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Task.pm
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Task.pm
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#!/usr/local/bin/perl -w
##---------------------------------------------------------------------------##
## File:
## @(#) Task.pm
## Author:
## Robert M. Hubley [email protected]
## Description:
## A lightweight job management system for RepeatMasker/RepeatModeler.
## This currently supports using the fork() command to run jobs locally
## or the Sun Grid Engine job batching system for running on clusters.
##
#******************************************************************************
#* Copyright (C) Institute for Systems Biology 2019 Developed by
#* Robert Hubley.
#*
#* This work is licensed under the Open Source License v2.1. To view a copy
#* of this license, visit http://www.opensource.org/licenses/osl-2.1.php or
#* see the license.txt file contained in this distribution.
#*
#******************************************************************************
###############################################################################
# ChangeLog
#
# $Log$
#
###############################################################################
# To Do:
#
#
=head1 NAME
Task
=head1 SYNOPSIS
use Task
Usage:
my $jb = Task->new();
=head1 DESCRIPTION
A class for grouping a set of Job objects for a given task
=head1 INSTANCE METHODS
=cut
package Task;
use strict;
use Data::Dumper;
use Carp;
use Time::Piece;
use Job;
use Storable qw(nstore retrieve);
use LockFile::Simple qw(lock trylock unlock);
use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION);
require Exporter;
@ISA = qw(Exporter);
@EXPORT = qw();
@EXPORT_OK = qw();
%EXPORT_TAGS = ( all => [ @EXPORT_OK ] );
my $CLASS = "Task";
my $DEBUG = 1;
##-------------------------------------------------------------------------##
## Constructor
##-------------------------------------------------------------------------##
sub new
{
my $class = shift;
my $arrayRef = shift;
# Create ourself as a hash
my $this = {};
# Bless this hash in the name of the father, the son...
bless $this, $class;
return $this;
}
##-------------------------------------------------------------------------##
## General Object Methods
##-------------------------------------------------------------------------##
##-------------------------------------------------------------------------##
=head2 get_setName()
Use: my $value = getName();
Use: my $oldValue = setName( $value );
Get/Set the name.
=cut
##-------------------------------------------------------------------------##
sub getName
{
my $obj = shift;
my $value = $obj->{'name'};
return $value;
}
sub setName
{
my $obj = shift;
my $value = shift;
my $oldValue = undef;
$oldValue = $obj->{'name'};
$obj->{'name'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 get_setExecutor()
Use: my $value = getExecutor();
Use: my $oldValue = setExecutor( $value );
Get/Set the executor.
=cut
##-------------------------------------------------------------------------##
sub getExecutor
{
my $obj = shift;
my $value = $obj->{'executor'};
return $value;
}
sub setExecutor
{
my $obj = shift;
my $value = shift;
my $oldValue = undef;
$oldValue = $obj->{'executor'};
$obj->{'executor'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 get_setQueue()
Use: my $value = getQueue();
Use: my $oldValue = setQueue( $value );
Get/Set the queue.
=cut
##-------------------------------------------------------------------------##
sub getQueue
{
my $obj = shift;
my $value = $obj->{'queue'};
return $value;
}
sub setQueue
{
my $obj = shift;
my $value = shift;
my $oldValue = undef;
$oldValue = $obj->{'queue'};
$obj->{'queue'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 get_setMaxLocalJobs()
Use: my $value = getMaxLocalJobs();
Use: my $oldValue = setMaxLocalJobs( $value );
Get/Set the maxLocalJobs.
=cut
##-------------------------------------------------------------------------##
sub getMaxLocalJobs
{
my $obj = shift;
my $value = $obj->{'maxLocalJobs'};
return $value;
}
sub setMaxLocalJobs
{
my $obj = shift;
my $value = shift;
my $oldValue = undef;
$oldValue = $obj->{'maxLocalJobs'};
$obj->{'maxLocalJobs'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 get_setMaxRetries()
Use: my $value = getMaxRetries();
Use: my $oldValue = setMaxRetries( $value );
Get/Set the maxRetries.
