view commons/pyRepetUnit/components/AbstractClusterLauncher.py @ 31:0ab839023fe4

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#!/usr/bin/env python

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software.  You can  use, 
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info". 
#
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# modify and redistribute granted by the license, users are provided only
# with a limited warranty  and the software's author,  the holder of the
# economic rights,  and the successive licensors  have only  limited
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# with loading,  using,  modifying and/or developing or reproducing the
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# therefore means  that it is reserved for developers  and  experienced
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# knowledge of the CeCILL license and that you accept its terms.

import getopt
import time
import glob
import sys
import os

from commons.core.checker.CheckerException import CheckerException
from commons.core.sql.RepetJob import RepetJob
from commons.core.sql.Job import Job
from commons.core.stat.Stat import Stat
from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher

GENERIC_IN_FILE = "zDUMMYz"


## Abstract class to launch a program in parallel on a cluster.
#
class AbstractClusterLauncher( object ):  #( IClusterLauncher )
     
    def __init__( self ):
        """
        Constructor.
        """
        self._inputDir = ""            # path to the directory with input files
        self._queueName = ""           # name of the queue on the cluster
        self._groupId = ""             # identifier of the group of jobs (groupid)
        self._inputFileSuffix = "fa"   # suffix of the input files (default='fa')
        self._prgAcronym = ""          # acronym of the program to launch
        self._configFile = ""          # name of the configuration file (connect to MySQL)
        self._currentDir = os.getcwd() # path to the current directory
        self._tmpDir = ""              # path to the temporary directory
        self._jobTable = "jobs"        # name of the table recording the jobs
        self._catOutFiles = False      # concatenate output files of all jobs
        self._clean = False            # clean job file, job stdout, job table...
        self._verbose = 1              # verbosity level
        self.jobdb = None              # RepetJob instance
        self.job = Job()               # Job instance
        
        self._nbJobs = 0
        self._cmdLineGenericOptions = "hi:Q:g:S:a:C:d:j:Zcv:"
        self._cmdLineSpecificOptions = ""
        
        self._exeWrapper = "AbstractProgramLauncher.py"
        self._prgLauncher = None
        # list of instances derived from AbstractProgramLauncher()
        # If several program are launched successively in the same job,
        # 'lPrgLaunchers' has to be filled before run().
        self.lPrgLaunchers = []
    
    def setProgramLauncherAttributeFromCmdLine(self, o, a=""):
        self.getProgramLauncherInstance().setASpecificAttributeFromCmdLine(o, a)
      
    def setClusterLauncherAttributeFromCmdLine(self, o, a=""):
        if o == "-h":
            print self.getHelpAsString()
            sys.exit(0)
        elif o == "-i":
            self.setInputDirectory(a)
        elif o == "-Q":
            self.setQueueName(a)
        elif o == "-g":
            self.setGroupIdentifier(a)
        elif o == "-S":
            self.setInputFileSuffix(a)
        elif o == "-a":
            self.setAcronym(a)
        elif o == "-C":
            self.setConfigFile(a)
        elif o == "-d":
            self.setTemporaryDirectory(a)
        elif o == "-j":
            self.setJobTableName(a)
        elif o == "-Z":
            self.setCatOutputFiles()
        elif o == "-c":
            self.setClean()
        elif o == "-v":
            self.setVerbosityLevel(a)

    def setAttributesFromCmdLine(self):
        try:
            opts, args = getopt.getopt(sys.argv[1:], self.getCmdLineOptions())
        except getopt.GetoptError, err:
            print str(err);
            print self.getHelpAsString()
            sys.exit(1)
        for o, a in opts:
            self.setClusterLauncherAttributeFromCmdLine(o, a)
            self.setProgramLauncherAttributeFromCmdLine(o, a)
    
    def setAGenericAttributeFromCmdLine( self, o, a="" ):
        self.setClusterLauncherAttributeFromCmdLine(o, a)
        
    def setASpecificAttributeFromCmdLine( self, o, a="" ):
        self.setProgramLauncherAttributeFromCmdLine(o, a)
        
    def setInputDirectory( self, arg ):
        self._inputDir = arg
        
    def setQueueName( self, arg ):
        self._queueName = arg
        
    def setGroupIdentifier( self, arg ):
        self._groupId = arg
        
    def setInputFileSuffix( self, arg ):
        self._inputFileSuffix = arg
        
    def setAcronym( self, arg ):
        self._prgAcronym = arg
        
    def setConfigFile( self, arg ):
        if os.path.dirname( arg ) == "":
            self._configFile = "%s/%s" % ( os.getcwd(), arg )
        else:
            self._configFile = arg
            
