Source code for stosim.sim.job_creator



This module sets up the stage - with it, you can make a configuration file
for each mix of parameter settings (for each job) that needs to be run.

import sys
import os
from math import ceil
    import configparser
except ImportError:
    import ConfigParser as configparser  # for py2

from . import utils

[docs]def create_jobs(main_conf, simfolder, limit_to={}, more=False): """ Writes a conf file for each run that the parameters in conf suggest. :param ConfigParser conf: main configuration :param string simfolder: relative path to simfolder :param dict limit_to: dict of configuration settings we should limit to (default is an empty dict) :param boolean more: True if runs should be appended to existing data (default is False) """ # these hold all parameter names and the different value configurations, per simulation #comb_options = [] # a list of param names #comb_values = [] # a list of lists with param values - one per job # --------------------------------------------------------------------------------------------- # define some helpful functions def combiner(lists): ''' :param list lists: list of lists with inputs :returns: all possible combinations of the input items in a nested list ''' res = [[]] for l in lists: tmp = [] for i in l: for j in res: tmp.append(j+[i]) res = tmp return res def get_options_values(sim_params, limit_to): ''' :param dict sim_params: dict of configuration for one simulation :param dict limit_to: dict of configuration settings we should limit to :returns: a list of option names and lists of values to use in every possible combination in one simulation. ''' # these hold all parameter names and the different value configurations, per simulation comb_options = [] # a list of param names comb_values = [] # a list of lists with param values - one per job for k, v in sim_params.items(): comb_options.append(k) comb_values.append(v) comb_values = combiner(comb_values) # if we filter the todo-list, remove some configs num = len(comb_values) for i in range(num-1, -1, -1): tmpcv = comb_values[i] matches = True for k, vals in limit_to.items(): if not str(tmpcv[comb_options.index(k)]) in vals: matches = False if not matches: comb_values.pop(i) return comb_options, comb_values def mk_option(opt_spec, sim_conf): ''' helper function to copy values in conf file from meta and control section ''' (opt, isint, sec) = opt_spec from_conf = sim_conf.has_option(sec, opt) and sim_conf or main_conf getter = isint and getattr(from_conf, 'getint') or getattr(from_conf, 'get') return '{}:{}\n'.format(opt, getter(sec, opt)) def write_job(values, sim='', run=1): ''' Write a job conf with these values for this sim ''' job_name = "sim{}_".format(sim) for i in range(len(values)): job_name += "{}{}".format(options[i], values[i]) if i < len(values) - 1: job_name += "_" job_conf_filename = '{}/jobs/{}_run{}.conf'.format(simfolder, job_name, run) job_conf = open(job_conf_filename, 'w') if more: run += utils.runs_in_folder(simfolder, job_name) # these meta sections settings are tricky - they might be overwritten # per simulation and we might want to start where we left off sim_conf = configparser.ConfigParser();"%s/%s" % (simfolder, sim)) job_conf.write('[meta]\n') for dat in [(opt, isint, 'meta') for (opt, isint) in [('name', 0), ('maintainer', 0)]]: job_conf.write(mk_option(dat, sim_conf)) job_conf.write('\n[fjd]\n') exe = mk_option(('executable', 0, 'control'), sim_conf) exe = 'executable: {}/{}\n'.format(os.path.abspath(simfolder), exe.split(':')[1].strip().strip('./')) job_conf.write(exe) # logfile, seed job_conf.write('\n[stosim]\n') logfile = '{}/data/{}/log{}.dat'.format(simfolder, job_name, run) if not os.path.exists('{}/data/{}'.format(simfolder, job_name)): os.mkdir('{}/data/{}'.format(simfolder, job_name)) job_conf.write('logfile: {}\n'.format(logfile)) if main_conf.has_option('seeds', str(run)): seed = main_conf.get('seeds', str(run)) job_conf.write('seed:{}\n'.format(seed)) job_conf.write('\n') # write param values job_conf.write('[params]\n') for i in range(len(values)): job_conf.write('{}:{}\n'.format(options[i], values[i])) job_conf.flush() job_conf.close() # --------------------------------------------------------------------------------------------- # now let's get going # get parameters from subsimulations: combine them with our normal params default_params = {} for param in main_conf.options('params'): default_params[param] = [v.strip() for v in main_conf.get('params', param).split(',')] simulations = {'': default_params} if 'simulations' in main_conf.sections() and main_conf.get('simulations', 'configs') != '': simulations = {} for sim in main_conf.get('simulations', 'configs').split(','): sim = sim.strip() simulations[sim] = default_params.copy() sim_conf = configparser.ConfigParser() sim_job_name = "%s/%s" % (simfolder, sim) if not os.path.exists(sim_job_name): print("[StoSim] Error: Can't find %s !" % sim_job_name) sys.exit() if sim_conf.has_section('params'): for param in sim_conf.options('params'): simulations[sim][param] = [v.strip() for v in sim_conf.get('params', param).split(',')] # now write all the conf files, once for each simulation and once for each seed job_count = 0 for sim in simulations: options, values = get_options_values(simulations[sim], limit_to) for _ in range(len(values)): # get a set of unique values act_values = values.pop() runs = main_conf.getint('control', 'runs') for run in range(1, runs+1): write_job(act_values, sim=sim, run=run) job_count += 1 # if running on PBS, write a PBS job per node we need scheduler = utils.get_scheduler(simfolder) if scheduler == 'pbs': num_cores = utils.get_numcores(simfolder) num_nodes = int(ceil(job_count / float(num_cores))) sim_name = utils.get_simulation_name(simfolder, "{}/stosim.conf".format(simfolder)) wall_time = utils.get_jobtime(simfolder) pbs_job = '''# Shell for the job: #PBS -S /bin/bash # request 1 node, {cores} core(s) #PBS -lnodes=1:cores{cores}:ppn={ppn} # job requires at most n hours wallclock time #PBS -lwalltime={wall_time} cd {path2sim} fjd-recruiter --project {sim_name} hire {cores} # create worker screens python -c "import time; time.sleep({seconds})" # keep PBS job alive fjd-recruiter --project {sim_name} fire # stop worker screens '''.format(cores=num_cores, path2sim=os.path.abspath(simfolder), ppn=num_cores, # processes per node wall_time=wall_time, sim_name=sim_name, seconds=(int(wall_time.split(':')[0]) + 1) * 60 * 60) for node in range(1, num_nodes + 1): pbs_job_file = open('{}/jobs/node{}.pbs'.format(simfolder, node, run), 'w') pbs_job_file.write(pbs_job) pbs_job_file.close()