lsst.ctrl.pool.parallel.PbsBatch Class Reference

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

Public Member Functions
def	preamble (self, walltime=None)
def	submitCommand (self, scriptName)
	Return command to submit script. 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	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

Batch submission with PBS

Definition at line 184 of file parallel.py.

Member Function Documentation

createScript()

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

inherited

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  )

inherited

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() [1/2]

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

inherited

Return preamble string for script to be submitted

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

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")
 

preamble() [2/2]

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

Definition at line 187 of file parallel.py.

    def preamble(self, walltime=None):
        if walltime is None:
            walltime = self.walltime
        if walltime <= 0:
            raise RuntimeError("Non-positive walltime: %s (did you forget '--time'?)" % (walltime,))
        if self.numNodes <= 0 or self.numProcsPerNode <= 0:
            raise RuntimeError(
                "Number of nodes (--nodes=%d) or number of processors per node (--procs=%d) not set" %
                (self.numNodes, self.numProcsPerNode))
        if self.numCores > 0:
            raise RuntimeError("PBS does not support setting the number of cores")
        return "\n".join([
            "#PBS %s" % self.options if self.options is not None else "",
            "#PBS -l nodes=%d:ppn=%d" % (self.numNodes, self.numProcsPerNode),
            "#PBS -l walltime=%d" % walltime if walltime is not None else "",
            "#PBS -o %s" % self.outputDir if self.outputDir is not None else "",
            "#PBS -N %s" % self.jobName if self.jobName is not None else "",
            "#PBS -q %s" % self.queue if self.queue is not None else "",
            "#PBS -j oe",
            "#PBS -W umask=%03o" % UMASK,
        ])
 

run()

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

inherited

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 )

inherited

Definition at line 107 of file parallel.py.

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

submitCommand()

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

Return command to submit script.

    @param scriptName: name of script on filesystem

Reimplemented from lsst.ctrl.pool.parallel.Batch.

Definition at line 209 of file parallel.py.

    def submitCommand(self, scriptName):
        return "qsub %s -V %s" % (self.submit if self.submit is not None else "", scriptName)
 
 

Member Data Documentation

doExec

lsst.ctrl.pool.parallel.Batch.doExec

inherited

Definition at line 101 of file parallel.py.

dryrun

lsst.ctrl.pool.parallel.Batch.dryrun

inherited

Definition at line 100 of file parallel.py.

jobName

lsst.ctrl.pool.parallel.Batch.jobName

inherited

Definition at line 98 of file parallel.py.

mpiexec

lsst.ctrl.pool.parallel.Batch.mpiexec

inherited

Definition at line 102 of file parallel.py.

numCores

lsst.ctrl.pool.parallel.Batch.numCores

inherited

Definition at line 96 of file parallel.py.

numNodes

lsst.ctrl.pool.parallel.Batch.numNodes

inherited

Definition at line 94 of file parallel.py.

numProcsPerNode

lsst.ctrl.pool.parallel.Batch.numProcsPerNode

inherited

Definition at line 95 of file parallel.py.

options

lsst.ctrl.pool.parallel.Batch.options

inherited

Definition at line 104 of file parallel.py.

outputDir

lsst.ctrl.pool.parallel.Batch.outputDir

inherited

Definition at line 93 of file parallel.py.

queue

lsst.ctrl.pool.parallel.Batch.queue

inherited

Definition at line 97 of file parallel.py.

submit

lsst.ctrl.pool.parallel.Batch.submit

inherited

Definition at line 103 of file parallel.py.

verbose

lsst.ctrl.pool.parallel.Batch.verbose

inherited

Definition at line 105 of file parallel.py.

walltime

lsst.ctrl.pool.parallel.Batch.walltime

inherited

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-0.7.0/Linux64/ctrl_pool/22.0.1-2-g92698f7+dcf3732eb2/python/lsst/ctrl/pool/parallel.py