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#! /usr/bin/env perl |
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=pod |
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=head1 NAME |
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Schedule::SGELK |
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=head1 SYNOPSIS |
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A module for submitting jobs to an SGE queue. |
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use Schedule::SGELK |
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my $sge=Schedule::SGELK->new(verbose=>1,numnodes=>5,numcpus=>8,workingdir=>"SGE/",waitForEachJobToStart=>1); |
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$sge->set("jobname","thisisaname"); |
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# run a series of jobs and wait for them all to finish |
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my $job=$sge->pleaseExecute("sleep 60"); |
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my $job2=$sge->pleaseExecute("sleep 60"); |
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$sge->wrapItUp(); |
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# or you can specify which jobs to wait for |
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$sge->waitOnJobs([$job,$job2],1); # 1 means wait for all jobs to finish; 0 to wait for any free node |
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# or in one step |
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$sge->pleaseExecute_andWait("sleep 60"); |
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A quick test for this module is the following one-liner |
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perl -MSchedule::SGELK -e '$sge=Schedule::SGELK->new(numnodes=>5); for(1..3){$sge->pleaseExecute("sleep 3");}$sge->wrapItUp();' |
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Another quick test is to use the test() method, if you want to see standardized text output (see test() below) |
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perl -MSchedule::SGELK -e '$sge=Schedule::SGELK->new(-numnodes=>2,-numcpus=>8); $sge->test(\%tmpSettings);' |
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=head1 DESCRIPTION |
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A module for submitting jobs to an SGE queue. Monitoring is |
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performed using a combination of monitoring files |
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written to the hard drive and qstat. |
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Submitting is performed internally by making a perl script. |
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=head1 AUTHOR |
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Author: Lee Katz |
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=cut |
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package Schedule::SGELK; |
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use strict; |
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use warnings; |
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use Data::Dumper; |
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use File::Basename qw/basename/; |
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use File::Spec; |
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use File::Slurp qw/read_file write_file/; |
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use File::Temp qw/tempdir/; |
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1
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542
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use String::Escape qw/escape/; |
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5769
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1
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1
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511
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use version 0.77; |
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1924
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54
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55
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our $VERSION = version->declare("v1.5"); |
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57
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my $has_threads=eval{ |
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return 0; # this isn't working yet |
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require threads; |
60
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return 1; |
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}; |
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63
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# some global variables |
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my @jobsToClean=(); |
65
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my @jobsToMonitor=(); |
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my $numSlots=0; # number of slots that are being used now |
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68
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4
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4
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0
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916
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sub logmsg {local $0=basename $0;my $FH = *STDOUT; print $FH "$0: ".(caller(1))[3].": @_\n";} |
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80
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4
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437
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69
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local $SIG{'__DIE__'} = sub { my $e = $_[0]; $e =~ s/(at [^\s]+? line \d+\.$)/\nStopped $1/; die("$0: ".(caller(1))[3].": ".$e); }; |
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local $SIG{INT} = sub{ cleanAllJobs(); }; |
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72
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# to be called when the script exits |
