Source code for abipy.flowtk

# flake8: noqa
import os
import tempfile

from monty.termcolor import cprint
from import *
from import Pseudo, PseudoTable, PseudoParser
from import NetcdfReader
from import GroundStateScfCycle, D2DEScfCycle, yaml_read_kpoints, yaml_read_irred_perts

from .launcher import PyFlowScheduler, PyLauncher
from .qadapters import show_qparams, all_qtypes
from .wrappers import Mrgscr, Mrgddb, Cut3D, Fold2Bloch
from .nodes import Status
from .tasks import *
from .tasks import EphTask, ElasticTask
from .works import *
from .flows import (Flow, G0W0WithQptdmFlow, bandstructure_flow, PhononFlow, phonon_conv_flow,
    g0w0_flow, NonLinearCoeffFlow)
from .abitimer import AbinitTimerParser, AbinitTimerSection
from .events import EventsParser, autodoc_event_handlers
#from import *
#from abipy.flowtk.gs_works import EosWork
from .dfpt_works import ElasticWork, NscfDdksWork
from .gw import ScreeningWork

[docs]def flow_main(main): # pragma: no cover """ This decorator is used to decorate main functions producing `Flows`. It adds the initialization of the logger and an argument parser that allows one to select the loglevel, the workdir of the flow as well as the YAML file with the parameters of the `TaskManager`. The main function shall have the signature: main(options) where options in the container with the command line options generated by `ArgumentParser`. Args: main: main function. """ from functools import wraps @wraps(main) def wrapper(*args, **kwargs): # Build the parse and parse input args. parser = build_flow_main_parser() options = parser.parse_args() # loglevel is bound to the string value obtained from the command line argument. # Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug import logging numeric_level = getattr(logging, options.loglevel.upper(), None) if not isinstance(numeric_level, int): raise ValueError('Invalid log level: %s' % options.loglevel) logging.basicConfig(level=numeric_level) # Istantiate the manager. options.manager = TaskManager.as_manager(options.manager) if options.tempdir: options.workdir = tempfile.mkdtemp() print("Working in temporary directory", options.workdir) def execute(): """This is the function that performs the work depending on options.""" flow = main(options) if options.plot: flow.plot_networkx(tight_layout=True, with_edge_labels=True) if options.graphviz: graph = flow.get_graphviz() #engine=options.engine) directory = tempfile.mkdtemp() print("Producing source files in:", directory) graph.view(directory=directory, cleanup=False) if options.abivalidate: print("Validating flow input files...") isok, errors = flow.abivalidate_inputs() if not isok: for e in errors: if e.retcode == 0: continue lines = e.log_file.readlines() i = len(lines) - 50 if len(lines) >= 50 else 0 print("Last 50 line from log file:") print("".join(lines[i:])) raise RuntimeError("flow.abivalidate_input failed. See messages above.") else: print("Validation succeeded") if options.remove and os.path.isdir(flow.workdir): print("Removing old directory:", flow.workdir) import shutil shutil.rmtree(flow.workdir) if options.dry_run: print("Dry-run mode.") retcode = 0 elif options.scheduler: retcode = flow.make_scheduler().start() if retcode == 0: retcode = 0 if flow.all_ok else 1 elif options.batch: retcode = flow.batch() else: # Default behaviour. retcode = flow.build_and_pickle_dump() cprint("Return code: %d" % retcode, "red" if retcode != 0 else "green") return retcode if # Profile execute import pstats, cProfile cProfile.runctx("execute()", globals(), locals(), "") s = pstats.Stats("") s.strip_dirs().sort_stats("time").print_stats() return 0 else: return execute() return wrapper
[docs]def build_flow_main_parser(): """ Build and return the parser used in the abipy/data/runs scripts. """ import argparse parser = argparse.ArgumentParser() parser.add_argument('--loglevel', default="ERROR", type=str, help="set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG") parser.add_argument("-w", '--workdir', default="", type=str, help="Working directory of the flow.") parser.add_argument("-m", '--manager', default=None, help="YAML file with the parameters of the task manager. " "Default None i.e. the manager is read from standard locations: " "working directory first then ~/.abinit/abipy/manager.yml.") parser.add_argument("-s", '--scheduler', action="store_true", default=False, help="Run the flow with the scheduler") parser.add_argument("-b", '--batch', action="store_true", default=False, help="Run the flow in batch mode") parser.add_argument("-r", "--remove", default=False, action="store_true", help="Remove old flow workdir") parser.add_argument("-p", "--plot", default=False, action="store_true", help="Plot flow with networkx.") parser.add_argument("-g", "--graphviz", default=False, action="store_true", help="Plot flow with graphviz.") parser.add_argument("-d", "--dry-run", default=False, action="store_true", help="Don't write directory with flow.") parser.add_argument("-a", "--abivalidate", default=False, action="store_true", help="Call Abinit to validate input files.") parser.add_argument("-t", "--tempdir", default=False, action="store_true", help="Execute flow in temporary directory.") parser.add_argument("--prof", action="store_true", default=False, help="Profile code wth cProfile ") return parser