    def setCurrentDirectory( self, arg =os.getcwd()):
        self._currentDir = arg
        
    def setTemporaryDirectory( self, arg ):
        self._tmpDir = arg
        
    def setJobTableName( self, arg ):
        self._jobTable = arg

    def setCatOutputFiles( self ):
        self._catOutFiles = True
   
    def setClean( self):
        self._clean = True
        
    def setVerbosityLevel( self, arg ):
        self._verbose = int(arg)
        
    def setExecutableWrapper( self, arg = "AbstractProgramLauncher.py" ):
        self._exeWrapper = arg

    def setSingleProgramLauncher( self ):
        """
        Set the wrapper and program command-lines of the program launcher.
        Append the program launcher to 'self.lPrgLaunchers'.
        """
        self.getProgramLauncherInstance().setWrapperCommandLine()
        self.getProgramLauncherInstance().setProgramCommandLine()
        self.lPrgLaunchers.append( self.getProgramLauncherInstance() )      
        
    def getGenericHelpAsString( self ):
        string = ""
        string += "usage: %s.py [options]" % (type(self).__name__ )
        string += "\ngeneric options:"
        string += "\n     -h: this help"
        string += "\n     -i: directory with input files (absolute path)"
        string += "\n     -Q: name of the queue on the cluster"
        string += "\n     -g: identifier of the group of jobs (groupid)"
        string += "\n     -S: suffix of the input files (default='fa')"
        string += "\n     -a: acronym of the program to be launched (default='%s')" % ( self.getAcronym() )
        string += "\n     -C: configuration file to connect to MySQL (absolute path or in current dir)"
        string += "\n     -d: temporary directory (absolute path, default=None)"
        string += "\n     -j: table recording the jobs (default='jobs')"
        string += "\n     -c: clean the temporary data"
        string += "\n     -v: verbosity level (default=0/1/2)"
        return string
        
    def getSpecificHelpAsString( self ):
        pass
    
    def getHelpAsString(self):
        return self.getGenericHelpAsString() + self.getSpecificHelpAsString()
    
    def getInputDirectory( self ):
        return self._inputDir
        
    def getQueueName( self ):
        return self._queueName
        
    def getGroupIdentifier( self ):
        return self._groupId
        
    def getInputFileSuffix( self ):
        return self._inputFileSuffix
    
    def getAcronym( self ):
        return self._prgAcronym
        
    def getConfigFile( self ):
        return self._configFile
        
    def getCurrentDirectory( self ):
        return self._currentDir
        
    def getTemporaryDirectory( self ):
        return self._tmpDir
        
    def getJobTableName( self ):
        return self._jobTable
    
    def getCatOutputFiles( self ):
        return self._catOutFiles
    
    def getClean( self ):
        return self._clean
        
    def getVerbosityLevel( self ):
        return self._verbose
    
    def getWrapperName( self ):
        return self.getProgramLauncherInstance().getWrapperName()
    
    def getProgramName( self ):
        return self.getProgramLauncherInstance().getProgramName()
    
    def getPatternToConcatenate( self ):
        return self.getProgramLauncherInstance().getOutputFile().replace( GENERIC_IN_FILE, "*" )
    
    def getProgramLauncherInstance( self ):
        if self._prgLauncher == None:
            self._prgLauncher = AbstractProgramLauncher()
        return self._prgLauncher
    
    def getInputFilesList(self):
        lInFiles = glob.glob("%s/*.%s" % (self._inputDir, self._inputFileSuffix))
        return lInFiles
    
    def getCmdLineOptions(self):
        return "hi:Q:g:S:a:C:d:j:Zcv:"