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sub cleanAllJobs{ |
74
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1
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50
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1
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0
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16
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return if(!@jobsToClean); |
75
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1
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14
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logmsg "Cleaning all jobs"; |
76
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1
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12
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for (@jobsToClean){ |
77
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2
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12
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cleanAJob($_); |
78
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} |
79
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} |
80
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END{ |
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cleanAllJobs(); |
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} |
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84
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=pod |
85
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86
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=head2 METHODS |
87
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88
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=over |
89
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90
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=item sub new |
91
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92
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create a new instance of a scheduler. |
93
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Arguments and their defaults: |
94
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numnodes=>50 maximum nodes to use |
95
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numcpus=>128 maximum cpus that will be used per node in a script |
96
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maxslots=>9999 maximum slots that you can use. Useful if you want to be limited by total slots instead of nodes or CPUs. E.g. {numnodes=>100,numcpus=>1,maxslots=>20} |
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verbose=>0 |
98
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workingdir=>$ENV{PWD} a directory that all nodes can access to read/write jobs and log files |
99
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waitForEachJobToStart=>0 Allow each job to start as it's run (0), or to wait until the qstat sees the job before continuing (1) |
100
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jobname=>... This is the name given to the job when you view it with qstat. By default, it will be named after the script that calls this module. |
101
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warn_on_error=>1 This will make the script give a warning instead of exiting |
102
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qsubxopts=>... These are extra options to pass to qsub. E.g., {qsubxopts=>"-V"} Options are overwritten by appending them to the within-script options. Therefore this is not the best way to choose a different queue but it is a way to change a job name or the number of processors. |
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noqsub=>1 Force performing a system call instead of using qsub |
104
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queue=>all.q Choose the queue to use for a new job. Default: all.q |
105
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106
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Examples: |
107
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{numnodes=>100,numcpus=>1,maxslots=>50} # for many small jobs |
108
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{numnodes=>5,numcpus=>8,maxslots=>40} # for a few larger jobs (note: maxslots should be >= numnodes * maxslots |
109
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110
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=back |
111
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112
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=cut |
113
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114
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sub new{ |
115
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1
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1
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1
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1610
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my($class,%args)=@_; |
116
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1
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3
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my $self=bless{},$class; |
117
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118
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# just start with verbosity = 0. This avoids an error in the >= checks |
119
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1
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6
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$self->{'settings'}={}; |
120
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1
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2
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$self->{'error'}=""; |
121
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1
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2
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$self->{'exit_code'}=0; |
122
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123
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# load up if we know what we have |
124
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1
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5
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foreach my $key (keys %args) { |
125
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6
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8
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my $nodash=$key; |
126
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6
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11
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$nodash =~ s/^\-//; |
127
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6
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11
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$self->set($nodash,$args{$key}); |
128
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} |
129
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130
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# set defaults if they are not set |
131
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1
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4
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my %default=(numnodes=>50,numcpus=>128,verbose=>0,waitForEachJobToStart=>0,maxslots=>9999,queue=>"all.q",scheduler=>"SGE"); |
132
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1
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5
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while(my($key,$value)=each(%default)){ |
133
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7
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100
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11
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$self->settings($key,$value) if(!defined($self->settings($key))); |
134
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} |
135
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1
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50
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2
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if(!$self->get("workingdir")){ |
136
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0
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0
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$self->set("workingdir",$self->mktempdir()); |
137
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0
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0
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logmsg "Working directory not set. Using ".$self->get("workingdir"); |
138
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} |
139
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140
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# executables |
141
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1
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3
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for(qw(qsub qstat qdel)){ |
142
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# See if it exists |
143
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3
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17510
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my $exec=`which $_ 2>/dev/null`; |
144
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3
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50
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77
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$exec="" if $?; |
145
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3
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14
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chomp($exec); |
146
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3
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101
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$self->set($_,$exec); |
147
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148
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3
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50
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26
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$self->set("scheduler","") if(!$exec); |
149
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} |
150
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151
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# See if SGE is present |
152
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1
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50
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33
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75
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if($ENV{SGE_ROOT} && -e $ENV{SGE_ROOT}){ |
153
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0
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0
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$self->set("scheduler","SGE"); |
154
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} else{ |
155
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1
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19
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logmsg "Env variable \$SGE_ROOT is not set. I will not use SGE"; |
156
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1
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39
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$self->set("scheduler",""); |
157
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1
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14
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$self->set("qsub",""); |
158
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} |
159
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160
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# Remove the scheduler option if the user explicitly |
161
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# chooses not to use it. |
162
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1
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50
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37
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$self->set("scheduler","") if($self->get("noqsub")); |
163
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164
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1
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61
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return $self; |
165
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} |
166
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167
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=pod |
168
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169
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=over |
170
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171
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=item sub error($msg,$exit_code) or error() |
172
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173
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Get or set the error. Can set the error code too, if provided. |
174
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175
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=back |
176
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177
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=cut |
178
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179
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# Sets the error and returns the previous error message. |
180
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# Or, simply returns the current error message. |
181
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sub error{ |
182
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0
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0
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1
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0
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my($self,$msg,$exit_code)=@_; |
183
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0
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0
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0
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return $self->{error} if(!defined($msg)); |
184
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0
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0
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my $oldmsg=$self->{error}; |
185
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0
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0
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$self->{error}=$msg; |
186
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0
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0
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0
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$self->{exit_code}=$exit_code if(defined($exit_code)); |
187
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0
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0
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return $oldmsg; |
188
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} |
189
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=pod |
190
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191
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=over |
192
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193
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=item sub set() get() settings() |
194
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195
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Get or set a setting. All settings are listed under sub new(). |
196
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If a setting is provided without a value, then nothing new will be set, |
197
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and only the value of the specified setting will be returned. |
198
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199
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=back |
200
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201
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=cut |
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sub set{ |
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1
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my($self,$key,$value)=@_; |
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100
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100
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252
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if(defined($key) && defined($value)){ |
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18
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$self->{'settings'}{$key}=$value; |
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} elsif (defined($key)){ |
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return $self->{'settings'}{$key}; |
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} |
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return %{$self->{'settings'}} if wantarray; |
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0
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0
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20
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return $self->{'settings'}; |
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} |
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# renaming of sub set() |
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sub get{ |
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1
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my($self,@args)=@_; |
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return $self->set(@args); |
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} |
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# renaming of sub set() |
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sub settings{ |
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14
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1
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95
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my($self,@args)=@_; |
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14
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48
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return $self->set(@args); |
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} |
223
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224
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=pod |
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226
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=over |
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228
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=item pleaseExecute() |
229
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This is the main method. It will submit a command to the cluster. |
231
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$sge->set("jobname","a_nu_start"); |
232
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$sge->pleaseExecute("someCommand with parameters"); |
233
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234
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If you are already occupying more than numnodes, then it will pause before |
235
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executing the command. It will also create many files under workingdir, so |
236
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be sure to specify it. The workingdir is the current directory by default. |
237
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238
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You can also specify temporary settings for this one command with a referenced hash. |
239
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240
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$sge->pleaseExecute("someCommand with parameters",{jobname=>"a_nu_start",numcpus=>2}); |
241
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242
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=back |
243
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244
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=cut |
245
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246
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sub pleaseExecute{ |
247
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2
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2
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1
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64
|
my($self,$cmd,$tmpSettings)=@_; |
248
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2
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308
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local $0=basename $0; |
249
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2
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11
|
my %settings=%{ $self->settings }; |
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2
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16
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250
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251
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# read in any temporary settings for this command |
252
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2
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50
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15
|
$tmpSettings={} if(!defined($tmpSettings)); |
253
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2
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19
|
$settings{$_}=$$tmpSettings{$_} for(keys(%$tmpSettings)); |
254
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255
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# default settings for undefined settings |
256
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2
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12
|
my $jobid=-1; # -1 is an error state |
257
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2
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33
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50
|
$settings{jobname}||="sgelk$0"; |
258
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2
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33
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44
|
$settings{logfile}||="$0.log"; |
259
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2
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50
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8
|
$settings{numcpus}||=1; |
260
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2
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50
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21
|
$settings{timeout}||=60; # how long we will wait for qsub to start |
261
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2
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50
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43
|
return 0 if($cmd=~/^\s*$/); # if there's no command, then no worries |
262
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263
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2
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29
|
$self->waitOnJobs(\@jobsToMonitor,0); # wait until the job can be submitted |
264
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265
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2
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75
|
my $rand=int(rand(999999)); |
266
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2
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10
|
my $tempdir=$settings{workingdir}; |
267
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|
# create a perl script with the literal command in it |
268
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2
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11
|
my $script="$tempdir/qsub.$rand.pl"; |
269
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270
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2
|
50
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32
|
my $prefix=($0 eq '-e')?"STDIN":$0; |
271
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2
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10
|
$prefix="$settings{workingdir}/$prefix.$rand"; |
272
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2
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26
|
my($submitted,$running,$finished,$died,$output)=("$prefix.submitted", "$prefix.running", "$prefix.finished","$prefix.died","$prefix.log"); |
273
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|
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274
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2
|
|
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|
|
8497
|
my $perl=`which perl`; chomp($perl); |
|
2
|
|
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|
|
58
|
|
275
|
2
|
50
|
|
|
|
349
|
open(SCRIPT,">",$script) or die "Could not write to temporary script $script: $!"; |
276
|
2
|
|
|
|
|
57
|
print SCRIPT "#! $perl\n\n"; |
277
|
|
|
|
|
|
|
# It has SGE params in it. |
278
|
2
|
|
|
|
|
23
|
print SCRIPT "#\$ -N $settings{jobname}\n"; |
279
|
2
|
|
|
|
|
48
|
print SCRIPT "#\$ -S $perl\n"; |
280
|
2
|
|
|
|
|
18
|
print SCRIPT "#\$ -V\n"; |
281
|
2
|
|
|
|
|
11
|
print SCRIPT "#\$ -wd $ENV{PWD}\n"; |
282
|
2
|
|
|
|
|
60
|
print SCRIPT "#\$ -pe smp $settings{numcpus}\n"; |
283
|
2
|
|
|
|
|
10
|
print SCRIPT "#\$ -o $output\n"; |
284
|
2
|
|
|
|
|
6
|
print SCRIPT "#\$ -e $output\n"; |
285
|
2
|
|
|
|
|
22
|
print SCRIPT "#\$ -q $settings{queue}\n"; |
286
|
|
|
|
|
|
|
# qsubxopts get to be in here first but will be overwritten by later qsubopts below |
287
|
2
|
50
|
|
|
|
29
|
if(my $opts=$settings{qsubxopts}){ |
288
|
0
|
|
|
|
|
0
|
print SCRIPT "# options specified by qsubxopts are in the next line:\n"; |
289
|
0
|
|
|
|
|
0
|
print SCRIPT "#\$ $opts\n"; |
290
|
|
|
|
|
|
|
} |
291
|
2
|
|
|
|
|
25
|
print SCRIPT "use strict;\nuse warnings;\n"; |
292
|
2
|
|
|
|
|
11
|
print SCRIPT "use File::Slurp qw/read_file write_file/;\n"; |
293
|
|
|
|
|
|
|
|
294
|
|
|
|
|
|
|
# announces that it was submitted |
295
|
2
|
|
|
|
|
121
|
my $sanitized=escape('qqbackslash',$cmd); |
296
|
2
|
|
|
|
|
667
|
print SCRIPT "write_file('$submitted',$sanitized);\n"; |
297
|
|
|
|
|
|
|
# it runs the command |
298
|
2
|
|
|
|
|
15
|
print SCRIPT "write_file('$running',$sanitized);\n"; |
299
|
2
|
|
|
|
|
14
|
print SCRIPT "system($sanitized);\n"; |
300
|
|
|
|
|
|
|
# let the script try one more time if it fails |
301
|
|
|
|
|
|
|
#print SCRIPT "system($sanitized) if \$?;\n"; |
302
|
|
|
|
|
|
|
# print a parsable error if the script dies. This error will be in $output and in file $died |
303
|
2
|
|
|
|
|
20
|
print SCRIPT <
|
304
|
|
|
|
|
|
|
if(\$?){ |
305
|
|
|
|
|
|
|
my \$error=\"QSUB ERROR\\n\$?\\n\$!\"; |
306
|
|
|
|
|
|
|
write_file('$died',$sanitized); |
307
|
|
|
|
|
|
|
write_file('$died',{append=>1},"\\n\$error\\n"); |
308
|
|
|
|
|
|
|
die \$error; |
309
|
|
|
|
|
|
|
} |
310
|
|
|
|
|
|
|
END |
311
|
|
|
|
|
|
|
# announces when it is finished |
312
|
2
|
|
|
|
|
27
|
print SCRIPT "write_file('$finished',$sanitized);\n"; |
313
|
2
|
|
|
|
|
132
|
close SCRIPT; |
314
|
2
|
50
|
|
|
|
7502
|
system("touch $script"); die if $?; # make the system close the script. Why isn't Perl closing it? |
|
2
|
|
|
|
|
118
|
|
315
|
|
|
|
|
|
|
#system("cat $script");sleep 60;die; |
316
|
|
|
|
|
|
|
|
317
|
|
|
|
|
|
|
# now run the script and get the jobid |
318
|
2
|
|
|
|
|
198
|
my %return=(submitted=>$submitted,running=>$running,finished=>$finished,died=>$died,tempdir=>$tempdir,output=>$output,cmd=>$cmd,script=>$script,jobname=>$settings{jobname},numcpus=>$settings{numcpus}); |
319
|
2
|
|
|
|
|
69
|
my $qsub=$self->get("qsub"); |
320
|
2
|
50
|
|
|
|
19
|
if(!$settings{scheduler}){ |
321
|
2
|
|
|
|
|
64
|
my $job=command("$perl $script",$has_threads,\%settings); |
322
|
2
|
50
|
|
|
|
44
|
$return{thread}=$job if($has_threads); |
323
|
2
|
50
|
|
|
|
65
|
$return{jobid}=$job->tid if($has_threads); |
324
|
2
|
50
|
|
|
|
56
|
push(@jobsToClean,\%return) if(!$self->settings("keep")); |
325
|
2
|
|
|
|
|
17
|
push(@jobsToMonitor,\%return); |
326
|
2
|
|
|
|
|
39
|
$numSlots+=$settings{numcpus}; # claim these cpus |
327
|
2
|
50
|
|
|
|
33
|
return %return if wantarray; |
328
|
2
|
|
|
|
|
358
|
return \%return; |
329
|
|
|
|
|
|
|
} |
330
|
|
|
|
|
|
|
|
331
|
|
|
|
|
|
|
# At this point, qsub is on this computer. Submit the job. |
332
|
0
|
|
|
|
|
0
|
my $out=`$qsub $script`; chomp($out); |
|
0
|
|
|
|
|
0
|
|
333
|
0
|
0
|
|
|
|
0
|
if($out=~/Your job (\d+)/){ |
334
|
0
|
|
|
|
|
0
|
$jobid=$1; |
335
|
0
|
|
|
|
|
0
|
$out.=" from $script"; |
336
|
0
|
0
|
|
|
|
0
|
logmsg $out if($settings{verbose}); |
337
|
|
|
|
|
|
|
} else { |
338
|
0
|
|
|
|
|
0
|
logmsg "WARNING: the last job submitted did not have an obvious jobid. It can't be tracked!"; |
339
|
|
|
|
|
|
|
} |
340
|
|
|
|
|
|
|
|
341
|
|
|
|
|
|
|
# monitor for the script to be running before moving on |
342
|
0
|
|
|
|
|
0
|
my $started=time; |
343
|
0
|
|
|
|
|
0
|
while(!-e $submitted){ |
344
|
0
|
0
|
|
|
|
0
|
last if(!$self->settings("waitForEachJobToStart")); |
345
|
0
|
|
|
|
|
0
|
sleep 1; |
346
|
0
|
0
|
|
|
|
0
|
die "Command timed out!\n $cmd" if((time-$started)>$settings{timeout}); |
347
|
0
|
0
|
|
|
|
0
|
die "Command resulted in an error. qstat -j $jobid for more info\n $cmd" if($self->jobStatus($jobid) eq 'Eqw'); |
348
|
|
|
|
|
|
|
} |
349
|
|
|
|
|
|
|
|
350
|
|
|
|
|
|
|
# TODO create a link from the jobid to the random id |
351
|
|
|
|
|
|
|
|
352
|
0
|
|
|
|
|
0
|
$return{jobid}=$jobid; |
353
|
0
|
0
|
|
|
|
0
|
push(@jobsToClean,\%return) if(!$self->settings("keep")); |
354
|
0
|
|
|
|
|
0
|
push(@jobsToMonitor,\%return); |
355
|
0
|
|
|
|
|
0
|
$numSlots+=$settings{numcpus}; # claim these cpus |
356
|
0
|
0
|
|
|
|
0
|
return %return if wantarray; |
357
|
0
|
|
|
|
|
0
|
return \%return; |
358
|
|
|
|
|
|
|
} |
359
|
|
|
|
|
|
|
|
360
|
|
|
|
|
|
|
=pod |
361
|
|
|
|
|
|
|
|
362
|
|
|
|
|
|
|
=over |
363
|
|
|
|
|
|
|
|
364
|
|
|
|
|
|
|
=item pleaseExecute_andWait() |
365
|
|
|
|
|
|
|
|
366
|
|
|
|
|
|
|
Exact same as pleaseExecute(), except it will wait for the command to finish |
367
|
|
|
|
|
|
|
before continuing. Internally calls pleaseExecute() and then waitOnJobs(). |
368
|
|
|
|
|
|
|
However one key difference between pleaseExecute() and this sub is that you can |
369
|
|
|
|
|
|
|
give a list of commands. |
370
|
|
|
|
|
|
|
|
371
|
|
|
|
|
|
|
# this will take 100 seconds because all commands have to finish. |
372
|
|
|
|
|
|
|
$sge->pleaseExecute_andWait(["sleep 60","sleep 100","sleep 3"]); |
373
|
|
|
|
|
|
|
|
374
|
|
|
|
|
|
|
=back |
375
|
|
|
|
|
|
|
|
376
|
|
|
|
|
|
|
=cut |
377
|
|
|
|
|
|
|
|
378
|
|
|
|
|
|
|
sub pleaseExecute_andWait{ |
379
|
0
|
|
|
0
|
1
|
0
|
my($self,$cmd)=@_; |
380
|
0
|
|
|
|
|
0
|
my %settings=$self->settings; |
381
|
0
|
|
|
|
|
0
|
my $mustfinish=$self->settings("mustfinish"); # should be restored later |
382
|
0
|
|
|
|
|
0
|
$self->set("mustfinish",0); |
383
|
0
|
0
|
|
|
|
0
|
$cmd=[$cmd] if(ref($cmd) eq ""); # let cmd be a string but turn it into a list internally |
384
|
0
|
|
|
|
|
0
|
my(@jobid); |
385
|
0
|
|
|
|
|
0
|
for(@$cmd){ |
386
|
0
|
|
|
|
|
0
|
my $jobid=$self->pleaseExecute($_); |
387
|
0
|
|
|
|
|
0
|
push(@jobid,$jobid); |
388
|
0
|
|
|
|
|
0
|
$self->waitOnJobs(\@jobid); |
389
|
|
|
|
|
|
|
} |
390
|
0
|
|
|
|
|
0
|
$self->waitOnJobs(\@jobid,1); |
391
|
|
|
|
|
|
|
} |
392
|
|
|
|
|
|
|
|
393
|
|
|
|
|
|
|
=pod |
394
|
|
|
|
|
|
|
|
395
|
|
|
|
|
|
|
=over |
396
|
|
|
|
|
|
|
|
397
|
|
|
|
|
|
|
=item checkJob($jobHash) |
398
|
|
|
|
|
|
|
|
399
|
|
|
|
|
|
|
Checks the status of a given job. The job variable is obtained from pleaseExecute(). |
400
|
|
|
|
|
|
|
$self->error can be set if there is an error in the job. Return values: |
401
|
|
|
|
|
|
|
1 for finished; 0 for still running or hasn't started; -1 for error. |
402
|
|
|
|
|
|
|
|
403
|
|
|
|
|
|
|
=back |
404
|
|
|
|
|
|
|
|
405
|
|
|
|
|
|
|
=cut |
406
|
|
|
|
|
|
|
|
407
|
|
|
|
|
|
|
sub checkJob{ |
408
|
0
|
|
|
0
|
1
|
0
|
my($self,$job)=@_; |
409
|
|
|
|
|
|
|
# See what the job status is {jobid} for fast checking |
410
|
0
|
|
|
|
|
0
|
my $status=$self->jobStatus($$job{jobid}); |
411
|
0
|
0
|
|
|
|
0
|
if($status eq 'qw'){ # queued but not running |
|
|
0
|
|
|
|
|
|
|
|
0
|
|
|
|
|
|
412
|
0
|
|
|
|
|
0
|
return 0; |
413
|
|
|
|
|
|
|
} elsif($status eq 'Eqw'){ # error |
414
|
0
|
|
|
|
|
0
|
$self->error("Command resulted in an error. qstat -j $$job{jobid} for more info\n $$job{cmd}"); |
415
|
0
|
|
|
|
|
0
|
return -1; |
416
|
|
|
|
|
|
|
} elsif($status=~/[rt]/){ # running or is delayed |
417
|
0
|
|
|
|
|
0
|
return 0; |
418
|
|
|
|
|
|
|
} |
419
|
|
|
|
|
|
|
|
420
|
|
|
|
|
|
|
# look at files to check on the job status, for slower checking. |
421
|
|
|
|
|
|
|
# see if the job has even started: {submitted} |
422
|
0
|
0
|
|
|
|
0
|
return 0 if(!-e $$job{submitted}); |
423
|
|
|
|
|
|
|
# if the job finished, then great! {finished} |
424
|
0
|
0
|
|
|
|
0
|
return 1 if(-e $$job{finished}); |
425
|
0
|
0
|
|
|
|
0
|
return 1 if(!keys(%$job)); # sometimes a job is blank... why? |
426
|
|
|
|
|
|
|
# if the job died |
427
|
0
|
0
|
|
|
|
0
|
if(-e $$job{died}){ |
428
|
0
|
|
|
|
|
0
|
my @content=read_file($$job{output}); |
429
|
0
|
|
|
|
|
0
|
chomp(@content); |
430
|
0
|
|
|
|
|
0
|
$self->error(join("\n",@content[-3..-1])); |
431
|
0
|
|
|
|
|
0
|
return -1; |
432
|
|
|
|
|
|
|
} |
433
|
|
|
|
|
|
|
# It's running if the die-file isn't there and if the running file is there |
434
|
0
|
0
|
|
|
|
0
|
return 0 if(-e $$job{running}); |
435
|
0
|
|
|
|
|
0
|
logmsg "ERROR: Could not understand what the status is of job $$job{jobid}!\n".Dumper($job); |
436
|
0
|
|
|
|
|
0
|
return -1; |
437
|
|
|
|
|
|
|
} |
438
|
|
|
|
|
|
|
|
439
|
|
|
|
|
|
|
=pod |
440
|
|
|
|
|
|
|
|
441
|
|
|
|
|
|
|
=over |
442
|
|
|
|
|
|
|
|
443
|
|
|
|
|
|
|
=item jobStatus(jobid) |
444
|
|
|
|
|
|
|
|
445
|
|
|
|
|
|
|
Given an SGE job id, it returns its qstat status |
446
|
|
|
|
|
|
|
|
447
|
|
|
|
|
|
|
=back |
448
|
|
|
|
|
|
|
|
449
|
|
|
|
|
|
|
=cut |
450
|
|
|
|
|
|
|
|
451
|
|
|
|
|
|
|
sub jobStatus{ |
452
|
0
|
|
|
0
|
1
|
0
|
my($self,$jobid)=@_; |
453
|
0
|
|
|
|
|
0
|
my $state=0; |
454
|
0
|
|
0
|
|
|
0
|
$jobid||=0; |
455
|
0
|
|
|
|
|
0
|
my $qstat=$self->qstat; |
456
|
0
|
|
|
|
|
0
|
for(split(/\n/,$qstat)){ |
457
|
0
|
|
|
|
|
0
|
my @F=split /\s+/; |
458
|
0
|
0
|
|
|
|
0
|
if($F[0] eq $jobid){ |
459
|
0
|
|
|
|
|
0
|
$state=$F[4]; |
460
|
|
|
|
|
|
|
} |
461
|
|
|
|
|
|
|
} |
462
|
0
|
|
|
|
|
0
|
close QSTAT; |
463
|
0
|
|
|
|
|
0
|
return $state; |
464
|
|
|
|
|
|
|
} |
465
|
|
|
|
|
|
|
|
466
|
|
|
|
|
|
|
=pod |
467
|
|
|
|
|
|
|
|
468
|
|
|
|
|
|
|
=over |
469
|
|
|
|
|
|
|
|
470
|
|
|
|
|
|
|
=item qstat |
471
|
|
|
|
|
|
|
|
472
|
|
|
|
|
|
|
Runs qstat and caches the result for one second. Or, returns the cached result of qstat |
473
|
|
|
|
|
|
|
|
474
|
|
|
|
|
|
|
=back |
475
|
|
|
|
|
|
|
|
476
|
|
|
|
|
|
|
=cut |
477
|
|
|
|
|
|
|
|
478
|
|
|
|
|
|
|
sub qstat{ |
479
|
0
|
|
|
0
|
1
|
0
|
my($self)=@_; |
480
|
|
|
|
|
|
|
# return the cached value if it was just accessed a second ago |
481
|
|
|
|
|
|
|
#return $self->get("qstat") if(defined($self->get("qstat")) && $self->get("qstat_timestamp") <= time - 1); |
482
|
|
|
|
|
|
|
|
483
|
0
|
|
|
|
|
0
|
my $content=""; |
484
|
0
|
0
|
|
|
|
0
|
open(QSTAT,"qstat|") or die "ERROR: could not execute qstat! $!"; |
485
|
0
|
|
|
|
|
0
|
while(my $line=){ |
486
|
0
|
|
|
|
|
0
|
$line=~s/^\s+|\s+$//g; |
487
|
0
|
|
|
|
|
0
|
$content.="$line\n"; |
488
|
|
|
|
|
|
|
} |
489
|
0
|
|
|
|
|
0
|
close QSTAT; |
490
|
0
|
|
|
|
|
0
|
$self->set("qstat",$content); |
491
|
0
|
|
|
|
|
0
|
$self->set("qstat_timestamp",time); |
492
|
0
|
|
|
|
|
0
|
return $self->get("qstat"); |
493
|
|
|
|
|
|
|
} |
494
|
|
|
|
|
|
|
|
495
|
|
|
|
|
|
|
=pod |
496
|
|
|
|
|
|
|
|
497
|
|
|
|
|
|
|
=over |
498
|
|
|
|
|
|
|
|
499
|
|
|
|
|
|
|
=item wrapItUp() |
500
|
|
|
|
|
|
|
|
501
|
|
|
|
|
|
|
Waits on all jobs to finish before pausing the program. |
502
|
|
|
|
|
|
|
Calls waitOnJobs or joinAllThreads internally. Does not take any parameters. |
503
|
|
|
|
|
|
|
|
504
|
|
|
|
|
|
|
=back |
505
|
|
|
|
|
|
|
|
506
|
|
|
|
|
|
|
=cut |
507
|
|
|
|
|
|
|
|
508
|
|
|
|
|
|
|
# Wait on all jobs to finish and clear out the queue. |
509
|
|
|
|
|
|
|
sub wrapItUp{ |
510
|
1
|
|
|
1
|
1
|
66
|
my($self)=@_; |
511
|
1
|
50
|
|
|
|
37
|
if($self->get("scheduler")){ |
|
|
50
|
|
|
|
|
|
512
|
0
|
|
|
|
|
0
|
$self->waitOnJobs(\@jobsToMonitor,1); |
513
|
|
|
|
|
|
|
} elsif($has_threads){ |
514
|
0
|
|
|
|
|
0
|
$self->joinAllThreads(\@jobsToMonitor,1); |
515
|
|
|
|
|
|
|
} |
516
|
1
|
|
|
|
|
12
|
return 1; |
517
|
|
|
|
|
|
|
} |
518
|
|
|
|
|
|
|
|
519
|
|
|
|
|
|
|
=pod |
520
|
|
|
|
|
|
|
|
521
|
|
|
|
|
|
|
=over |
522
|
|
|
|
|
|
|
|
523
|
|
|
|
|
|
|
=item joinAllThreads($jobList) |
524
|
|
|
|
|
|
|
|
525
|
|
|
|
|
|
|
Joins all threads. This is if you have ithreads and if the scheduler is not set. |
526
