#!/usr/bin/env python """ This is free and unencumbered software released into the public domain. Anyone is free to copy, modify, publish, use, compile, sell, or distribute this software, either in source code form or as a compiled binary, for any purpose, commercial or non-commercial, and by any means. In jurisdictions that recognize copyright laws, the author or authors of this software dedicate any and all copyright interest in the software to the public domain. We make this dedication for the benefit of the public at large and to the detriment of our heirs and successors. We intend this dedication to be an overt act of relinquishment in perpetuity of all present and future rights to this software under copyright law. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. For more information, please refer to [http://unlicense.org] """ import os import sys import shutil import glob import argparse import itertools import multiprocessing import re import subprocess MCELL_PATH = '' RUNNING_MARKER = 'running.marker' FINISHED_MARKER = 'finished.marker' LOGS_DIR = 'logs' class Options: def __init__(self): self.seeds_str = None self.extra_arg = '' self.args_file = None self.max_cores = None self.main_model_file = None def create_argparse(name): parser = argparse.ArgumentParser(description=name + ' Runner') parser.add_argument( '-s', '--seeds', type=str, help='seeds in the form first:last:step, e.g. 1:100:2 will use seeds 1 through 100 in steps of 2, ' 'model must accept "-seed N" argument, ' 'model must make sure that the output directories are different for different seeds, ' 'can be used with argument -x') parser.add_argument( '-x', '--extra-arg', type=str, help='optional extra argument to be passed when -s is used') parser.add_argument( '-a', '--args-file', type=str, help='arguments file where each line contains arguments passed to the main model file, ' 'model must make sure that the output directories are different for different arguments') parser.add_argument('-j', '--max-cores', type=int, help='sets maximum number of cores for running, default is all if -j is not used') parser.add_argument('main_model_file', help='sets path to the MCell4 model') return parser def process_opts(name = 'MCell4'): parser = create_argparse(name) args = parser.parse_args() opts = Options() if args.seeds and args.args_file: sys.exit("Error: only one argument -s/--seeds or -a/--args-file must be specified, not both.") if not args.seeds and not args.args_file: sys.exit("Error: one of arguments -s/--seeds or -a/--args-file must be specified.") if args.seeds: opts.seeds_str = args.seeds if args.extra_arg: opts.extra_arg = args.extra_arg if args.args_file: if os.path.exists(args.args_file): opts.args_file = args.args_file else: sys.exit("Error: file " + args.args_file + " does not exist.") if args.extra_arg: sys.exit("Error: argument -x/-extra-args cannot be used with -a/--args-file.") if args.max_cores: opts.max_cores = args.max_cores if args.main_model_file: if os.path.exists(args.main_model_file): opts.main_model_file = args.main_model_file else: sys.exit("Error: file " + args.main_model_file + " does not exist.") else: sys.exit("Error: main model file must be specified as a positional argument.") return opts def check_prerequisites(): global MCELL_PATH MCELL_PATH = os.environ.get('MCELL_PATH', '') if MCELL_PATH: sys.path.append(os.path.join(MCELL_PATH, 'lib')) else: sys.exit("Error: system variable MCELL_PATH that is used to find the mcell library was not set.") if os.name == 'nt': ext = '.pyd' else: ext = '.so' mcell_so_path = os.path.join(MCELL_PATH, 'lib', 'mcell' + ext) if not os.path.exists(mcell_so_path): sys.exit("Could not find library '" + mcell_so_path + ".") def generate_seeds(seeds_str): seeds_info = seeds_str.split(':') if len(seeds_info) != 3 or \ not seeds_info[0].isdigit() or \ not seeds_info[1].isdigit() or \ not seeds_info[2].isdigit(): sys.exit("Error: invalid seed string, must be in for form min:max:step, given '" + seeds_str + "'.") res = [] for i in range(int(seeds_info[0]), int(seeds_info[1]) + 1, int(seeds_info[2])): res.append(i) return res def prepare_args(opts): if opts.seeds_str: seeds = generate_seeds(opts.seeds_str) return ['-seed ' + str(i) + ' ' + opts.extra_arg for i in seeds ] elif opts.args_file: res = [] with open(opts.args_file, 'r') as f: for line in f: if not line.isspace(): if line.endswith('\n'): res.append(line[:-1]) else: res.append(line[:-1]) return res def run_mcell4(args_str_w_opts): args_str = args_str_w_opts[0] opts = args_str_w_opts[1] cmd_str = sys.executable + ' ' + opts.main_model_file + ' ' cmd_str += args_str print("Running " + cmd_str) args_log = args_str.replace(' ', '_').replace('-', '_').replace('\\', '_').replace('/', '_') log_name = os.path.join( LOGS_DIR, os.path.splitext(os.path.basename(opts.main_model_file))[0] + '_' + args_log + '.mcell4.log') with open(log_name, "w") as f: f.write("DIR:" + os.getcwd() + "\n") f.write("CMD:" + cmd_str + "\n") exit_code = 1 with open(log_name, "a") as f: proc = subprocess.Popen(cmd_str, shell=True, cwd=os.getcwd(), stdout=f, stderr=subprocess.STDOUT) proc.communicate() exit_code = proc.returncode if exit_code != 0: print("MCell4 failed, see '" + os.path.join(os.getcwd(), log_name) + "'.") return exit_code else: return 0 def run_mcell4_parallel(opts, args): # set up the parallel task pool to use all available processors ot the # maximum specified if opts.max_cores: cpu_count = int(opts.max_cores) else: cpu_count = multiprocessing.cpu_count() # create logs directory if not os.path.exists(LOGS_DIR): os.mkdir(LOGS_DIR) # run the jobs pool = multiprocessing.Pool(processes=cpu_count) args_str_w_opts = zip(args, itertools.repeat(opts)) res_codes = pool.map(run_mcell4, args_str_w_opts, 1) num_total = 0 num_failed = 0 for i in range(len(res_codes)): c = res_codes[i] if c != 0: print("MCell run with args '" + args[i] + "' failed with exit code " + str(c) + ".") num_failed += 1 num_total += 1 if num_failed == 0: print("Finished, all runs passed.") return 0 else: print("Finished with errors, " + str(num_failed) + "/" + str(num_total) + " runs failed.") return 1 def my_touch(fname): # emulates 'touch', pathlib.Path(FINISHED_MARKER).touch() may not be available try: if os.path.exists(fname): os.utime(fname, None) else: open(fname, 'a').close() except: print("Warning: could not 'touch' file " + fname + ".") def file_markers_start(): if (os.path.exists(FINISHED_MARKER)): os.remove(FINISHED_MARKER) my_touch(RUNNING_MARKER) def file_markers_finish(): if (os.path.exists(RUNNING_MARKER)): os.remove(RUNNING_MARKER) my_touch(FINISHED_MARKER) if __name__ == '__main__': file_markers_start() check_prerequisites() opts = process_opts() args = prepare_args(opts) exit_code = run_mcell4_parallel(opts, args) file_markers_finish() sys.exit(exit_code)