carputils.job.job.Job Class Reference

A sequence of commands plus the tools to execute them. More...

Public Member Functions
def	__init__ (self, ID)
def	register (self, command, delayed=False)
	Register a command to be executed. More...
def	script (self)
	Generate a bash script running the command sequence. More...
def	submit (self, argv=None)
	Submit the command sequence to the batch system. More...
def	bash (self, cmd, message=None, delayed=False, *args, **kwargs)
	Execute an arbitrary command in the shell. More...
def	mpi (self, cmd, message='Executing MPI Command', *args, **kwargs)
	Execute a command with MPI. More...
def	bench (self, cmd, simname=None, msg=None, *args, **kwargs)
	Execute a BENCH simulation. More...
def	carp (self, cmd, simname=None, polling_subdirs=True, *args, **kwargs)
	Execute an openCARP simulation. More...
def	python (self, cmd, *args, **kwargs)
	Execute a python script. More...
def	meshtool (self, cmd, *args, stdout=None, stderr=None, **kwargs)
	Execute meshtool. More...
def	cvstool (self, cmd, stdout=None, stderr=None, *args, **kwargs)
	Execute cvstool. More...
def	mkdir (self, directory, parents=False, *args, **kwargs)
	Make a directory. More...
def	cp (self, path_from, path_to, cpdir=False, *args, **kwargs)
	Copy a file. More...
def	mv (self, path_from, path_to, *args, **kwargs)
	Move a file. More...
def	rm (self, filename, rmdir=False, *args, **kwargs)
	Remove a file or a directory. More...
def	link (self, target, link_name=None, *args, **kwargs)
	Make a symbolic link. More...
def	gunzip (self, filename, *args, **kwargs)
	Unzip a .gz file. More...
def	meshalyzer (self, geom, *args, **kwargs)
	Run meshalyzer. More...

Public Attributes
	ID

Detailed Description

A sequence of commands plus the tools to execute them.

A job defines a series of commands that can be executed in different ways. Each job has an ID, which defines where the output of its commands is placed, plus a series of commands that can either be run immediately as they are registered or delayed for later execution in different ways.

A job is instantiated with its ID:

>>> job = Job('2015-11-25_important_sim')

and its ID can then be accessed as an attribute:

>>> print job.ID

2015-11-25_important_sim

Commands are then registered for the job with the :meth:~Job.register method:

>>> from carputils.job.command import ShellCommand
>>> job.register(ShellCommand(['ls', '-l'], 'List directory'))

however, for convenience, a number of methods such as :meth:~Job.bash are provided to avoid the need to construct your own commands manually:

>>> job.bash(['ls', '-l'])

On a normal system, commands are executed immeditately once registered (unless the 'delayed' keyword argument is set to True), however on batch systems, commands are stored. The :meth:~Job.script method may then be used to generate a bash script executing the stored commands.

The :meth:~Job.submit method may also be used to automatically generate and submit the job on HPC systems, using the carputils platform.

>>> job.submit()

Users will generally only need to use the convenience submission methods, as the job creation and batch script generation and submission is done automatically by the carputils framework.

Parameters

ID	str The identifier for this job, both the name of the output directory and the identifier on batch systems

Constructor & Destructor Documentation

__init__()

def carputils.job.job.Job.__init__	(		self,
			ID
	)

Member Function Documentation

bash()

def carputils.job.job.Job.bash	(		self,
			cmd,
			message = None,
			delayed = False,
		*	args,
		**	kwargs
	)

Execute an arbitrary command in the shell.

Parameters

cmd	list Command to be executed
message	str, optional Descriptive message to display when running command

bench()

def carputils.job.job.Job.bench	(		self,
			cmd,
			simname = None,
			msg = None,
		*	args,
		**	kwargs
	)

Execute a BENCH simulation.

   Runs a BENCH sim with mpiexec, automatically adding the number of
   processes and command configuration.

Parameters

cmd	list The command to be executed with MPI
simname	str, optional Name to display when running command, defaults to job ID

carp()

def carputils.job.job.Job.carp	(		self,
			cmd,
			simname = None,
			polling_subdirs = True,
		*	args,
		**	kwargs
	)

Execute an openCARP simulation.

