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import re |
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from collections import OrderedDict |
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regex_walltime = re.compile("(\d+:){1,4}") |
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regex_resource_nodes = re.compile("[a-zA-Z0-9]+(:ppn=\d+)?(:gpus=\d+)?(:[a-zA-Z0-9]+)*") |
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regex_resource_pmem = re.compile("[0-9]+(b|kb|mb|gb|tb)?") |
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class PBS(object): |
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""" Offers functionalities to manage a PBS file. |
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For more information about the PBS file format see: |
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`http://docs.adaptivecomputing.com/suite/8-0/basic/help.htm#topics/torque/2-jobs/requestingRes.htm?TocPath=TORQUE Resource Manager|Submitting and managing jobs|Job submission|_____3` |
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Parameters |
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---------- |
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queue_name : str |
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name of the queue on which commands will be executed |
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walltime : str |
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maximum time allocated to execute every commands (DD:HH:MM:SS) |
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""" |
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def __init__(self, queue_name, walltime): |
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if queue_name is None or len(queue_name) == 0: |
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raise ValueError("Queue's name must be provided.") |
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self.queue_name = queue_name |
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self.modules = [] |
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self.commands = [] |
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self.resources = OrderedDict() |
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self.add_resources(walltime=walltime) |
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self.options = OrderedDict() |
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self.add_options(q=queue_name) |
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# Declares that all environment variables in the qsub command's environment are to be exported to the batch job. |
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self.add_options(V="") |
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def add_options(self, **options): |
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""" Adds options to this PBS file. |
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Parameters |
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---------- |
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**options : dict |
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each key is the name of a PBS option (see `Options`) |
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Options |
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------- |
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*A* : account_string |
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Defines the account string associated with the job. |
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*N* : name (up to 64 characters) |
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Declares a name for the job. It must consist of printable, |
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non white space characters with the first character alphabetic. |
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""" |
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for option_name, option_value in options.items(): |
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# If known option, validate it. |
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if option_name.strip('-') == 'N': |
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if len(option_name) > 64: |
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raise ValueError("Maximum number of characters for the name is: 64") |
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self.options["-" + option_name] = option_value |
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def add_resources(self, **resources): |
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""" Adds resources to this PBS file. |
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Parameters |
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---------- |
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**resources : dict |
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each key is the name of a PBS resource (see `Resources`) |
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Resources |
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--------- |
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*nodes* : nodes={<node_count>|<hostname>}[:ppn=<ppn>][:gpus=<gpu>][:<property>[:<property>]...] |
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Specifies how many and what type of nodes to use |
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**nodes={<node_count>|<hostname>}**: type of nodes |
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**ppn=#**: Number of process per node requested for this job |
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**gpus=#**: Number of process per node requested for this job |
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**property**: A string specifying a node's feature |
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*pmem*: pmem=[0-9]+(b|kb|mb|gb|tb) |
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Specifies the maximum amount of physical memory used by any single process of the job. |
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""" |
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for resource_name, resource_value in resources.items(): |
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# If known ressource, validate it. |
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if resource_name == 'nodes': |
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if re.match(regex_resource_nodes, str(resource_value)) is None: |
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raise ValueError("Unknown format for PBS resource: nodes") |
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elif resource_name == 'pmem': |
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if re.match(regex_resource_pmem, str(resource_value)) is None: |
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raise ValueError("Unknown format for PBS resource: pmem") |
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elif resource_name == 'walltime': |
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if re.match(regex_walltime, str(resource_value)) is None: |
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raise ValueError("Unknown format for PBS resource: walltime (dd:hh:mm:ss)") |
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self.resources[resource_name] = resource_value |
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def add_modules_to_load(self, *modules): |
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""" Adds modules to load prior to execute the job on a node. |
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Parameters |
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---------- |
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*modules : list of str |
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each string represents the name of the module to load |
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""" |
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self.modules += modules |
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def add_commands(self, *commands): |
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""" Sets commands to execute on a node. |
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Parameters |
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---------- |
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*commands : list of str |
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each string represents a command that is part of this job |
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""" |
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self.commands += commands |
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def save(self, filename): |
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""" Saves this PBS job to a file. |
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Parameters |
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---------- |
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filename : str |
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specified where to save this PBS file |
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""" |
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with open(filename, 'w') as pbs_file: |
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pbs_file.write(str(self)) |
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def __str__(self): |
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pbs = [] |
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pbs += ["#!/bin/bash"] |
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for option_name, option_value in self.options.items(): |
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if option_value == "": |
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pbs += ["#PBS {0}".format(option_name)] |
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else: |
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pbs += ["#PBS {0} {1}".format(option_name, option_value)] |
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for resource_name, resource_value in self.resources.items(): |
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pbs += ["#PBS -l {0}={1}".format(resource_name, resource_value)] |
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pbs += ["\n# Modules #"] |
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for module in self.modules: |
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pbs += ["module load " + module] |
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pbs += ["\n# Commands #"] |
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pbs += ["{command} &".format(command=command) for command in self.commands] |
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pbs += ["\nwait"] |
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return "\n".join(pbs) |
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SMART-Lab /
smartdispatch
