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Merge pull request #120 from valeriupredoi/dev_parrallel_ts
Batch timeseries analysis in slurm
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,152 @@ | ||
| #!/usr/bin/env python | ||
| # | ||
| # Copyright 2015, Plymouth Marine Laboratory | ||
| # | ||
| # This file is part of the bgc-val library. | ||
| # | ||
| # bgc-val is free software: you can redistribute it and/or modify it | ||
| # under the terms of the Revised Berkeley Software Distribution (BSD) 3-clause license. | ||
|
|
||
| # bgc-val is distributed in the hope that it will be useful, but | ||
| # without any warranty; without even the implied warranty of merchantability | ||
| # or fitness for a particular purpose. See the revised BSD license for more details. | ||
| # You should have received a copy of the revised BSD license along with bgc-val. | ||
| # If not, see <http://opensource.org/licenses/BSD-3-Clause>. | ||
| # | ||
| # Address: | ||
| # Plymouth Marine Laboratory | ||
| # Prospect Place, The Hoe | ||
| # Plymouth, PL1 3DH, UK | ||
| # | ||
| # Email: | ||
| # [email protected] | ||
| # | ||
| """ | ||
| .. module:: batch_timeseries | ||
| :platform: Unix | ||
| :synopsis: A script to submit slurm scripts time series. | ||
| .. moduleauthor:: Lee de Mora <[email protected]> | ||
| """ | ||
| import argparse | ||
| import subprocess | ||
| import os | ||
| import sys | ||
|
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| from getpass import getuser | ||
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| from bgcval2.analysis_compare import load_comparison_yml | ||
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| def get_args(): | ||
| """Parse command line arguments.""" | ||
| parser = argparse.ArgumentParser( | ||
| description=__doc__, | ||
| formatter_class=argparse.RawDescriptionHelpFormatter) | ||
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| parser.add_argument('-y', | ||
| '--compare_yml', | ||
| nargs='+', | ||
| type=str, | ||
| help='One or more Comparison Analysis configuration file, for examples see bgcval2 input_yml directory.', | ||
| required=True, | ||
| ) | ||
|
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| parser.add_argument('-c', | ||
| '--config-file', | ||
| default=os.path.join(os.path.dirname(os.path.realpath(__file__)), | ||
| 'default-bgcval2-config.yml'), | ||
| help='User configuration file (for paths).', | ||
| required=False) | ||
|
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| parser.add_argument('--dry_run', | ||
| '-d', | ||
| default=False, | ||
| help='When True: Do not submit the jobs to lotus.', | ||
| action=argparse.BooleanOptionalAction, | ||
| required=False) | ||
|
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| args = parser.parse_args() | ||
| return args | ||
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| def submits_lotus(compare_yml, config_user, dry_run=False): | ||
| """ | ||
| Loads the yaml file and submits individual time series to sbatch. | ||
| """ | ||
| # Load details from yml file | ||
| details = load_comparison_yml(compare_yml) | ||
|
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| # list of job IDS | ||
| jobs = details['jobs'] | ||
|
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| # username | ||
| user = getuser() | ||
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| # Load current on-going list of this users slurm jobs: | ||
| out = str(subprocess.check_output(["squeue", "--user="+user])) | ||
|
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| # loop over jobs: | ||
| for job in jobs: | ||
| # Check whether there's already a job running for this jobID | ||
| if out.find(job) > -1: | ||
| print("That job exists already: skipping", job) | ||
| continue | ||
|
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| # Get list of suites for each job | ||
| suites = details['suites'][job] | ||
|
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| # Make it a list: | ||
| if isinstance(suites, str): | ||
| suites = suites.split(' ') | ||
|
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| # prepare the command | ||
| command_txt = ['sbatch', | ||
| '-J', job, | ||
| ''.join(['--error=logs/', job,'.err']), | ||
| ''.join(['--output=logs/', job,'.out']), | ||
| 'lotus_timeseries.sh', job] | ||
| for suite in suites: | ||
| command_txt.append(suite) | ||
|
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| # Send it! | ||
| if dry_run: | ||
| print('Not submitting (dry-run):', ' '.join(command_txt)) | ||
| else: | ||
| # Submit job: | ||
| print('Submitting:', ' '.join(command_txt)) | ||
| #command1 = subprocess.Popen(command_txt) | ||
| command1 = subprocess.Popen( | ||
| command_txt, | ||
| stdout=subprocess.PIPE, | ||
| stderr=subprocess.STDOUT, | ||
| ) | ||
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| def main(): | ||
|
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| """Run the main routine.""" | ||
| args = get_args() | ||
|
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| # This has a sensible default value. | ||
| config_user=args.config_file | ||
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| # This shouldn't fail as it's a required argument. | ||
| compare_ymls = args.compare_yml | ||
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| for compare_yml in compare_ymls: | ||
| print(f"analysis_timeseries: Comparison config file {compare_yml}") | ||
|
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| if not os.path.isfile(compare_yml): | ||
| print(f"analysis_timeseries: Could not find comparison config file {compare_yml}") | ||
| sys.exit(1) | ||
| dry_run = args.dry_run | ||
| submits_lotus(compare_yml, config_user, dry_run) | ||
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| if __name__ == "__main__": | ||
| from ._version import __version__ | ||
| print(f'BGCVal2: {__version__}') | ||
| main() | ||
|
|
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