Source code for matador.cli.run3

# coding: utf-8
# Distributed under the terms of the MIT License.

""" Run calculations in a folder with BatchRun
such that there are no clashes.
import os
import argparse
from matador import __version__, script_epilog
from matador.utils.print_utils import print_notify
from matador.utils.errors import InputError
from matador.compute import BatchRun

[docs]def main(): """ Parse args and run any remaining jobs. """ parser = argparse.ArgumentParser( prog='run3', description='Run multiple calculations from a series of .res \ files and single cell and param files, typically CASTEP geometry \ optimisations. The geometry optimization will \ be split into "--rough" (default: 4) chunks of "--rough_iter" (default: 2) \ iterations, followed by chunks of "--fine_iter" (default: 20) \ iterations, until geom_max_iter is reached in the param file. \ Successful runs will be moved to "completed", crashes/failures will go to \ "bad_castep" and initial res files will go into "input". Running jobs will \ be listed in jobs.txt and those that completed cleanly will be listed \ in finished_cleanly.txt.', epilog=script_epilog ) parser.add_argument('--version', action='version', version='matador version ' + __version__ + '.') parser.add_argument('seed', type=str, nargs='+', help='cell and param seed to use as template for CASTEP calculations OR list of files\ to apply run executable on') parser.add_argument('-nc', '--ncores', type=int, help='number of cores per node per job [DEFAULT=cpu_count/nprocesses]') parser.add_argument('-np', '--nprocesses', type=int, default=1, help='number of concurrent calculations, i.e. number \ of concurrent mpiruns [DEFAULT=1]') parser.add_argument('-nn', '--nnodes', type=int, default=1, help='number of nodes per job, i.e. number of nodes \ using -nc cores [DEFAULT=1].') parser.add_argument('-t', '--max_walltime', type=int, help='maximum walltime in seconds (job will quit early to clean up if specified)') parser.add_argument('-exec', '--executable', type=str, help='specify path to or name of executable (DEFAULT: castep)') parser.add_argument('--no_reopt', action='store_true', default=False, help='do not run geometry optimisation again after first success') parser.add_argument('--redirect', type=str, help='filename to redirect output to, can use $seed macro') parser.add_argument('--mode', type=str, default='castep', help='either castep or generic') parser.add_argument('--noise', action='store_true', help=('add 0.1 A of random noise to positions on every cell, ' 'useful for converging forces (DEFAULT: off)')) parser.add_argument('--squeeze', action='store_true', help='add external pressure to the rough steps of geom opts') parser.add_argument('--ignore_jobs_file', action='store_true', help='whether to use the jobs.txt file to avoid clashes') parser.add_argument('-d', '--debug', action='store_true', default=False, help='debug output') parser.add_argument('-cust', '--custom_params', action='store_true', default=False, help='use custom param file per structure') parser.add_argument('-v', '--verbosity', type=int, default=2, help='integer to set level of verbosity') parser.add_argument('--archer', action='store_true', default=False, help='use aprun over mpirun') parser.add_argument('--slurm', action='store_true', default=False, help='use srun over mpirun') parser.add_argument('--intel', action='store_true', default=False, help='use Intel\'s mpirun') parser.add_argument('--conv_cutoff', action='store_true', default=False, help='run all res files at cutoff defined in cutoff.conv file') parser.add_argument('--conv_kpt', action='store_true', default=False, help='run all res files at kpoint spacings defined in kpt.conv file') parser.add_argument('--memcheck', action='store_true', default=False, help='enable memcheck via castep dryrun') parser.add_argument('--scratch_prefix', type=str, help='specify absolute path prefix for compute dir e.g. ' '--scratch_prefix /scratch/user/ will set the compute directory to /scratch/user/$hostname. ' 'default value is taken from .matadorrc.') parser.add_argument('--maxmem', type=int, help='override max memory for memcheck') parser.add_argument('--killcheck', action='store_true', default=True, help='check for $seed.kill file and quit job if present') parser.add_argument('--kpts_1D', action='store_true', default=False, help='recalculate a 1D kpoint mesh of spacing specified in template cell') parser.add_argument('--spin', type=int, nargs='?', const=5, default=None, help=('if not specified in .cell file, break spin symmetry on first atom using the spin specified by ' 'the user [DEFAULT: 5]')) parser.add_argument('--rough', type=int, default=4, help='choose how many <rough_iter> geometry optimizations \ to perform, decrease if lattice is nearly correct. [DEFAULT: 4].') parser.add_argument('--rough_iter', type=int, default=2, help='choose how many relaxation steps per rough geometry optimization\ to perform, [DEFAULT: 2].') parser.add_argument('--fine_iter', type=int, default=20, help='choose how many relaxation steps per fine geometry optimization\ to perform, [DEFAULT: 20].') parser.add_argument('-l', '--limit', type=int, default=None, help='limit to n structures per run') parser.add_argument('--profile', action='store_true', help='profile code with cProfile') args = parser.parse_args() seed = vars(args)['seed'] kwargs = vars(args) del kwargs['seed'] from matador.config import load_custom_settings settings = load_custom_settings(debug=kwargs.get('debug')).get('run3') if settings is not None: if kwargs['scratch_prefix'] is None: kwargs['scratch_prefix'] = settings.get('scratch_prefix') if kwargs['scratch_prefix'] == '.': kwargs['scratch_prefix'] = None if kwargs['executable'] is None: kwargs['executable'] = settings.get('castep_executable', 'castep') kwargs['run3_settings'] = settings if sum([vars(args)['slurm'], vars(args)['archer'], vars(args)['intel']]) > 1: exit('Incompatible MPI arguments specified, please use at most one of --archer/--intel/--slurm.') if vars(args).get('profile'): import cProfile import pstats from sys import version_info hostname = os.uname()[1] pr = cProfile.Profile() pr.enable() try: runner = BatchRun(seed, **kwargs) runner.spawn() except InputError as exc: print_notify(exc) except RuntimeError: print_notify('Some jobs failed, exiting...') except Exception as exc: raise exc if vars(args).get('profile'): pr.disable() fname = 'run3-{}-{}-{}.{}.{}'.format(__version__, hostname, version_info.major, version_info.minor, version_info.micro) pr.dump_stats(fname + '.prof') with open(fname + '.pstats', 'w') as s: sortby = 'cumulative' ps = pstats.Stats(pr, stream=s).sort_stats(sortby) ps.print_stats()
if __name__ == '__main__': main()