                        
    def getProgramCommandLineAsString( self ):
        """
        Return the command-line to launch in each job.
        Specified in each wrapper.
        """
        pass
    
    
    def getListFilesToKeep( self ):
        """
        Return the list of files to keep at the end of each job.
        Specified in each wrapper.
        """
        pass
    
    
    def getListFilesToRemove( self ):
        """
        Return the list of files to remove at the end of each job.
        Specified in each wrapper.
        """
        pass
    
    
    def getJobFileNameAsString( self, count ):
        """
        Return the name of the job file as a string.
        @param count: job number (e.g. '1') or '*'
        @type count: integer or string
        """
        jobFile = "ClusterLauncher"
        jobFile += "_groupid%s" % ( self.getGroupIdentifier() )
        if count != "*":
            jobFile += "_job%i" % ( count )
            jobFile += "_time%s" % ( time.strftime("%Y-%m-%d-%H-%M-%S") )
        else:
            jobFile += "_job*"
            jobFile += "_time%s-*" % ( time.strftime("%Y-%m") )
        jobFile += ".py"
        return jobFile
    
    
    def getCmdUpdateJobStatusAsString( self, newStatus ):
        """
        Return the command to update the job status in the table.
        """
        prg = os.environ["REPET_PATH"] + "/bin/srptChangeJobStatus.py"
        cmd = prg
        cmd += " -t %s" % ( self.job.tablename )
        if str(self.job.jobid).isdigit():
            cmd += " -j %s" % ( self.job.jobname )
        else:
            cmd += " -j %s" % ( self.job.jobid )
        cmd += " -g %s" % ( self.job.groupid )
        if self.job.queue != "":
            cmd += " -q %s" % ( self.job.queue )
        cmd += " -s %s" % ( newStatus )
        cmd += " -c %s" % ( self.getConfigFile() )
        cmd += " -v %i" % ( self._verbose )
        return "os.system( \"%s\" )\n" % ( cmd )
    
    
    def getCmdToLaunchWrapper( self, fileName, genericCmd, exeWrapper ):
        """
        Return the launching command as a string.
        Launch the wrapper, retrieve its exit status, update status if error.
        """
        specificCmd = genericCmd.replace( GENERIC_IN_FILE, fileName )
        cmd = ""
        cmd += "print \"LAUNCH: %s\"\n" % ( specificCmd )
        cmd += "sys.stdout.flush()\n"
        cmd += "exitStatus = os.system ( \"%s\" )\n" % ( specificCmd )
        cmd += "if exitStatus != 0:\n"
        cmd += "\tprint \"ERROR: wrapper '%s'" % ( exeWrapper )
        cmd += " returned exit status '%i'\" % ( exitStatus )\n"
        cmd += "\tos.chdir( \"%s\" )\n" % ( self.getTemporaryDirectory() )
        cmd += "\tshutil.move( newDir, '%s' )\n" % ( self.getCurrentDirectory() )
        cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
        cmd += "\tsys.exit(1)\n"
        return cmd
    
    
    def getCmdToKeepFiles( self, fileName, lFilesToKeep ):
        """
        Return the commands to keep the output files.
        """
        cmd = ""
        for f in lFilesToKeep:
            f = f.replace( GENERIC_IN_FILE, fileName )
            cmd += "if not os.path.exists( \"%s\" ):\n" % ( f )
            cmd += "\tprint \"ERROR: output file '%s' doesn't exist\"\n" % ( f )
            cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
            cmd += "\tsys.exit(1)\n"
            cmd += "if not os.path.exists( \"%s/%s\" ):\n" \
                   % ( self._currentDir, f )
            cmd += "\tshutil.copy( \"%s\", \"%s/%s\" )\n" % ( f, self.getCurrentDirectory(), f )
        return cmd
    
    
    def getCmdToRemoveFiles( self, fileName, lFilesToRemove ):
        """
        Return the commands to remove the temporary files.
        """
        cmd = ""
        if lFilesToRemove != []:
            for f in lFilesToRemove:
                f = f.replace( GENERIC_IN_FILE, fileName )
                cmd += "if os.path.exists( \"%s\" ):\n" % ( f )
                cmd += "\tos.remove( \"%s\" )\n" % ( f )
        return cmd
    
