mirror of
https://github.com/JHUAPL/kaipy.git
synced 2026-01-09 14:28:02 -05:00
Removed obsolete script.
This commit is contained in:
Eric Winter
@@ -1,743 +0,0 @@
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#!/usr/bin/env python
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"""Run a SuperMag comparison for a MAGE magnetosphere run.
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Perform a comparison of ground magnetic field perturbations computed for a
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MAGE magnetosphere simulation with measured data from SuperMag. This is done
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in a set of PBS jobs run in the specified MAGE results directory.
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NOTE: If the calcdb.x binary was built with a module set other than that
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listed below, change the module set in the PBS scripts appropriately.
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Author
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------
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Eric Winter (eric.winter@jhuapl.edu)
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"""
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# Import standard modules.
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import argparse
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import copy
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import os
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import pathlib
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import re
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import shutil
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import sys
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# Import 3rd-party modules.
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from jinja2 import Template
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# Import project-specific modules.
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from kaipy import kaiH5
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from kaipy import kaiTools
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# Program constants and defaults
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# Program description.
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DESCRIPTION = "Compare MAGE ground delta-B to SuperMag measurements."
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# Default values for command-line arguments.
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DEFAULT_ARGUMENTS = {
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"calcdb": "calcdb.x",
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"debug": False,
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"dt": 60.0,
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"parintime": 1,
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"pbs_account": "",
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"smuser": "",
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"verbose": False,
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"mage_results_path": None,
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}
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# Location of template XML file for calcdb.x.
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CALCDB_XML_TEMPLATE = os.path.join(
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pathlib.Path(__file__).parent.resolve(), "calcdb-template.xml"
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)
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# # Location of template PBS file for calcdb.x.
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# CALCDB_PBS_TEMPLATE = os.path.join(
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# pathlib.Path(__file__).parent.resolve(), "calcdb-template.pbs"
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# )
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# # Default options for filling in the calcdb.x PBS template.
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# DEFAULT_CALCDB_PBS_OPTIONS = {
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# "job_name": None,
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# "queue": "normal",
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# "select": "1:ncpus=28:model=bro",
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# "walltime": "01:00:00",
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# "modules": [
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# "nas",
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# "pkgsrc/2022Q1-rome",
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# "comp-intel/2020.4.304",
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# "mpi-hpe/mpt.2.23",
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# "hdf5/1.8.18_mpt",
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# ],
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# "conda_environment": "kaiju-3.8",
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# "kaipyhome": os.environ["KAIPYHOME"],
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# "kaijuhome": os.environ["KAIJUHOME"],
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# }
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# # Location of template PBS file for pitmerge.py.
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# PITMERGE_PBS_TEMPLATE = os.path.join(
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# pathlib.Path(__file__).parent.resolve(), "pitmerge-template.pbs"
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# )
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# # Default options for filling in the pitmerge.py PBS template.
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# DEFAULT_PITMERGE_PBS_OPTIONS = {
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# "job_name": None,
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# "queue": "normal",
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# "select": "1:ncpus=28:model=bro",
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# "walltime": "01:00:00",
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# "modules": [
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# "nas",
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# "pkgsrc/2022Q1-rome",
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# "comp-intel/2020.4.304",
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# "mpi-hpe/mpt.2.23",
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# "hdf5/1.8.18_mpt",
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# ],
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# "conda_environment": "kaiju-3.8",
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# "kaipyhome": os.environ["KAIPYHOME"],
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# "kaijuhome": os.environ["KAIJUHOME"],
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# }
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# # Location of template PBS file for supermag_comparison.py.
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# SUPERMAG_COMPARISON_PBS_TEMPLATE = os.path.join(
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# pathlib.Path(__file__).parent.resolve(), "supermag_comparison-template.pbs"
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# )
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# # Default options for filling in the pitmerge.py PBS template.
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# DEFAULT_SUPERMAG_COMPARISON_PBS_OPTIONS = {
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# "job_name": None,
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# "queue": "normal",
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# "select": "1:ncpus=28:model=bro",
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# "walltime": "01:00:00",
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# "modules": [
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# "nas",
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# "pkgsrc/2022Q1-rome",
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# "comp-intel/2020.4.304",
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# "mpi-hpe/mpt.2.23",
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# "hdf5/1.8.18_mpt",
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# ],
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# "conda_environment": "kaiju-3.8",
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# "kaipyhome": os.environ["KAIPYHOME"],
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# "kaijuhome": os.environ["KAIJUHOME"],
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# }
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def create_command_line_parser():
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"""Create the command-line parser.
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Create the parser for the command line.
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Parameters
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----------
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None
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Returns
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-------
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parser : argparse.ArgumentParser
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Command-line parser for this script.
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Raises
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------
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None
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"""
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parser = argparse.ArgumentParser(description=DESCRIPTION)
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parser.add_argument(
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"--calcdb", default=DEFAULT_ARGUMENTS["calcdb"],
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help="Path to calcdb.x binary (default: %(default)s)."
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)
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parser.add_argument(
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"--debug", "-d", action="store_true",
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help="Print debugging output (default: %(default)s)."
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)
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parser.add_argument(
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"--dt", type=float, default=DEFAULT_ARGUMENTS["dt"],
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help="Time interval for delta-B computation (seconds)"
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" (default: %(default)s)."
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)
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parser.add_argument(
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"--parintime", type=int, default=DEFAULT_ARGUMENTS["parintime"],
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help="Split the calculation into this many parallel chunks"
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" (default: %(default)s)."
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)
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parser.add_argument(
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"--pbs_account", type=str, default=DEFAULT_ARGUMENTS["pbs_account"],
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help="Split the calculation into this many parallel chunks"
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" (default: %(default)s)."
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)
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parser.add_argument(
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"--smuser", type=str, default=DEFAULT_ARGUMENTS["smuser"],
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help="Account name for SuperMag database access"
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" (default: %(default)s)."
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)
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parser.add_argument(
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"--verbose", "-v", action="store_true",
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help="Print verbose output (default: %(default)s)."
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)
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parser.add_argument(
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"mage_results_path",
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help="Path to a result file for a MAGE magnetosphere run."
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)
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return parser
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def filename_to_runid(filename: str):
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"""Parse the runid from a MAGE results file name.
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Parse the runid from a MAGE results file name.
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For a result file from an MPI run, the runid is all text before the
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underscore before the set of 6 underscore-separated 4-digit sequences at
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the end of the name and the terminal .gam.h5 string.
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For a result file from a serial run, the runid is the name of the file,
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less the .gam.h5 extension.
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Parameters
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----------
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filename : str
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Name of MAGE results file.
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Returns
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-------
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runid : str
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The MAGE runid for the file.
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Raises
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------
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None
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"""
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# Check to see if the result file is for an MPI run. If not, it must be
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# for a serial run.
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mpi_pattern = (
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r"^(.+)_(\d{4})_(\d{4})_(\d{4})_(\d{4})_(\d{4})_(\d{4})\.gam.h5$"
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)
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serial_pattern = r"^(.+)\.gam.h5$"
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mpi_re = re.compile(mpi_pattern)
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serial_re = re.compile(serial_pattern)
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m = mpi_re.match(filename)
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if not m:
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m = serial_re.match(filename)
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runid = m.groups()[0]
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return runid
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def create_calcdb_xml_file(runid: str, parintime: int, dt: float,
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debug: bool = False):
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"""Create the XML input file for calcdb.x from a template.
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Create the XML input file for calcdb.x from a template. The file is
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created in the current directory.
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Parameters
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----------
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runid : str
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runid for MAGE results file.
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parintime : int
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Number of threads to use for calcdb.x computation.
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dt : infloatt
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Time interval for calcdb.x calculations (seconds).
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debug : bool, default False
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Set to True to produce debugging output.
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Returns
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-------
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xml_file : str
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Name of XML file.
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Raises
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------
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TypeError
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If the MAGE result file contains no steps for time >= 0.
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"""
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# Fetch run information from the MAGE result file.
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filename, isMPI, Ri, Rj, Rk = kaiTools.getRunInfo(".", runid)
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if debug:
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print(f"filename = {filename}")
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print(f"isMPI = {isMPI}")
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print(f"Ri = {Ri}")
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print(f"Rj = {Rj}")
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print(f"Rk = {Rk}")
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# Get the number of steps and the step IDs from the MAGE results file.
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nSteps, sIds = kaiH5.cntSteps(filename)
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if debug:
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print(f"nSteps = {nSteps}")
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print(f"sIds = {sIds}")
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# Determine the start and end time of the MAGE results.