=cut
##-------------------------------------------------------------------------##
sub getMaxRetries
{
my $obj = shift;
my $value = $obj->{'maxRetries'};
return $value;
}
sub setMaxRetries
{
my $obj = shift;
my $value = shift;
my $oldValue = undef;
$oldValue = $obj->{'maxRetries'};
$obj->{'maxRetries'} = $value;
return $oldValue;
}
sub job
{
my $obj = shift;
if ( @_ )
{
my $jb = Job->new( @_ );
push @{ $obj->{'jobs'} }, $jb;
}
}
##-------------------------------------------------------------------------##
=head2 execute()
Use: $task->execute();
=cut
##-------------------------------------------------------------------------##
sub execute
{
my $obj = shift;
# Save state of jobs to disk
# Decide where to execute
if ( !defined $obj->{'executor'}
|| $obj->{'executor'} =~ /local/i )
{
$obj->_non_blocking_local_execute();
} elsif ( $obj->{'executor'} =~ /sge/i )
{
if ( !defined $obj->{'queue'} )
{
croak "$CLASS"
. "::execute(): Queue is not set. A queue a required parameter for excutor SGE.\n";
}
$obj->_sge_execute();
} else
{
croak "$CLASS" . "::execute(): Unknown executor \"$obj->{'executor'}\".\n";
}
}
sub getEstimatedCompletionTime()
{
my $obj = shift;
my $avgRuntime = $obj->averageJobRuntime();
my $remainingJobs = $obj->queuedJobsCount();
if ( $avgRuntime <= 0 )
{
#
return ( -1 );
}else {
return( $remainingJobs * $avgRuntime );
}
}
sub queuedJobsCount()
{
my $obj = shift;
my $jobQueue = $obj->_queueStatus();
my $jobsCnt = 0;
foreach my $jobNum ( keys( %{$jobQueue} ) )
{
if ( $jobQueue->{$jobNum}->{'status'} eq "queued" )
{
$jobsCnt++;
}
}
return $jobsCnt;
}
sub averageJobRuntime()
{
my $obj = shift;
my $jobQueue = $obj->_queueStatus();
my $sumRuntimes = 0;
my $finishedJobs = 0;
foreach my $jobNum ( keys( %{$jobQueue} ) )
{
if ( $jobQueue->{$jobNum}->{'status'} eq "finished" )
{
my $runTime = $jobQueue->{$jobNum}->{'end_time'} - $jobQueue->{$jobNum}->{'start_time'};
#print "Runtime: $runTime\n";
$sumRuntimes += $runTime;
$finishedJobs++;
}
}
if ( $finishedJobs == 0 )
{
return -1;
}
return ( $sumRuntimes / $finishedJobs );
}
sub isComplete()
{
my $obj = shift;
my $jobQueue = $obj->_queueStatus();
#print "" . Dumper($jobQueue) . "\n";
my $flagComplete = 1;
foreach my $jobNum ( keys( %{$jobQueue} ) )
{
if ( $jobQueue->{$jobNum}->{'status'} ne "finished" )
{
$flagComplete = 0;
last;
}
}
return $flagComplete;
}
##
## Execute jobs using an Sun Grid Engine queue
##
sub _sge_execute
{
my $obj = shift;
my $date = localtime( time() );
$date =~ s/[ ,\t,\n:]//g;
my $uid = "$$" . ".$date";
my $name = "unnamed_task";
if ( defined $obj->getName()
&& $obj->getName() ne "" )
{
$name = $obj->getName();
}
my $jobDataStore = "$name-$uid.dat";
$obj->{'job_data_store'} = $jobDataStore;
my %jobsQueue = ();
my $jobNum = 0;
foreach my $job ( @{ $obj->{'jobs'} } )
{
# TODO: Allow use of extra flags
# Set -o/-e
# Set -S /bin/bash
# Turn command into script?
my $qsubCmd = "qsub -q " . $obj->{'queue'} . " -N "
. $job->getName()
. " -b y -cwd "
. $job->getCommand()
. "";
my $retVal = `$qsubCmd`;
if ( $retVal =~ /Your job\s+(\d+)\s/ ) {
$jobsQueue{$jobNum}->{'pid'} = $1;
$jobsQueue{$jobNum}->{'status'} = 'queued';
}else
{
# TODO: What do we do if we can't queue
}
$jobNum++;
}
&_saveDataStore( \%jobsQueue, $jobDataStore );
}
##
## _non_blocking_local_execute
##
sub _non_blocking_local_execute
{
my $obj = shift;
my $date = localtime( time() );
$date =~ s/[ ,\t,\n:]//g;
my $uid = "$$" . ".$date";
my $name = "unnamed_task";
if ( defined $obj->getName()
&& $obj->getName() ne "" )
{
$name = $obj->getName();
}
my $jobDataStore = "$name-$uid.dat";
$obj->{'job_data_store'} = $jobDataStore;
my $maxJobs = $obj->getMaxLocalJobs();
if ( !defined $maxJobs || $maxJobs < 1 )
{
croak "$CLASS"
. "::local_execute(): MaxLocalJobs is not defined or is less than 1.\n";
}
my $maxRetries = $obj->getMaxRetries();
$maxRetries = 0 if ( !defined $maxRetries );
my %jobsQueue = ();
my $jobNum = 0;
foreach my $job ( @{ $obj->{'jobs'} } )
{
$jobsQueue{$jobNum}->{'status'} = 'queued';
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'retval'} = undef;
$jobsQueue{$jobNum}->{'retries'} = 0;
$jobsQueue{$jobNum}->{'start_time'} = undef;
$jobsQueue{$jobNum}->{'end_time'} = undef;
$jobNum++;
}
&_saveDataStore( \%jobsQueue, $jobDataStore );
# In order to be non-blocking we fork off a task manager that is
# responsible for processing the job queue. We then keep queue
# state in a "Storable" file for asynchronous status checking.
my $taskManagerPID = fork();
if ( not $taskManagerPID )
{
#
# TASK Manager Code
#
my %children = ();
my $badForkCount = 0;
while ( 1 )
{
if ( keys( %children ) )
{
# Wait for at least one to exit;
print "Waiting for a child to finish or die ( "
. scalar( keys( %children ) )
. " running )\n"
if ( $DEBUG );
my $childPID = wait();
my $retVal = ( $? >> 8 );
# Check if we returned with a valid PID
if ( $childPID > 0 )
{
## Child process is gone
# Find out what batch it was working on
my $jobNum = $children{$childPID};
# Delete it from the children list
delete $children{$childPID};
# Check it's status
if ( $retVal == 0 )
{
print "Child finished. PID=$childPID, "
. "jobNum=$jobNum, RetVal=$retVal\n"
if ( $DEBUG );
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'status'} = 'finished';
$jobsQueue{$jobNum}->{'end_time'} = localtime;
# TODO: Other validation?
} else
{
## Process failed.
print "Child die'd. Organize the funeral for PID=$childPID, "
. "jobNum=$jobNum, RetVal=$retVal\n"
if ( $DEBUG );
# Check how many times we have run it
if ( $jobsQueue{$jobNum}->{'retries'} < $maxRetries )
{
## Under the retry limit...rerun it!
print "Child for batch=$jobNum failed ($retVal) " . "retry#"
. $jobsQueue{$jobNum}->{'retries'} . "\n"
if ( $DEBUG );
$jobsQueue{$jobNum}->{'retries'}++;
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'status'} = 'queued';
print "WARNING: Retrying job ( $jobNum ) [ $retVal ]...\n";
} else
{
## Too many retries.
## We are out of here!
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'status'} = 'failed';
# TODO: Gracefully exit
}
}
&_saveDataStore( \%jobsQueue, $jobDataStore );
}
}
# Gather a list of batches to work on
my @queuedJobs = grep { ( $jobsQueue{$_}->{'status'} eq 'queued' ) }
sort( { $a <=> $b } keys( %jobsQueue ) );
# Decide how many jobs to start
my $numberToStart = scalar( @queuedJobs );
$numberToStart = ( $maxJobs - keys( %children ) )
if ( ( $maxJobs - keys( %children ) ) < $numberToStart );
if ( @queuedJobs == 0 && !keys( %children ) )
{
# Looks like our work here is done
last;
}
#
# Loop through and fork to our hearts
# content.
#
for ( my $k = 0 ; $k < $numberToStart ; $k++ )
{
my $job = $obj->{'jobs'}->[ $queuedJobs[ $k ] ];
print "Forking ( " . $job->getName() . " )\n" if ( $DEBUG );
FORK:
my $pid = fork();
if ( not $pid )
{
# Child
print "Child Running " . $job->getName() . "\n";
system( $job->getCommand() );
exit;
} elsif ( $pid )
{
# Parent
$children{$pid} = $queuedJobs[ $k ];
$jobsQueue{ $queuedJobs[ $k ] }->{'pid'} = $pid;
$jobsQueue{ $queuedJobs[ $k ] }->{'status'} = 'running';
$jobsQueue{ $queuedJobs[ $k ] }->{'start_time'} = localtime;
# TODO: Update job info on disk
} elsif ( $! =~ /No more process/ )
{
$badForkCount++;
sleep 5;
redo FORK;
} else
{
# Weird fork error
print "\nWARNING: Cannot fork...for unknown reasons!\n";
$badForkCount++;
last;
}
}
if ( $numberToStart )
{
&_saveDataStore( \%jobsQueue, $jobDataStore );
}
}
exit;
} elsif ( $taskManagerPID )
{
print "Task manager started (PID=$taskManagerPID). Executing jobs...\n";
} elsif ( $! =~ /No more process/ )
{
# TODO: more sanity
print "No more processes!!!!...\n";
} else
{
# TODO: more sanity
# Weird fork error
print "\nWARNING: Cannot fork...for unknown reasons!\n";
}
}
##
## _queueStatus
##
sub _queueStatus {
my $obj = shift;
my $jobQueue;
if ( !defined $obj->{'executor'}
|| $obj->{'executor'} =~ /local/i )
{
$jobQueue = $obj->_localQueueStatus();
} elsif ( $obj->{'executor'} =~ /sge/i )
{
$jobQueue = $obj->_SGEQueueStatus();
} else
{
croak "$CLASS" . "::execute(): Unknown executor \"$obj->{'executor'}\".\n";
}
return $jobQueue;
}
##
## _localQueueStatus
##
sub _localQueueStatus {
my $obj = shift;
if ( !defined $obj->{'job_data_store'}
|| $obj->{'job_data_store'} eq "" )
{
return undef;
}
my $jobQueue = _retrieveDataStore( $obj->{'job_data_store'} );
if ( scalar( keys( %{$jobQueue} ) ) != scalar( @{ $obj->{'jobs'} } ) )
