lsst.ctrl.pool.parallel.Batch Class Reference

Inheritance diagram for lsst.ctrl.pool.parallel.Batch:

Public Member Functions
def	__init__ (self, outputDir=None, numNodes=0, numProcsPerNode=0, numCores=0, queue=None, jobName=None, walltime=0.0, dryrun=False, doExec=False, mpiexec="", submit=None, options=None, verbose=False)
	Constructor. More...
def	shebang (self)
def	preamble (self, command, walltime=None)
def	execution (self, command)
def	createScript (self, command, walltime=None)
	Create script to be submitted. More...
def	submitCommand (self, scriptName)
	Return command to submit script. More...
def	run (self, command, walltime=None)
	Run the batch system. More...

Public Attributes
	outputDir
	numNodes
	numProcsPerNode
	numCores
	queue
	jobName
	walltime
	dryrun
	doExec
	mpiexec
	submit
	options
	verbose

Detailed Description

Base class for batch submission

Definition at line 68 of file parallel.py.

Constructor & Destructor Documentation

__init__()

def lsst.ctrl.pool.parallel.Batch.__init__	(		self,
			outputDir = None,
			numNodes = 0,
			numProcsPerNode = 0,
			numCores = 0,
			queue = None,
			jobName = None,
			walltime = 0.0,
			dryrun = False,
			doExec = False,
			mpiexec = "",
			submit = None,
			options = None,
			verbose = False
	)

Constructor.

    @param outputDir: output directory, or None
    @param numNodes: number of nodes
    @param numProcsPerNode: number of processors per node
    @param numCores: number of cores (Slurm, SMP only)
    @param queue: name of queue, or None
    @param jobName: name of job, or None
    @param walltime: maximum wall clock time for job
    @param dryrun: Dry run (only print actions that would be taken)?
    @param doExec: exec the script instead of submitting to batch system?
    @param mpiexec: options for mpiexec
    @param submit: command-line options for batch submission (e.g., for qsub, sbatch)
    @param options: options to append to script header (e.g., #PBS or #SBATCH)
    @param verbose: produce verbose output?

Reimplemented in lsst.ctrl.pool.parallel.SmpBatch.

Definition at line 71 of file parallel.py.

                 verbose=False):
        """!Constructor
 
        @param outputDir: output directory, or None
        @param numNodes: number of nodes
        @param numProcsPerNode: number of processors per node
        @param numCores: number of cores (Slurm, SMP only)
        @param queue: name of queue, or None
        @param jobName: name of job, or None
        @param walltime: maximum wall clock time for job
        @param dryrun: Dry run (only print actions that would be taken)?
        @param doExec: exec the script instead of submitting to batch system?
        @param mpiexec: options for mpiexec
        @param submit: command-line options for batch submission (e.g., for qsub, sbatch)
        @param options: options to append to script header (e.g., #PBS or #SBATCH)
        @param verbose: produce verbose output?
        """
        if (numNodes <= 0 or numProcsPerNode <= 0) and numCores <= 0:
            raise RuntimeError("Must specify numNodes+numProcs or numCores")
 
        self.outputDir = outputDir
        self.numNodes = numNodes
        self.numProcsPerNode = numProcsPerNode
        self.numCores = numCores
        self.queue = queue
        self.jobName = jobName
        self.walltime = walltime
        self.dryrun = dryrun
        self.doExec = doExec
        self.mpiexec = mpiexec
        self.submit = submit
        self.options = options
        self.verbose = verbose
 

Member Function Documentation

createScript()

def lsst.ctrl.pool.parallel.Batch.createScript	(		self,
			command,
			walltime = None
	)

Create script to be submitted.

    @param command: command to run
    @param walltime: maximum wall clock time, overrides value to constructor
    @return name of script on filesystem

Definition at line 138 of file parallel.py.

    def createScript(self, command, walltime=None):
        """!Create script to be submitted
 
        @param command: command to run
        @param walltime: maximum wall clock time, overrides value to constructor
        @return name of script on filesystem
        """
        fd, scriptName = tempfile.mkstemp()
        with os.fdopen(fd, "w") as f:
            f.write(self.shebang())
            f.write('\n')
            f.write(self.preamble(walltime))
            f.write('\n')
            f.write(self.execution(command))
            f.write('\n')
 
        os.chmod(scriptName, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)
        return scriptName
 

execution()

def lsst.ctrl.pool.parallel.Batch.execution	(		self,
			command
	)

Return execution string for script to be submitted

Definition at line 117 of file parallel.py.

