-
Notifications
You must be signed in to change notification settings - Fork 6
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
5 changed files
with
222 additions
and
54 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| #!/usr/bin/env python3 | ||
|
|
||
| import argparse | ||
| import os | ||
| import shutil | ||
| import mpet.main as main | ||
|
|
||
| from dask_jobqueue import SLURMCluster, PBSCluster | ||
| from dask.distributed import Client, LocalCluster | ||
|
|
||
|
|
||
| def create_slurm_cluster(time, nproc, mem, queue, dashboard_port): | ||
| """Create a SLURM cluster for use with dask""" | ||
| cluster = SLURMCluster(cores=nproc, | ||
| processes=nproc, | ||
| memory=mem, | ||
| queue=queue, | ||
| walltime=time, | ||
| scheduler_options={'dashboard_address': dashboard_port}) | ||
| return cluster | ||
|
|
||
|
|
||
| def create_pbs_cluster(time, nproc, mem, queue, dashboard_port): | ||
| """Create a PBS cluster for use with dask""" | ||
| cluster = PBSCluster(cores=nproc, | ||
| processes=nproc, | ||
| memory=mem, | ||
| resource_spec=f'nodes=1:ppn={nproc}', | ||
| queue=queue, | ||
| walltime=time, | ||
| scheduler_options={'dashboard_address': dashboard_port}) | ||
| return cluster | ||
|
|
||
|
|
||
| def create_local_cluster(mem, dashboard_port): | ||
| """Create a local cluster for use with dask""" | ||
| cluster = LocalCluster(memory_limit=mem, | ||
| dashboard_address=dashboard_port) | ||
| return cluster | ||
|
|
||
|
|
||
| def run_mpet(client, output_folder, mpet_configs): | ||
| """Run MPET on each config file present in the mpet_configs folder""" | ||
| # In order to copy or move simulation output to current directory, remove old existing folder | ||
| tmpDir = os.path.join(os.getcwd(), "sim_output") | ||
| shutil.rmtree(tmpDir, ignore_errors=True) | ||
|
|
||
| with open(mpet_configs, 'r') as fp: | ||
| config_files = fp.readlines() | ||
|
|
||
| folder = os.path.dirname(mpet_configs) | ||
| files = [f'{os.path.join(folder, fname.strip())}' for fname in config_files] | ||
| print('Running mpet for these config files:', files) | ||
|
|
||
| # function to run MPET in directory given as input to run_mpet | ||
| def run_mpet_instance(*args, **kwargs): | ||
| print(f"Running in {output_folder} with {args=} and {kwargs=}") | ||
| os.chdir(output_folder) | ||
| try: | ||
| main.main(*args, **kwargs) | ||
| except Exception as e: | ||
| print(f'MPET crashed with error: {e}') | ||
|
|
||
| futures = client.map(run_mpet_instance, files, keepFullRun=True) | ||
| print('Waiting for MPET to finish') | ||
| client.gather(futures) | ||
| client.close() | ||
| print('Done') | ||
|
|
||
| return | ||
|
|
||
|
|
||
| if __name__ == '__main__': | ||
| parser = argparse.ArgumentParser(description='Runs several instances of MPET on a SLURM or' | ||
| ' PBS cluster, or local cluster') | ||
| # cluster settings | ||
| parser.add_argument('--time', '-t', required=True, | ||
| help='Maximum walltime per job (hh:mm:ss format)') | ||
| parser.add_argument('--nproc', '-n', type=int, required=True, | ||
| help='Number of CPU cores per job') | ||
| parser.add_argument('--mem', '-m', required=True, | ||
| help=('Max memory usage per job. When using a ' | ||
| 'local cluster it sets the memory limit per worker process.')) | ||
| parser.add_argument('--queue', '-q', default='default', | ||
| help='Queue to use (default: %(default)s)') | ||
| parser.add_argument('--dashboard_port', '-d', type=int, default=4096, | ||
| help='Port for dask dashboard (default: %(default)s)') | ||
|
|
||
| # script settings | ||
| parser.add_argument('--scheduler', '-s', default='slurm', choices=('slurm', 'pbs', 'local'), | ||
| help='Scheduling system to use (default: %(default)s)') | ||
| parser.add_argument('--min_jobs', type=int, default=1, | ||
| help='Minimum number of jobs to launch (default: %(default)s)') | ||
| parser.add_argument('--max_jobs', type=int, default=1, | ||
| help='Maximum number of jobs to launch (default: %(default)s)') | ||
| parser.add_argument('mpet_configs', | ||
| help='Text file containg the path to each MPET config file to run') | ||
|
|
||
| args = parser.parse_args() | ||
| # split cluster settings from the rest | ||
| main_settings = {} | ||
| for arg in ['scheduler', 'mpet_configs', 'min_jobs', 'max_jobs']: | ||
| main_settings[arg] = getattr(args, arg) | ||
| delattr(args, arg) | ||
| cluster_settings = vars(args) | ||
|
|
||
| # create cluster | ||
| if main_settings['scheduler'] == 'slurm': | ||
| cluster = create_slurm_cluster(**cluster_settings) | ||
| elif main_settings['scheduler'] == 'pbs': | ||
| cluster = create_pbs_cluster(**cluster_settings) | ||
| elif main_settings['scheduler'] == 'local': | ||
| cluster = create_local_cluster(args.mem, args.dashboard_port) | ||
|
|
||
| # Scale Dask cluster automatically based on scheduler activity (only if not local cluster) | ||
| if main_settings['scheduler'] != 'local': | ||
| cluster.adapt(minimum_jobs=main_settings['min_jobs'], | ||
| maximum_jobs=main_settings['max_jobs']) | ||
| client = Client(cluster) | ||
|
|
||
| # Store output in folder this script was called from | ||
| output_folder = os.getcwd() | ||
|
|
||
| run_mpet(client, output_folder, os.path.abspath(main_settings['mpet_configs'])) | ||
|
|
||
| client.shutdown() |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| [Particles] | ||
| type = CHR | ||
| discretization = 0.5e-9 | ||
| shape = sphere | ||
| thickness = 20e-9 | ||
|
|
||
| [Material] | ||
| muRfunc = LiFePO4 | ||
| noise = false | ||
| noise_prefac = 1e-5 | ||
| numnoise = 200 | ||
| Omega_a = 1.8560e-20 | ||
| kappa = 2.0148e-10 | ||
| B = 0.001e9 | ||
| rho_s = 1.3793e28 | ||
| D = 3.5e-15 | ||
| Dfunc = lattice | ||
| dgammadc = 0e-30 | ||
| cwet = 0.98 | ||
|
|
||
| [Reactions] | ||
| rxnType = CIET | ||
| k0 = 30 | ||
| E_A = 13000 | ||
| alpha = 0.5 | ||
| lambda = 3.4113e-20 | ||
| Rfilm = 0e-0 | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters