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#!/usr/bin/env python |
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# -*- coding: utf-8 -*- |
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import os |
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import sys |
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import argparse |
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import time as t |
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import numpy as np |
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from os.path import join as pjoin |
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from subprocess import check_output |
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from textwrap import dedent |
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from smartdispatch.command_manager import CommandManager |
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from smartdispatch.queue import Queue |
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from smartdispatch.job_generator import job_generator_factory |
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from smartdispatch import get_available_queues |
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from smartdispatch import utils |
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import logging |
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import smartdispatch |
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LOGS_FOLDERNAME = "SMART_DISPATCH_LOGS" |
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CLUSTER_NAME = utils.detect_cluster() |
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AVAILABLE_QUEUES = get_available_queues(CLUSTER_NAME) |
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LAUNCHER = utils.get_launcher(CLUSTER_NAME) |
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def main(): |
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# Necessary if we want 'logging.info' to appear in stderr. |
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logging.root.setLevel(logging.INFO) |
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args = parse_arguments() |
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path_smartdispatch_logs = pjoin(os.getcwd(), LOGS_FOLDERNAME) |
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# Check if RESUME or LAUNCH mode |
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if args.mode == "launch": |
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if args.commandsFile is not None: |
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# Commands are listed in a file. |
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jobname = os.path.basename(args.commandsFile.name) |
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commands = smartdispatch.get_commands_from_file(args.commandsFile) |
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else: |
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# Command that needs to be parsed and unfolded. |
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command = " ".join(args.commandAndOptions) |
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jobname = smartdispatch.generate_name_from_command(command, max_length=235) |
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commands = smartdispatch.unfold_command(command) |
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commands = smartdispatch.replace_uid_tag(commands) |
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nb_commands = len(commands) # For print at the end |
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elif args.mode == "resume": |
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jobname = args.batch_uid |
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if os.path.isdir(jobname): |
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# We assume `jobname` is `path_job` repo, we extract the real `jobname`. |
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jobname = os.path.basename(os.path.abspath(jobname)) |
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if not os.path.isdir(pjoin(path_smartdispatch_logs, jobname)): |
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raise LookupError("Batch UID ({0}) does not exist! Cannot resume.".format(jobname)) |
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else: |
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raise ValueError("Unknown subcommand!") |
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job_folders_paths = smartdispatch.get_job_folders(path_smartdispatch_logs, jobname) |
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path_job, path_job_logs, path_job_commands = job_folders_paths |
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# Keep a log of the command line in the job folder. |
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command_line = " ".join(sys.argv) |
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smartdispatch.log_command_line(path_job, command_line) |
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command_manager = CommandManager(pjoin(path_job_commands, "commands.txt")) |
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# If resume mode, reset running jobs |
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if args.mode == "launch": |
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command_manager.set_commands_to_run(commands) |
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elif args.mode == "resume": |
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# Verifying if there are failed commands |
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failed_commands = command_manager.get_failed_commands() |
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if len(failed_commands) > 0: |
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FAILED_COMMAND_MESSAGE = dedent("""\ |
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{nb_failed} command(s) are in a failed state. They won't be resumed. |
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Failed commands: |
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{failed_commands} |
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The actual errors can be found in the log folder under: |
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{failed_commands_err_file}""") |
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utils.print_boxed(FAILED_COMMAND_MESSAGE.format( |
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nb_failed=len(failed_commands), |
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failed_commands=''.join(failed_commands), |
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failed_commands_err_file='\n'.join([utils.generate_uid_from_string(c[:-1]) + '.err' for c in failed_commands]) |
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)) |
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if not utils.yes_no_prompt("Do you want to continue?", 'n'): |
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exit() |
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if not args.onlyPending: |
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command_manager.reset_running_commands() |
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nb_commands = command_manager.get_nb_commands_to_run() |
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# If no pool size is specified the number of commands is taken |
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if args.pool is None: |
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args.pool = command_manager.get_nb_commands_to_run(command_line) |
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# Generating all the worker commands |
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COMMAND_STRING = 'cd "{cwd}"; smart_worker.py "{commands_file}" "{log_folder}" '\ |
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'1>> "{log_folder}/worker/$PBS_JOBID\"\"_worker_{{ID}}.o" '\ |
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'2>> "{log_folder}/worker/$PBS_JOBID\"\"_worker_{{ID}}.e" ' |
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COMMAND_STRING = COMMAND_STRING.format(cwd=os.getcwd(), commands_file=command_manager._commands_filename, log_folder=path_job_logs) |
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commands = [COMMAND_STRING.format(ID=i) for i in range(args.pool)] |
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# TODO: use args.memPerNode instead of args.memPerNode |
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queue = Queue(args.queueName, CLUSTER_NAME, args.walltime, args.coresPerNode, args.gpusPerNode, np.inf, args.modules) |
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command_params = {'nb_cores_per_command': args.coresPerCommand, |
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'nb_gpus_per_command': args.gpusPerCommand, |
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'mem_per_command': None # args.memPerCommand |
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} |
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job_generator = job_generator_factory(queue, commands, command_params, CLUSTER_NAME, path_job) |
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pbs_filenames = job_generator.write_pbs_files(path_job_commands) |
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# Launch the jobs |
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print "## {nb_commands} command(s) will be executed in {nb_jobs} job(s) ##".format(nb_commands=nb_commands, nb_jobs=len(pbs_filenames)) |
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print "Batch UID:\n{batch_uid}".format(batch_uid=jobname) |
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if not args.doNotLaunch: |
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jobs_id = [] |
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for pbs_filename in pbs_filenames: |
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qsub_output = check_output('{launcher} {pbs_filename}'.format(launcher=LAUNCHER if args.launcher is None else args.launcher, pbs_filename=pbs_filename), shell=True) |
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jobs_id += [qsub_output.strip()] |
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with utils.open_with_lock(pjoin(path_job, "jobs_id.txt"), 'a') as jobs_id_file: |
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jobs_id_file.writelines(t.strftime("## %Y-%m-%d %H:%M:%S ##\n")) |
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jobs_id_file.writelines("\n".join(jobs_id) + "\n") |
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print "\nJobs id:\n{jobs_id}".format(jobs_id=" ".join(jobs_id)) |
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print "\nLogs, command, and jobs id related to this batch will be in:\n {smartdispatch_folder}".format(smartdispatch_folder=path_job) |
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def parse_arguments(): |
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parser = argparse.ArgumentParser() |
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parser.add_argument('-q', '--queueName', required=True, help='Queue used (ex: qwork@mp2, qfat256@mp2, qfat512@mp2)') |
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parser.add_argument('-t', '--walltime', required=False, help='Set the estimated running time of your jobs using the DD:HH:MM:SS format. Note that they will be killed when this time limit is reached.') |
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parser.add_argument('-L', '--launcher', choices=['qsub', 'msub'], required=False, help='Which launcher to use. Default: qsub') |
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parser.add_argument('-C', '--coresPerNode', type=int, required=False, help='How many cores there are per node.') |
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parser.add_argument('-G', '--gpusPerNode', type=int, required=False, help='How many gpus there are per node.') |
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# parser.add_argument('-M', '--memPerNode', type=int, required=False, help='How much memory there are per node (in Gb).') |
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parser.add_argument('-c', '--coresPerCommand', type=int, required=False, help='How many cores a command needs.', default=1) |
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parser.add_argument('-g', '--gpusPerCommand', type=int, required=False, help='How many gpus a command needs.', default=1) |
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# parser.add_argument('-m', '--memPerCommand', type=float, required=False, help='How much memory a command needs (in Gb).') |
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parser.add_argument('-f', '--commandsFile', type=file, required=False, help='File containing commands to launch. Each command must be on a seperate line. (Replaces commandAndOptions)') |
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parser.add_argument('-l', '--modules', type=str, required=False, help='List of additional modules to load.', nargs='+') |
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parser.add_argument('-x', '--doNotLaunch', action='store_true', help='Creates the QSUB files without launching them.') |
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parser.add_argument('-p', '--pool', type=int, help="Number of workers that will be consuming commands. Default: Nb commands") |
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subparsers = parser.add_subparsers(dest="mode") |
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launch_parser = subparsers.add_parser('launch', help="Launch jobs.") |
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launch_parser.add_argument("commandAndOptions", help="Options for the commands.", nargs=argparse.REMAINDER) |
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resume_parser = subparsers.add_parser('resume', help="Resume jobs from batch UID.") |
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resume_parser.add_argument('--onlyPending', action='store_true', help='Resume only pending commands.') |
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resume_parser.add_argument("batch_uid", help="Batch UID of the jobs to resume.") |
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args = parser.parse_args() |
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# Check for invalid arguments in |
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if args.mode == "launch": |
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if args.commandsFile is None and len(args.commandAndOptions) < 1: |
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parser.error("You need to specify a command to launch.") |
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if args.queueName not in AVAILABLE_QUEUES and ((args.coresPerNode is None and args.gpusPerNode is None) or args.walltime is None): |
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parser.error("Unknown queue, --coresPerNode/--gpusPerNode and --walltime must be set.") |
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return args |
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if __name__ == "__main__": |
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main() |
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SMART-Lab /
smartdispatch