{
# Either the count of jobs changed since the last execution or
# something went wrong. Either way it's "not complete".
return undef;
}
return $jobQueue;
}
##
## _SGEQueueStatus
##
sub _SGEQueueStatus {
my $obj = shift;
if ( !defined $obj->{'job_data_store'}
|| $obj->{'job_data_store'} eq "" )
{
return undef;
}
my $jobQueue = _retrieveDataStore( $obj->{'job_data_store'} );
if ( scalar( keys( %{$jobQueue} ) ) != scalar( @{ $obj->{'jobs'} } ) )
{
# Either the count of jobs changed since the last execution or
# something went wrong. Either way it's "not complete".
return undef;
}
#
# Update the job queue stats
#
# job-ID prior name user state submit/start at queue slots ja-task-ID
# -----------------------------------------------------------------------------------------------------------------
# 50441 0.25000 rmblast-jo rhubley r 03/14/2019 13:57:31 [email protected] 1
open QSTAT, "qstat |" or die "$CLASS" ."::isComplete(): Could not run qstat: $|\n";
my %qstatStates = ();
while ( <QSTAT> ) {
if ( /^\s*(\d+)\s+\d+\.\d+\s+\S+\s+\S+\s+(\S+)\s+(\S+)\s+(\S+)/ )
{
$qstatStates{$1} = $2;
#my $timeStr = "$3 $4";
}
}
close QSTAT;
for ( my $i = 0; $i <= $#{$obj->{'jobs'}}; $i++ )
{
my $qjob = $jobQueue->{$i};
my $stateCodes = $qstatStates{ $qjob->{'pid'} };
if ( ! defined $stateCodes || $stateCodes eq "" )
{
# Check qacct
my $qacctCmd = "qacct -j " . $qjob->{'pid'} . " 2>&1";
my $status = `$qacctCmd`;
if ( $status =~ /start_time\s+(\S+\s+\S+\s+\d+\s+\S+\s+\d\d\d\d)/ )
{
# E.g Thu Mar 14 16:40:33 2019
my $t = Time::Piece->strptime("$1", "%a %b %d %T %Y");
$qjob->{'start_time'} = $t;
}
if ( $status =~ /end_time\s+(\S+\s+\S+\s+\d+\s+\S+\s+\d\d\d\d)/ )
{
# E.g Thu Mar 14 16:40:33 2019
my $t = Time::Piece->strptime("$1", "%a %b %d %T %Y");
$qjob->{'end_time'} = $t;
}
if ( $status =~ /failed\s+(\d+)/ )
{
if ( $1 == 1 )
{
$qjob->{'status'} = 'failed';
# TODO What else to do here
}else {
$qjob->{'status'} = 'finished';
}
}
if ( $status =~ /exit_status\s+(\d+)/ )
{
$qjob->{'retval'} = $1;
}
}elsif ( $stateCodes =~ /r/ ) {
$qjob->{'status'} = "running";
}elsif ( $stateCodes =~ /q/ ) {
$qjob->{'status'} = "queued";
}
}
&_saveDataStore( $jobQueue, $obj->{'job_data_store'} );
return $jobQueue;
}
##
## _retrieveDataStore
##
sub _retrieveDataStore
{
my $filename = shift;
my $limit = 100;
for ( my $i = 0 ; $i < $limit ; $i++ )
{
if ( lock( $filename ) )
{
my $dataRef = retrieve( $filename );
unlock( $filename );
return $dataRef;
}
}
return undef;
}
##
## _saveDataStore
##
sub _saveDataStore
{
my $dataRef = shift;
my $filename = shift;
my $limit = 100;
for ( my $i = 0 ; $i < $limit ; $i++ )
{
if ( lock( $filename ) )
{
nstore( $dataRef, $filename );
unlock( $filename );
return 1;
}
}
return 0;
}
##########################################
################OLD CODE##################
##########################################
sub blocking_local_execute
{
my $obj = shift;
my $jobDataStore = "task-name-date.dat";
my $maxJobs = $obj->getMaxLocalJobs();
if ( !defined $maxJobs || $maxJobs < 1 )
{
croak "$CLASS"
. "::local_execute(): MaxLocalJobs is not defined or is less than 1.\n";
}
my $maxRetries = $obj->getMaxRetries();