    
    def getJobCommandsAsString( self, fileName, jobName, minFreeGigaInTmpDir=1 ):
        """
        Return all the job commands as a string.
        """
        cmd = "#!/usr/bin/env python\n"
        cmd += "\n"
        cmd += "import os\n"
        cmd += "import sys\n"
        cmd += "import shutil\n"
        cmd += "import time\n"
        cmd += "\n"
        cmd += "print \"system:\", os.uname()\n"
        cmd += "beginTime = time.time()\n"
        cmd += "print 'beginTime=%f' % ( beginTime )\n"
        cmd += "\n"
        cmd += self.getCmdUpdateJobStatusAsString( "running" )
        cmd += "\n"
        cmd += "if not os.path.exists( \"%s\" ):\n" % ( self.getTemporaryDirectory() )
        cmd += "\tprint \"ERROR: working dir '%s' doesn't exist\"\n" % ( \
            self.getTemporaryDirectory() )
        cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
        cmd += "\tsys.exit(1)\n"
        cmd += "freeSpace = os.statvfs( \"%s\" )\n" % ( self.getTemporaryDirectory() )
        cmd += "if ( freeSpace.f_bavail * freeSpace.f_frsize ) / 1073741824.0 < %i:\n" % ( minFreeGigaInTmpDir ) # nb blocs * bloc size in bytes > 1 GigaByte ?
        cmd += "\tprint \"ERROR: less than %iGb in '%s'\"\n" % ( minFreeGigaInTmpDir, self.getTemporaryDirectory() )
        cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) )
        cmd += "\tsys.exit(1)\n"
        cmd += "print \"working dir: %s\"\n" % ( self.getTemporaryDirectory() )
        cmd += "sys.stdout.flush()\n"
        cmd += "os.chdir( \"%s\" )\n" % ( self.getTemporaryDirectory() )
        cmd += "\n"
        cmd += "newDir = \"%s_%s_%s\"\n" % ( self.getGroupIdentifier(), jobName, time.strftime("%Y%m%d-%H%M%S") )
        cmd += "if os.path.exists( newDir ):\n"
        cmd += "\tshutil.rmtree( newDir )\n"
        cmd += "os.mkdir( newDir )\n"
        cmd += "os.chdir( newDir )\n"
        cmd += "\n"
        cmd += "if not os.path.exists( \"%s\" ):\n" % ( fileName )
        cmd += "\tos.symlink( \"%s/%s\", \"%s\" )\n" % \
               ( self._inputDir, fileName, fileName )
        cmd += "\n"
        
        for pL in self.lPrgLaunchers:
            cmd += self.getCmdToLaunchWrapper( \
                fileName, \
                pL.getWrapperCommandLine(), \
                "%s.py" % ( type(pL).__name__ ) )
            cmd += "\n"
            cmd += self.getCmdToKeepFiles( fileName, pL.getListFilesToKeep() )
            cmd += "\n"
            cmd += self.getCmdToRemoveFiles( fileName, \
                                             pL.getListFilesToRemove() )
            
        cmd += "if os.path.exists( \"%s\" ):\n" % ( fileName )
        cmd += "\tos.remove( \"%s\" )\n" % ( fileName )
        cmd += "os.chdir( \"..\" )\n"
        cmd += "shutil.rmtree( newDir )\n"
        cmd += self.getCmdUpdateJobStatusAsString( "finished" )
        cmd += "\n"
        cmd += "endTime = time.time()\n"
        cmd += "print 'endTime=%f' % ( endTime)\n"
        cmd += "print 'executionTime=%f' % ( endTime - beginTime )\n"
        cmd += "print \"system:\", os.uname()\n"
        cmd += "sys.exit(0)\n"
        return cmd
    
    def getStatsOfExecutionTime( self ):
        """
        Return a Stat object about the execution time of each job as a
        float expressed in seconds since the epoch, in UTC.
        """
        stat = Stat()
        pattern = "%s/%s*.o*" % ( self.getCurrentDirectory(), \
                                  self.getAcronym() )
        lJobFiles = glob.glob( pattern )
        for f in lJobFiles:
            fH = open( f, "r" )
            while True:
                line = fH.readline()
                if line == "":
                    break
                if "executionTime" in line:
                    stat.add( float(line[:-1].split("=")[1] ) )
                    break
            fH.close()
        return stat
    
    
    def formatGroupidAndTime(self):
        return self.job.groupid + " " + time.strftime("%Y-%m-%d %H:%M:%S") + ""

    def submitJob(self, lInFiles):
        count = 0
        for inFile in lInFiles:
            count += 1
            fileName = os.path.basename(inFile)
            if self._verbose > 1:
                print "processing '%s' # %i..." % (fileName, count)
                sys.stdout.flush()
            
            self.initializeJob(fileName, count)
            time.sleep(0.5)
            exitStatus = self.jobdb.submitJob(self.job)
            if exitStatus != 0:
                print "ERROR while submitting job '%i' to the cluster" % (count)
                sys.exit(1)

