LENGTH_RANGE="85"
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POLAR_ANGLE_RANGE="0"
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AZIMUTHAL_ANGLE_RANGE="0"
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NUM_ATOMS_LIST="[90000]"
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CHUNK_SIZE=1
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# Convert parameter ranges into arrays
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scatteringLengths=($(eval echo {$SCATTERING_LENGTH_RANGE}))
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polarAngles=($(eval echo {$POLAR_ANGLE_RANGE}))
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azimuthalAngles=($(eval echo {$AZIMUTHAL_ANGLE_RANGE}))
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numAtoms=($(eval echo {$NUM_ATOMS_LIST}))
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# Calculate the total number of jobs (combinations of parameters)
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totalJobs=$((${#scatteringLengths[@]} * ${#polarAngles[@]} * ${#azimuthalAngles[@]} * ${#numAtoms[@]}))
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# Calculate the number of array jobs based on total jobs and chunk size
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numArrayJobs=$(( (totalJobs + CHUNK_SIZE - 1) / CHUNK_SIZE ))
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# Print the total number of jobs and array jobs for debugging
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echo "Total number of jobs: $totalJobs"
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echo "Number of SLURM array jobs: $numArrayJobs"
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# Create the SLURM job submission command
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sbatch --export=SCATTERING_LENGTH_RANGE="$SCATTERING_LENGTH_RANGE",POLAR_ANGLE_RANGE="$POLAR_ANGLE_RANGE",AZIMUTHAL_ANGLE_RANGE="$AZIMUTHAL_ANGLE_RANGE",NUM_ATOMS_LIST="$NUM_ATOMS_LIST",CHUNK_SIZE=$CHUNK_SIZE << EOF
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#!/bin/bash
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########### Begin SLURM header ###########
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#SBATCH --partition=gpu-single
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#SBATCH --nodes=1
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#SBATCH --ntasks-per-node=1
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#SBATCH --cpus-per-task=8
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#SBATCH --gres=gpu:1
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#SBATCH --mem=16G
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#SBATCH --time=00:40:00
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#SBATCH --job-name=simulation
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#SBATCH --error=simulation_%A_%a.err
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#SBATCH --output=simulation_%A_%a.out
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#SBATCH --array=1-${numArrayJobs}
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########### End SLURM header ##########
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echo "Working Directory: $PWD"
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echo "Running on host $HOSTNAME"
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echo "Job id: $SLURM_JOB_ID"
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echo "Job name: $SLURM_JOB_NAME"
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echo "Number of nodes allocated to job: $SLURM_JOB_NUM_NODES"
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echo "Number of GPUs allocated to job: $SLURM_GPUS"
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# Load module
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module load math/matlab/R2023a
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echo Directory is `pwd`
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echo "Initiating Job..."
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# Inside SLURM job array
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echo "Running SLURM job array from 1 to ${numArrayJobs}"
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# Start MATLAB job with the batch index
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matlab -nodisplay -nosplash -r "Scripts.run_hybrid_worker_wrapper(\$SLURM_ARRAY_TASK_ID)"
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# notice for tests
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echo "Job terminated successfully"
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exit
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EOF
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