$maxRetries = 0 if ( !defined $maxRetries );
my %jobsQueue = ();
my $jobNum = 0;
foreach my $job ( @{ $obj->{'jobs'} } )
{
$jobsQueue{$jobNum}->{'status'} = 'queued';
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'retval'} = undef;
$jobsQueue{$jobNum}->{'retries'} = 0;
$jobNum++;
}
&_saveDataStore( \%jobsQueue, $jobDataStore );
my %children = ();
my $badForkCount = 0;
while ( 1 )
{
if ( keys( %children ) )
{
# Wait for at least one to exit;
print "Waiting for a child to finish or die ( "
. scalar( keys( %children ) )
. " running )\n"
if ( $DEBUG );
my $childPID = wait();
my $retVal = ( $? >> 8 );
# Check if we returned with a valid PID
if ( $childPID > 0 )
{
## Child process is gone
# Find out what batch it was working on
my $jobNum = $children{$childPID};
# Delete it from the children list
delete $children{$childPID};
# Check it's status
if ( $retVal == 0 )
{
print "Child finished. PID=$childPID, "
. "jobNum=$jobNum, RetVal=$retVal\n"
if ( $DEBUG );
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'status'} = 'finished';
# Other validation
} else
{
## Process failed.
print "Child die'd. Organize the funeral for PID=$childPID, "
. "jobNum=$jobNum, RetVal=$retVal\n"
if ( $DEBUG );
# Check how many times we have run it
if ( $jobsQueue{$jobNum}->{'retries'} < $maxRetries )
{
## Under the retry limit...rerun it!
print "Child for batch=$jobNum failed ($retVal) " . "retry#"
. $jobsQueue{$jobNum}->{'retries'} . "\n"
if ( $DEBUG );
$jobsQueue{$jobNum}->{'retries'}++;
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'status'} = 'queued';
print "WARNING: Retrying job ( $jobNum ) [ $retVal ]...\n";
} else
{
## Too many retries.
## We are out of here!
$jobsQueue{$jobNum}->{'pid'} = -1;
$jobsQueue{$jobNum}->{'status'} = 'failed';
# TODO: Gracefully exit
}
}
&_saveDataStore( \%jobsQueue, $jobDataStore );
}
}
# Gather a list of batches to work on
my @queuedJobs = grep { ( $jobsQueue{$_}->{'status'} eq 'queued' ) }
sort( { $a <=> $b } keys( %jobsQueue ) );
# Decide how many jobs to start
my $numberToStart = scalar( @queuedJobs );
$numberToStart = ( $maxJobs - keys( %children ) )
if ( ( $maxJobs - keys( %children ) ) < $numberToStart );
if ( @queuedJobs == 0 && !keys( %children ) )
{
# Looks like our work here is done
last;
}
#
# Loop through and fork to our hearts
# content.
#
for ( my $k = 0 ; $k < $numberToStart ; $k++ )
{
my $job = $obj->{'jobs'}->[ $queuedJobs[ $k ] ];
print "Forking ( " . $job->getName() . " )\n" if ( $DEBUG );
FORK:
my $pid = fork();
if ( not $pid )
{
# Child
print "Child Running " . $job->getName() . "\n";
system( $job->getCommand() );
exit;
} elsif ( $pid )
{
# Parent
$children{$pid} = $queuedJobs[ $k ];
$jobsQueue{ $queuedJobs[ $k ] }->{'pid'} = $pid;
$jobsQueue{ $queuedJobs[ $k ] }->{'status'} = 'running';
# TODO: Update job info on disk
} elsif ( $! =~ /No more process/ )
{
$badForkCount++;
sleep 5;
redo FORK;
} else
{
# Weird fork error
print "\nWARNING: Cannot fork...for unknown reasons!\n";
$badForkCount++;
last;
}
}
if ( $numberToStart )
{
&_saveDataStore( \%jobsQueue, $jobDataStore );
}
}
print "Done local_execute()\n";
}
1;