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# Find the step for the first value of time >= 0, and that time.
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T0 = None
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for i_step in sIds:
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t_step = kaiH5.tStep(filename, sIds[i_step], aID="time")
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if t_step >= 0.0:
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T0 = t_step
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break
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if debug:
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print(f"T0 = {T0}")
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if T0 is None:
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raise TypeError("MAGE results contain no steps for t >= 0!")
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# Find the time for the last step.
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tFin = kaiH5.tStep(filename, sIds[-1], aID="time")
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if debug:
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print(f"tFin = {tFin}")
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# Read the template XML file.
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with open(CALCDB_XML_TEMPLATE, "r", encoding="utf-8") as f:
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template_content = f.read()
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if debug:
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print(f"template_content = {template_content}")
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template = Template(template_content)
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if debug:
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print(f"template = {template}")
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# Fill in the template options.
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ismpi = "false"
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if isMPI:
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ismpi = "true"
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options = {
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"runid": runid,
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"T0": T0,
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"dt": dt,
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"tFin": tFin,
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"ebfile": runid,
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"ismpi": ismpi,
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"Ri": Ri,
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"Rj": Rj,
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"Rk": Rk,
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"NumB": parintime,
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}
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if debug:
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print(f"options = {options}")
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# Render the template.
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xml_file = f"calcdb-{runid}.xml"
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xml_content = template.render(options)
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with open(xml_file, "w", encoding="utf-8") as f:
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f.write(xml_content)
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# Return the name of the XML file.
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return xml_file
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def create_calcdb_pbs_script(args: dict):
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"""Create the PBS script for calcdb.x from a template.
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Create the PBS script for calcdb.x from a template. The PBS script is
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created in the directory containing the MAGE results to compare to
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SuperMag data. The script will set up and run calcdb.x on the specified
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set of MAGE results, in the results directory.
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Parameters
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----------
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args : dict
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Dictionary of command-line and other options.
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Returns
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-------
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calcdb_pbs_script : str
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Path to PBS script.
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Raises
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------
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None
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"""
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# Local convenience variables.
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debug = args["debug"]
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mage_results_path = args["mage_results_path"]
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# Split the MAGE results path into a directory and a file.
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(mage_results_dir, mage_results_file) = os.path.split(mage_results_path)
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if debug:
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print(f"mage_results_dir = {mage_results_dir}")
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print(f"mage_results_file = {mage_results_file}")
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# Save the current directory.
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start_directory = os.getcwd()
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if debug:
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print(f"start_directory = {start_directory}")
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# Move to the results directory.
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os.chdir(mage_results_dir)
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# Compute the runid from the file name.
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runid = filename_to_runid(mage_results_file)
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if debug:
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print(f"runid = {runid}")
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# Create the XML input file for calcdb.x.
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calcdb_xml_file = create_calcdb_xml_file(
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runid, args["parintime"], args["dt"], debug)
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if debug:
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print(f"calcdb_xml_file = {calcdb_xml_file}")
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# # Copy the calcdb.x binary to the results directory, then make it
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# # executable.
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# shutil.copyfile(args["calcdb"], "./calcdb.x")
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# os.chmod("./calcdb.x", 0o755)
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# # Read the PBS script template for calcdb.x.
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# with open(CALCDB_PBS_TEMPLATE, "r", encoding="utf-8") as f:
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# template_content = f.read()
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# if debug:
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# print(f"template_content = {template_content}")
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# template = Template(template_content)
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# if debug:
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# print(f"template = {template}")
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# # Fill in the template options.
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# options = copy.deepcopy(DEFAULT_CALCDB_PBS_OPTIONS)
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# options.update({
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# "job_name": f"calcdb-{runid}",
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# "account": args["pbs_account"],
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# "select": f"{options['select']}:ompthreads={args['parintime']}",
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# "omp_num_threads": args["parintime"],
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# "calcdb_xml_file": calcdb_xml_file,
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# "runid": runid,
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# })
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# if debug:
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# print(f"options = {options}")
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# # Render the template.
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# calcdb_pbs_script = f"calcdb-{runid}.pbs"
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# xml_content = template.render(options)
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# with open(calcdb_pbs_script, "w", encoding="utf-8") as f:
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# f.write(xml_content)
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# # Move back to the start directory.