   Runs an openCARP sim with mpiexec, automatically adding the number of
   processes and debugger/profiler options from the current run
   configuration.

Parameters

cmd	list The command to be executed with MPI
simname	str, optional Name to display when running command, defaults to job ID

cp()

def carputils.job.job.Job.cp	(		self,
			path_from,
			path_to,
			cpdir = False,
		*	args,
		**	kwargs
	)

Copy a file.

Parameters

path_from	str Path of file to copy
path_to	str Path to copy file to

cvstool()

def carputils.job.job.Job.cvstool	(		self,
			cmd,
			stdout = None,
			stderr = None,
		*	args,
		**	kwargs
	)

Execute cvstool.

Parameters

cmd	list The command to be executed with cvstool

gunzip()

def carputils.job.job.Job.gunzip	(		self,
			filename,
		*	args,
		**	kwargs
	)

Unzip a .gz file.

Parameters

filename

str Path of file to unzip

link()

def carputils.job.job.Job.link	(		self,
			target,
			link_name = None,
		*	args,
		**	kwargs
	)

Make a symbolic link.

Parameters

target	str Target of link (first arg to 'ln -s')
link_name	str, optional Place to put link (second arg to 'ln -s')

meshalyzer()

def carputils.job.job.Job.meshalyzer	(		self,
			geom,
		*	args,
		**	kwargs
	)

Run meshalyzer.

Parameters

geom	str Basename of mesh to visualise
args	str Additional data/display config files to pass as command line arguments to meshalyzer
compsurf	bool, optional If True, generate a surface on the fly (default: False)
monitor	int Delay in seconds before spawning visualization process after job launched (default: none) Return the spawned process.

meshtool()

def carputils.job.job.Job.meshtool	(		self,
			cmd,
		*	args,
			stdout = None,
			stderr = None,
		**	kwargs
	)

Execute meshtool.

Parameters

cmd	list The command to be executed with meshtool

mkdir()

def carputils.job.job.Job.mkdir	(		self,
			directory,
			parents = False,
		*	args,
		**	kwargs
	)

Make a directory.

Parameters

directory	str Path of directory to make
parents	bool, optional True to automatically generate parents (mkdir -p)

mpi()

def carputils.job.job.Job.mpi	(		self,
			cmd,
			message = 'Executing MPI Command',
		*	args,
		**	kwargs
	)

Execute a command with MPI.

   Runs a command with mpiexec, automatically adding the number of
   processes and debugger/profiler options from the current run
   configuration.

Parameters

cmd	list The command to be executed with MPI
message	str, optional Descriptive message to display when running command

mv()

def carputils.job.job.Job.mv	(		self,
			path_from,
			path_to,
		*	args,
		**	kwargs
	)

Move a file.

Parameters

path_from	str Path of file to move
path_to	str Path to move file to

python()

def carputils.job.job.Job.python	(		self,
			cmd,
		*	args,
		**	kwargs
	)

Execute a python script.

# FIXME: update documentation

Runs a pythonCARP sim with mpiexec, automatically adding the number of processes and debugger/profiler options from the current run configuration.

Parameters

cmd	callable The function to be executed with python

register()

def carputils.job.job.Job.register	(		self,
			command,
			delayed = False
	)

Register a command to be executed.

Parameters

command	carputils.job.command.Command The command object
delayed	bool, optional If True, never execute immediately - instead wait until first non- delayed command before processing the whole series

rm()

def carputils.job.job.Job.rm	(		self,
			filename,
			rmdir = False,
		*	args,
		**	kwargs
	)

Remove a file or a directory.

Parameters

filename	str Path of file to remove
rmdir	str Set to True if removing directory

script()

def carputils.job.job.Job.script

(

self

)

Generate a bash script running the command sequence.

Returns

str The content of the batch script

submit()

def carputils.job.job.Job.submit	(		self,
			argv = None
	)

Submit the command sequence to the batch system.

Parameters

argv	list, optional If provided, include the command line in the generated script, for
providence

Member Data Documentation

ID

carputils.job.job.Job.ID

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The documentation for this class was generated from the following file:

• carputils/job/job.py