mcell/utils/mcell4_runner/bng_runner.py

#!/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)