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# os.chdir(start_directory)
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# # Return the name of the PBS script.
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# return calcdb_pbs_script
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def create_pitmerge_pbs_script(args: dict):
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"""Create the PBS script for pitmerge.py to stitch calcdb output.
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|
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Create the PBS script for stitching together calcdb output using the
|
||||
pitmerge.py script.
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||||
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||||
Parameters
|
||||
----------
|
||||
args : dict
|
||||
Dictionary of command-line and other options.
|
||||
|
||||
Returns
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||||
-------
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stitching_pbs_script : str
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Path to PBS script.
|
||||
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||||
Raises
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||||
------
|
||||
None
|
||||
"""
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||||
# Local convenience variables.
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||||
debug = args["debug"]
|
||||
mage_results_path = args["mage_results_path"]
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||||
|
||||
# Split the MAGE results path into a directory and a file.
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(mage_results_dir, mage_results_file) = os.path.split(mage_results_path)
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if debug:
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print(f"mage_results_dir = {mage_results_dir}")
|
||||
print(f"mage_results_file = {mage_results_file}")
|
||||
|
||||
# Save the current directory.
|
||||
start_directory = os.getcwd()
|
||||
if debug:
|
||||
print(f"start_directory = {start_directory}")
|
||||
|
||||
# Move to the results directory.
|
||||
os.chdir(mage_results_dir)
|
||||
|
||||
# Compute the runid from the file name.
|
||||
runid = filename_to_runid(mage_results_file)
|
||||
if debug:
|
||||
print(f"runid = {runid}")
|
||||
|
||||
# Read the PBS script template for pitmerge.py.
|
||||
with open(PITMERGE_PBS_TEMPLATE, "r", encoding="utf-8") as f:
|
||||
template_content = f.read()
|
||||
if debug:
|
||||
print(f"template_content = {template_content}")
|
||||
template = Template(template_content)
|
||||
if debug:
|
||||
print(f"template = {template}")
|
||||
|
||||
# Fill in the template options.
|
||||
options = copy.deepcopy(DEFAULT_PITMERGE_PBS_OPTIONS)
|
||||
options.update({
|
||||
"job_name": f"pitmerge-{runid}",
|
||||
"account": args["pbs_account"],
|
||||
"runid": runid,
|
||||
})
|
||||
if debug:
|
||||
print(f"options = {options}")
|
||||
|
||||
# Render the template.
|
||||
pitmerge_pbs_script = f"pitmerge-{runid}.pbs"
|
||||
xml_content = template.render(options)
|
||||
with open(pitmerge_pbs_script, "w", encoding="utf-8") as f:
|
||||
f.write(xml_content)
|
||||
|
||||
# Move back to the start directory.
|
||||
os.chdir(start_directory)
|
||||
|
||||
# Return the name of the PBS script.
|
||||
return pitmerge_pbs_script
|
||||
|
||||
|
||||
def create_supermag_comparison_pbs_script(args: dict):
|
||||
"""Create the PBS script for the MAGE-SuperMag comparison from a template.
|
||||
|
||||
Create the PBS script for the MAGE-SuperMag comparison from a template.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
args : dict
|
||||
Dictionary of command-line and other options.
|
||||
|
||||
Returns
|
||||
-------
|
||||
supermag_comparison_pbs_script : str
|
||||
Path to PBS script.
|
||||
|
||||
Raises
|
||||
------
|
||||
None
|
||||
"""
|
||||
# Local convenience variables.
|
||||
debug = args["debug"]
|
||||
mage_results_path = args["mage_results_path"]
|
||||
|
||||
# Split the MAGE results path into a directory and a file.
|
||||
(mage_results_dir, mage_results_file) = os.path.split(mage_results_path)
|
||||
if debug:
|
||||
print(f"mage_results_dir = {mage_results_dir}")
|
||||
print(f"mage_results_file = {mage_results_file}")
|
||||
|
||||
# Save the current directory.
|
||||
start_directory = os.getcwd()
|
||||
if debug:
|
||||
print(f"start_directory = {start_directory}")
|
||||
|
||||
# Move to the results directory.
|
||||
os.chdir(mage_results_dir)
|
||||
|
||||
# Compute the runid from the file name.
|
||||
runid = filename_to_runid(mage_results_file)
|
||||
if debug:
|
||||
print(f"runid = {runid}")
|
||||
|
||||
# Read the PBS script template for supermag_comparison.py.
|
||||
with open(SUPERMAG_COMPARISON_PBS_TEMPLATE, "r", encoding="utf-8") as f:
|
||||
template_content = f.read()
|
||||
if debug:
|
||||
print(f"template_content = {template_content}")
|
||||
template = Template(template_content)
|
||||
if debug:
|
||||
print(f"template = {template}")
|
||||
|
||||
# Fill in the template options.
|
||||
options = copy.deepcopy(DEFAULT_SUPERMAG_COMPARISON_PBS_OPTIONS)
|
||||
options.update({
|
||||
"job_name": f"supermag_comparison-{runid}",
|
||||
"account": args["pbs_account"],
|
||||
"runid": runid,
|
||||
"smuser": args["smuser"],
|
||||
"calcdb_results_path": f"./{runid}.deltab.h5",
|
||||
})
|
||||
if debug:
|
||||
print(f"options = {options}")
|
||||
|
||||
# Render the template.
|
||||
supermag_comparison_pbs_script = f"supermag_comparison-{runid}.pbs"
|
||||
xml_content = template.render(options)
|
||||
with open(supermag_comparison_pbs_script, "w", encoding="utf-8") as f:
|
||||
f.write(xml_content)
|
||||
|
||||
# Move back to the start directory.
|
||||
os.chdir(start_directory)
|
||||
|
||||
# Return the name of the PBS script.
|
||||
return supermag_comparison_pbs_script
|
||||
|
||||
|
||||
def create_submit_script(
|
||||
calcdb_pbs_script: str, pitmerge_pbs_script: str,
|
||||
supermag_comparison_pbs_script: str, args: dict):
|
||||
"""Create the PBS script for the MAGE-SuperMag comparison from a template.
|
||||
|
||||
Create the PBS script for the MAGE-SuperMag comparison from a template.
|
||||
The submit script submits the job to run calcdb.x, then submits the
|
||||
follow-up comparison job to run only if the calcdb.x job completes
|
||||
successfully.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
calcdb_pbs_script : str
|
||||
Path to calcdb.x PBS script.
|
||||
pitmerge_pbs_script : str
|
||||
Path to pitmerge.py PBS script.
|
||||
supermag_comparison_pbs_script : str
|
||||
Path to comparison PBS script.
|
||||
args : dict
|
||||
Dictionary of command-line and other options.
|
||||
|
||||
Returns
|
||||
-------
|
||||
submit_script : str
|
||||
Path to bash script to submit PBS jobs.
|
||||
|
||||
Raises
|
||||
------
|
||||
None
|
||||
"""
|
||||
# Local convenience variables.
|
||||
debug = args["debug"]
|
||||
mage_results_path = args["mage_results_path"]
|
||||
|
||||
# Split the MAGE results path into a directory and a file.
|
||||
(mage_results_dir, mage_results_file) = os.path.split(mage_results_path)
|
||||
if debug:
|
||||
print(f"mage_results_dir = {mage_results_dir}")
|
||||
print(f"mage_results_file = {mage_results_file}")
|
||||
|
||||
# Save the current directory.
|
||||
start_directory = os.getcwd()
|
||||
if debug:
|
||||
print(f"start_directory = {start_directory}")
|
||||
|
||||
# Move to the results directory.
|
||||
os.chdir(mage_results_dir)
|
||||
|
||||
# Compute the runid from the file name.
|
||||
runid = filename_to_runid(mage_results_file)
|
||||
if debug:
|
||||
print(f"runid = {runid}")