    def execution(self, command):
        """Return execution string for script to be submitted"""
        script = [exportEnv(),
                  "umask %03o" % UMASK,
                  "cd %s" % pipes.quote(os.getcwd()),
                  ]
        if self.verbose:
            script += ["echo \"mpiexec is at: $(which mpiexec)\"",
                       "ulimit -a",
                       "echo 'umask: ' $(umask)",
                       "eups list -s",
                       "export",
                       "date",
                       ]
        script += ["mpiexec %s %s" % (self.mpiexec, command)]
        if self.verbose:
            script += ["date",
                       "echo Done.",
                       ]
        return "\n".join(script)
 

preamble()

def lsst.ctrl.pool.parallel.Batch.preamble	(		self,
			command,
			walltime = None
	)

Return preamble string for script to be submitted

Most batch systems allow you to embed submission options as comments here.

Reimplemented in lsst.ctrl.pool.parallel.PbsBatch, lsst.ctrl.pool.parallel.SlurmBatch, and lsst.ctrl.pool.parallel.SmpBatch.

Definition at line 110 of file parallel.py.

    def preamble(self, command, walltime=None):
        """Return preamble string for script to be submitted
 
        Most batch systems allow you to embed submission options as comments here.
        """
        raise NotImplementedError("Not implemented for base class")
 

run()

def lsst.ctrl.pool.parallel.Batch.run	(		self,
			command,
			walltime = None
	)

Run the batch system.

    Creates and submits the script to execute the provided command

    @param command: command to run
    @param walltime: maximum wall clock time, overrides value to constructor
    @return name of script on filesystem

Definition at line 164 of file parallel.py.

    def run(self, command, walltime=None):
        """!Run the batch system
 
        Creates and submits the script to execute the provided command
 
        @param command: command to run
        @param walltime: maximum wall clock time, overrides value to constructor
        @return name of script on filesystem
        """
        scriptName = self.createScript(command, walltime=walltime)
        command = self.submitCommand(scriptName)
        if self.dryrun:
            print("Would run: %s" % command)
        elif self.doExec:
            os.execl(scriptName, scriptName)
        else:
            os.system(command)
        return scriptName
 
 

shebang()

def lsst.ctrl.pool.parallel.Batch.shebang

(

self

)

Definition at line 107 of file parallel.py.

    def shebang(self):
        return "#!/bin/bash"
 

submitCommand()

def lsst.ctrl.pool.parallel.Batch.submitCommand	(		self,
			scriptName
	)

Return command to submit script.

    @param scriptName: name of script on filesystem

Reimplemented in lsst.ctrl.pool.parallel.PbsBatch, lsst.ctrl.pool.parallel.SlurmBatch, and lsst.ctrl.pool.parallel.SmpBatch.

Definition at line 157 of file parallel.py.

    def submitCommand(self, scriptName):
        """!Return command to submit script
 
        @param scriptName: name of script on filesystem
        """
        raise NotImplementedError("No implementation for base class")
 

Member Data Documentation

doExec

lsst.ctrl.pool.parallel.Batch.doExec

Definition at line 101 of file parallel.py.

dryrun

lsst.ctrl.pool.parallel.Batch.dryrun

Definition at line 100 of file parallel.py.

jobName

lsst.ctrl.pool.parallel.Batch.jobName

Definition at line 98 of file parallel.py.

mpiexec

lsst.ctrl.pool.parallel.Batch.mpiexec

Definition at line 102 of file parallel.py.

numCores

lsst.ctrl.pool.parallel.Batch.numCores

Definition at line 96 of file parallel.py.

numNodes

lsst.ctrl.pool.parallel.Batch.numNodes

Definition at line 94 of file parallel.py.

numProcsPerNode

lsst.ctrl.pool.parallel.Batch.numProcsPerNode

Definition at line 95 of file parallel.py.

options

lsst.ctrl.pool.parallel.Batch.options

Definition at line 104 of file parallel.py.

outputDir

lsst.ctrl.pool.parallel.Batch.outputDir

Definition at line 93 of file parallel.py.

queue

lsst.ctrl.pool.parallel.Batch.queue

Definition at line 97 of file parallel.py.

submit

lsst.ctrl.pool.parallel.Batch.submit

Definition at line 103 of file parallel.py.

verbose

lsst.ctrl.pool.parallel.Batch.verbose

Definition at line 105 of file parallel.py.

walltime

lsst.ctrl.pool.parallel.Batch.walltime

Definition at line 99 of file parallel.py.

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

• /j/snowflake/release/lsstsw/stack/lsst-scipipe-5.0.1/Linux64/ctrl_pool/g295839609d+8ef6456700/python/lsst/ctrl/pool/parallel.py