#!/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 pathlib import argparse import itertools import multiprocessing import re import subprocess from mcell4_runner import file_markers_start, file_markers_finish, generate_seeds TEST_BNGL = 'test.bngl' class Options: def __init__(self): self.seeds_str = None self.bng2pl_path = None self.max_cores = None self.main_model_file = None def create_argparse(): parser = argparse.ArgumentParser(description='MCell4 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, ' 'the output directories are different for different seeds, ODE model ignores this argument') 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('-b', '--bng2pl', type=str, help='sets path to BNG2.pl') parser.add_argument('main_model_file', help='sets path to the BNGL model') return parser def process_opts(): parser = create_argparse() args = parser.parse_args() opts = Options() if args.seeds: opts.seeds_str = args.seeds else: print("Error: argument -s/--seeds must be specified.") sys.exit(1) if args.bng2pl: if os.path.exists(args.bng2pl): opts.bng2pl_path = args.bng2pl else: print("Error: file " + args.bng2pl + " does not exist.") sys.exit(1) else: print("Error: argument -b/--bng2pl must be specified.") sys.exit(1) 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: print("Error: file " + args.main_model_file + " does not exist.") sys.exit(1) else: print("Error: main model file must be specified as a positional argument.") sys.exit(1) return opts def run_bng(abs_dir, opts): os.chdir(abs_dir) cmd_str = 'perl ' + opts.bng2pl_path + ' ' + TEST_BNGL print("Running " + cmd_str + " in " + abs_dir) log_name = opts.main_model_file + '_' + os.path.basename(abs_dir) + '.bng2pl.log' exit_code = 1 with open(log_name, "w") as f: proc = subprocess.Popen(cmd_str, shell=True, cwd=os.getcwd(), stdout=f, stderr=subprocess.STDOUT) proc.communicate() exit_code = proc.returncode with open(log_name, "a") as f: f.write("DIR:" + os.getcwd() + "\n") f.write("CMD:" + cmd_str + "\n") if exit_code != 0: print("BNG2.pl failed, see '" + os.path.join(os.getcwd(), log_name) + "'.") return exit_code else: return 0 def find_in_file(fname, search_for): lines = [] with open(fname, "r") as infile: for line in infile: if search_for in line: return line return '' def replace_in_file(fname, search_for, replace_with): lines = [] with open(fname, "r") as infile: for line in infile: line = line.replace(search_for, replace_with) lines.append(line) with open(fname, "w") as outfile: for line in lines: outfile.write(line) def run_bng_parallel(opts, seeds): # nfsim or ode? # does not handle comments line_nf = find_in_file(opts.main_model_file, 'method=>"nf"') line_ssa = find_in_file(opts.main_model_file, 'method=>"ssa"') if not line_nf and not line_ssa: # ODE dir = os.path.join('bng', 'ode') os.makedirs(dir) shutil.copy(TEST_BNGL, dir) run_bng(dir, opts) else: # NFSim - multiple runs are needed cwd = os.getcwd() dirs = [] for s in seeds: dir = os.path.join('bng', 'nf_' + str(s).zfill(5)) if not os.path.exists(dir): os.makedirs(dir) shutil.copy(opts.main_model_file, os.path.join(dir, TEST_BNGL)) # copy also all other .bngl files from the main file's directory files = glob.iglob(os.path.join(os.path.dirname(opts.main_model_file), "*.bngl")) for file in files: if file != opts.main_model_file and os.path.isfile(file): shutil.copy2(file, dir) # update seed value replace_in_file(os.path.join(dir, TEST_BNGL), 'seed=>1', 'seed=>' + str(s)) dirs.append(os.path.join(cwd, dir)) if opts.max_cores: # maximum number of processes specified cpu_count = int(opts.max_cores) else: cpu_count = multiprocessing.cpu_count() pool = multiprocessing.Pool(processes=cpu_count) # run in parallel res_codes = pool.starmap(run_bng, zip(dirs, itertools.repeat(opts)), 1) num_total = 0 num_failed = 0 for i in range(len(res_codes)): c = res_codes[i] if c != 0: print("BNG run with seed '" + str(seeds[i]) + "' failed with exit code " + str(c) + ".") num_failed += 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 if __name__ == '__main__': file_markers_start() opts = process_opts() seeds = generate_seeds(opts.seeds_str) exit_code = run_bng_parallel(opts, seeds) file_markers_finish() sys.exit(exit_code)