|
||||
|
||||
# Submit the scripts in dependency order.
|
||||
submit_script = f"submit-{runid}.sh"
|
||||
with open(submit_script, "w", encoding="utf-8") as f:
|
||||
cmd = f"job_id=`qsub -J 1-{args['parintime']} {calcdb_pbs_script}`\n"
|
||||
f.write(cmd)
|
||||
cmd = "echo $job_id\n"
|
||||
f.write(cmd)
|
||||
cmd = "old_job_id=$job_id\n"
|
||||
f.write(cmd)
|
||||
cmd = (
|
||||
"job_id=`qsub -W depend=afterok:$old_job_id "
|
||||
f"{pitmerge_pbs_script}`\n"
|
||||
)
|
||||
f.write(cmd)
|
||||
cmd = "echo $job_id\n"
|
||||
f.write(cmd)
|
||||
cmd = "old_job_id=$job_id\n"
|
||||
f.write(cmd)
|
||||
cmd = (
|
||||
"job_id=`qsub -W depend=afterok:$old_job_id "
|
||||
f"{supermag_comparison_pbs_script}`\n"
|
||||
)
|
||||
f.write(cmd)
|
||||
cmd = "echo $job_id\n"
|
||||
f.write(cmd)
|
||||
|
||||
# Return the name of the PBS script.
|
||||
return submit_script
|
||||
|
||||
|
||||
def run_supermag_comparison(args: dict):
|
||||
"""Compare MAGE results for ground dB to SuperMag data.
|
||||
|
||||
Compare MAGE results for ground dB to SuperMag data.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
args: dict
|
||||
Dictionary of command-line options.
|
||||
|
||||
Returns
|
||||
-------
|
||||
int 0 on success
|
||||
|
||||
Raises
|
||||
------
|
||||
None
|
||||
"""
|
||||
# Set defaults for command-line options, then update with values passed
|
||||
# from the caller.
|
||||
local_args = copy.deepcopy(DEFAULT_ARGUMENTS)
|
||||
local_args.update(args)
|
||||
args = local_args
|
||||
|
||||
# Local convenience variables.
|
||||
debug = args["debug"]
|
||||
verbose = args["verbose"]
|
||||
|
||||
# ------------------------------------------------------------------------
|
||||
|
||||
# Create the PBS script to run calcdb.x.
|
||||
if verbose:
|
||||
print("Creating PBS script to run the calcdb.x job.")
|
||||
calcdb_pbs_script = create_calcdb_pbs_script(args)
|
||||
if debug:
|
||||
print(f"calcdb_pbs_script = {calcdb_pbs_script}")
|
||||
|
||||
# # Create the PBS script to stitch together the output from calcdb.x
|
||||
# # using pitmerge.py.
|
||||
# if verbose:
|
||||
# print("Creating PBS script to stitch together the calcdb.x output.")
|
||||
# pitmerge_pbs_script = create_pitmerge_pbs_script(args)
|
||||
# if debug:
|
||||
# print(f"pitmerge_pbs_script = {pitmerge_pbs_script}")
|
||||
|
||||
# # Create the PBS script to compare the calcdb.x results with SuperMag
|
||||
# # data.
|
||||
# if verbose:
|
||||
# print("Creating PBS script to run the MAGE-SuperMag comparison job.")
|
||||
# supermag_comparison_pbs_script = create_supermag_comparison_pbs_script(args)
|
||||
# if debug:
|
||||
# print(f"supermag_comparison_pbs_script = {supermag_comparison_pbs_script}")
|
||||
|
||||
# # Create the bash script to submit the PBS scripts in the proper order.
|
||||
# if verbose:
|
||||
# print("Creating bash script to submit the PBS jobs.")
|
||||
# submit_script = create_submit_script(
|
||||
# calcdb_pbs_script, pitmerge_pbs_script,
|
||||
# supermag_comparison_pbs_script, args
|
||||
# )
|
||||
# if debug:
|
||||
# print(f"submit_script = {submit_script}")
|
||||
|
||||
# if verbose:
|
||||
# print(f"Please run {submit_script} (in the MAGE result directory) to "
|
||||
# "submit the PBS jobs to run perform the MAGE-SuperMag "
|
||||
# "comparison.")
|
||||
|
||||
# Return normally.
|
||||
return 0
|
||||
|
||||
|
||||
def main():
|
||||
"""Driver for command-line version of code."""
|
||||
# Set up the command-line parser.
|
||||
parser = create_command_line_parser()
|
||||
|
||||
# Parse the command-line arguments.
|
||||
args = parser.parse_args()
|
||||
if args.debug:
|
||||
print(f"args = {args}")
|
||||
|
||||
# Convert the arguments from Namespace to dict.
|
||||
args = vars(args)
|
||||
|
||||
# Pass the command-line arguments to the main function as a dict.
|
||||
return_code = run_supermag_comparison(args)
|
||||
sys.exit(return_code)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Reference in New Issue
Block a user