    def checkClusterLauncherAttributes( self ):
        if self.getInputDirectory() == "":
            message = "ERROR: missing input directory"
            raise CheckerException(message)
        if not os.path.exists( self.getInputDirectory() ):
            message = "ERROR: input directory '%s' doesn't exist" % ( self.getInputDirectory() )
            raise CheckerException(message)
        if self.getGroupIdentifier() == "":
            message = "ERROR: missing group identifier"
            raise CheckerException(message)
        if self.getAcronym() == "":
            message = "ERROR: missing program acronym"
            raise CheckerException(message)
        if self.getConfigFile() == "":
            message = "ERROR: missing config file to access MySQL"
            raise CheckerException(message)
        if not os.path.exists( self.getConfigFile() ):
            message = "ERROR: config file '%s' doesn't exist" % ( self.getConfigFile() )
            raise CheckerException(message)   
        if self.getTemporaryDirectory() == "":
            self.setTemporaryDirectory(self._currentDir)
    
    def checkGenericAttributes( self ):
        self.checkClusterLauncherAttributes()
        
    def checkProgramLauncherAttributes( self ):
        self.getProgramLauncherInstance().checkSpecificAttributes()
    
    def checkSpecificAttributes( self ):
        self.checkProgramLauncherAttributes()
        
    def start( self ):
            
        if self.lPrgLaunchers == []:
            self.setSingleProgramLauncher()
        for pL in self.lPrgLaunchers:
            if pL.getWrapperCommandLine() == "":
                string = "ERROR: wrapper command is empty !"
                print string
                sys.exit(1)
            if pL.getProgramCommandLine() == "":
                string = "ERROR: program command is empty !"
                print string
                sys.exit(1)
        self.checkProgramAvailability()
        
        try:
            self.checkProgramLauncherAttributes()
        except CheckerException, msg:
            print msg
            print self.getHelpAsString()
            sys.exit(1)
        
        if self.getVerbosityLevel() > 0:
            string = "START %s" % ( type(self).__name__ )
            print string
        self.job.tablename = self.getJobTableName()
        self.job.groupid = self.getGroupIdentifier()
        tokens = self.getQueueName().replace("'","").split(" ")
        self.job.setQueue( tokens[0] )
        if len(tokens) > 1:
            lResources = tokens[1:]
            self.job.lResources = lResources
        if self.getVerbosityLevel() > 0:
            print "groupid: %s" % ( self.getGroupIdentifier() )
        self.jobdb = RepetJob( cfgFileName=self.getConfigFile() )
        if self.jobdb.hasUnfinishedJob( self.job.tablename, \
                                          self.job.groupid ):
            self.jobdb.waitJobGroup( self.job.tablename, self.job.groupid )
            return
        self.jobdb.cleanJobGroup( self.job.tablename, self.job.groupid )
        sys.stdout.flush()
   
    def end( self ):
        if self.getClean():
            self.removeAllJobFiles()
            self.removeAllJobStdouts()
            self.removeAllJobStderrs()
            
        if self.getCatOutputFiles():
            self.catOutputFiles()
        
        self.jobdb.close()
        
        if self.getVerbosityLevel() > 0:
            string = "END %s" % ( type(self).__name__ )
            print string
        sys.stdout.flush()
        
    def run( self ):
        try:
            self.checkClusterLauncherAttributes()
        except CheckerException, msg:
            print msg
            print self.getHelpAsString()
            sys.exit(1)
            
        self.start()
        
        lInFiles = self.getInputFilesList()
        self._nbJobs = len(lInFiles)
        
        if self._verbose > 0:
            string = "submitting " + str(self._nbJobs) +  " jobs... " + self.formatGroupidAndTime() 
            print string; sys.stdout.flush()
        
        self.submitJob(lInFiles)
        
        if self._verbose > 0:        
            string = "waiting for jobs... " + self.formatGroupidAndTime() 
            print string; sys.stdout.flush()
        
        self.jobdb.waitJobGroup( self.job.tablename, self.job.groupid )
        
        if self._verbose > 0:
            string = "all jobs completed ! " + self.formatGroupidAndTime() 
            print string; sys.stdout.flush()
            statsExecutionTime = self.getStatsOfExecutionTime()
            print "execution time of all jobs (seconds): %f" % statsExecutionTime.getSum()
            print "execution time per job: %s" % statsExecutionTime.string()
            sys.stdout.flush()
            
        self.jobdb.cleanJobGroup( self.job.tablename, self.job.groupid )
        
        self.end()