|
|
|
|
|
|
|
For example, if you specify noqsub or if qsub executable is not found. |
527
|
|
|
|
|
|
|
|
528
|
|
|
|
|
|
|
=back |
529
|
|
|
|
|
|
|
|
530
|
|
|
|
|
|
|
=cut |
531
|
|
|
|
|
|
|
|
532
|
|
|
|
|
|
|
sub joinAllThreads{ |
533
|
0
|
|
|
0
|
1
|
0
|
my($self,$job)=@_; |
534
|
|
|
|
|
|
|
|
535
|
|
|
|
|
|
|
JOINALLTHREADS: |
536
|
0
|
|
|
|
|
0
|
for my $j(@$job){ |
537
|
0
|
0
|
|
|
|
0
|
next if(!$$j{thread}); |
538
|
0
|
0
|
0
|
|
|
0
|
next if($$j{thread} && !$$j{thread}->is_joinable); |
539
|
0
|
|
|
|
|
0
|
logmsg "Joining TID".$$j{jobid}; |
540
|
0
|
|
|
|
|
0
|
$$j{thread}->join; |
541
|
0
|
|
|
|
|
0
|
$$j{thread}=0; |
542
|
|
|
|
|
|
|
} |
543
|
|
|
|
|
|
|
|
544
|
|
|
|
|
|
|
# clean out the joined jobs |
545
|
0
|
|
|
|
|
0
|
my @newjob; |
546
|
0
|
|
|
|
|
0
|
for my $j(@$job){ |
547
|
0
|
0
|
|
|
|
0
|
push(@newjob,$j) if($$j{thread}); |
548
|
|
|
|
|
|
|
} |
549
|
0
|
|
|
|
|
0
|
$job=\@newjob; |
550
|
|
|
|
|
|
|
|
551
|
|
|
|
|
|
|
# if there is still something in @$job, then go for another round |
552
|
0
|
0
|
|
|
|
0
|
if(@$job){ |
553
|
0
|
|
|
|
|
0
|
logmsg "Waiting for ".scalar(@$job)." more jobs to finish..."; |
554
|
0
|
|
|
|
|
0
|
sleep 1; |
555
|
0
|
|
|
|
|
0
|
goto JOINALLTHREADS; |
556
|
|
|
|
|
|
|
} |
557
|
|
|
|
|
|
|
|
558
|
|
|
|
|
|
|
} |
559
|
|
|
|
|
|
|
|
560
|
|
|
|
|
|
|
|
561
|
|
|
|
|
|
|
=pod |
562
|
|
|
|
|
|
|
|
563
|
|
|
|
|
|
|
=over |
564
|
|
|
|
|
|
|
|
565
|
|
|
|
|
|
|
=item waitOnJobs($jobList,[$mustFinish]) |
566
|
|
|
|
|
|
|
|
567
|
|
|
|
|
|
|
Waits on all given jobs to finish. The job list are jobs as given by pleaseExecute(). |
568
|
|
|
|
|
|
|
If $mustFinish evaluates to true, then the program will pause until |
569
|
|
|
|
|
|
|
all jobs are finished. |
570
|
|
|
|
|
|
|
Calls on checkJob() internally. Will die with an error message if a job dies. |
571
|
|
|
|
|
|
|
|
572
|
|
|
|
|
|
|
=back |
573
|
|
|
|
|
|
|
|
574
|
|
|
|
|
|
|
=cut |
575
|
|
|
|
|
|
|
|
576
|
|
|
|
|
|
|
# Wait on enough jobs to finish before returning. |
577
|
|
|
|
|
|
|
# If a job finishes, splice it from the job array. |
578
|
|
|
|
|
|
|
sub waitOnJobs{ |
579
|
3
|
|
|
3
|
1
|
26
|
my($self,$job,$mustfinish)=@_; |
580
|
|
|
|
|
|
|
|
581
|
|
|
|
|
|
|
# if there is no qsub, then every job is only going one at a time |
582
|
3
|
|
|
|
|
13
|
my $qsub=$self->get("qsub"); |
583
|
3
|
50
|
|
|
|
15
|
return @$job if(!$qsub); |
584
|
|
|
|
|
|
|
|
585
|
0
|
|
|
|
|
0
|
my %settings=$self->settings; |
586
|
0
|
0
|
|
|
|
0
|
$settings{mustfinish}=$mustfinish if(defined($mustfinish)); |
587
|
0
|
0
|
|
|
|
0
|
if($settings{verbose}){ |
588
|
0
|
0
|
|
|
|
0
|
logmsg "We have reached node capacity ($settings{numnodes})! Waiting for a job to finish." if(@$job >= $settings{numnodes}); |
589
|
0
|
0
|
|
|
|
0
|
logmsg "We have reached slot capacity ($settings{maxslots})! Waiting for a job to finish." if($numSlots >= $settings{maxslots}); |
590
|
|
|
|
|
|
|
} |
591
|
0
|
|
|
|
|
0
|
while(@$job > 0){ |
592
|
0
|
|
|
|
|
0
|
for(my $i=0;$i<@$job;$i++){ |
593
|
0
|
|
0
|
|
|
0
|
$$job[$i]{jobid}||=0; |
594
|
0
|
|
|
|
|
0
|
my $state=$self->checkJob($$job[$i]); |
595
|
0
|
0
|
|
|
|
0
|
if($state==1){ |
|
|
0
|
|
|
|
|
|
596
|
0
|
0
|
|
|
|
0
|
logmsg "A job finished: $$job[$i]{jobname} ($$job[$i]{jobid})" if($settings{verbose}); |
597
|
0
|
|
|
|
|
0
|
$numSlots = $numSlots - $$job[$i]{numcpus}; # not using these slots anymore |
598
|
0
|
|
|
|
|
0
|
splice(@$job,$i,1); |
599
|
0
|
|
|
|
|
0
|
last; |
600
|
|
|
|
|
|
|
} elsif($state==-1){ |
601
|
0
|
|
|
|
|
0
|
my $msg="A job failed ($$job[$i]{jobname} [$$job[$i]{jobid}]! Look at $$job[$i]{output} for more details.\nError message was ".$self->error()."\n".Dumper($$job[$i]); |
602
|
0
|
0
|
|
|
|
0
|
die $msg if(!$settings{warn_on_error}); |
603
|
|
|
|
|
|
|
# just print the warning if the script didn't die and forget about this dead job |
604
|
0
|
|
|
|
|
0
|
logmsg $msg; |
605
|
0
|
|
|
|
|
0
|
$numSlots = $numSlots - $$job[$i]{numcpus}; # not using these slots anymore |
606
|
0
|
|
|
|
|
0
|
$self->error($msg); |
607
|
0
|
|
|
|
|
0
|
splice(@$job,$i,1); |
608
|
0
|
|
|
|
|
0
|
last; |
609
|
|
|
|
|
|
|
} |
610
|
|
|
|
|
|
|
} |
611
|
0
|
|
|
|
|
0
|
sleep 1; |
612
|
|
|
|
|
|
|
# break out if you don't have to finish yet but you can still add in another job |
613
|
0
|
0
|
0
|
|
|
0
|
last if(!$settings{mustfinish} && @$job<$settings{numnodes} && $numSlots<$settings{maxslots}); |
|
|
|
0
|
|
|
|
|
614
|
|
|
|
|
|
|
} |
615
|
0
|
|
|
|
|
0
|
return @$job; |
616
|
|
|
|
|
|
|
} |
617
|
|
|
|
|
|
|
|
618
|
|
|
|
|
|
|
=pod |
619
|
|
|
|
|
|
|
|
620
|
|
|
|
|
|
|
=over |
621
|
|
|
|
|
|
|
|
622
|
|
|
|
|
|
|
=item cleanAJob |
623
|
|
|
|
|
|
|
|
624
|
|
|
|
|
|
|
This is internally used for cleaning up files after a job is done. |
625
|
|
|
|
|
|
|
Do not use externally. |
626
|
|
|
|
|
|
|
|
627
|
|
|
|
|
|
|
=back |
628
|
|
|
|
|
|
|
|
629
|
|
|
|
|
|
|
=cut |
630
|
|
|
|
|
|
|
|
631
|
|
|
|
|
|
|
sub cleanAJob{ |
632
|
2
|
|
|
2
|
1
|
6
|
my($job)=@_; |
633
|
2
|
|
50
|
|
|
69
|
my $jobid=$$job{jobid} || return 0; |
634
|
0
|
|
|
|
|
0
|
logmsg $jobid; |
635
|
0
|
|
|
|
|
0
|
for (qw(running submitted finished output script died)){ |
636
|
0
|
|
|
|
|
0
|
unlink $$job{$_}; |
637
|
|
|
|
|
|
|
} |
638
|
|
|
|
|
|
|
|
639
|
0
|
|
|
|
|
0
|
system("qdel $$job{jobid} 2>/dev/null | grep -v 'does not exist'"); |
640
|
|
|
|
|
|
|
#die "Internal error" if $?; |
641
|
0
|
|
|
|
|
0
|
return 1; |
642
|
|
|
|
|
|
|
} |
643
|
|
|
|
|
|
|
|
644
|
|
|
|
|
|
|
sub mktempdir{ |
645
|
0
|
|
|
0
|
0
|
0
|
my ($self,$settings) = @_; |
646
|
0
|
|
0
|
|
|
0
|
$settings||={}; |
647
|
|
|
|
|
|
|
# SGELK.22623.XXXXX |
648
|
|
|
|
|
|
|
#my $tempdir_path = File::Spec->join(File::Spec->tmpdir(), (split("::",(caller(1))[3]))[1].".$$.XXXXX"); |
649
|
0
|
0
|
|
|
|
0
|
mkdir "./.SGELK" if(!-d "./.SGELK"); |
650
|
0
|
0
|
|
|
|
0
|
die if $?; |
651
|
0
|
|
|
|
|
0
|
my $tempdir_path = File::Spec->join("./.SGELK",(split("::",(caller(1))[3]))[1].".$$.XXXXX"); |
652
|
0
|
|
|
|
|
0
|
my $tempdir = tempdir($tempdir_path, CLEANUP => !($$settings{keep})); |
653
|
0
|
|
|
|
|
0
|
return $tempdir; |
654
|
|
|
|
|
|
|
} |
655
|
|
|
|
|
|
|
|
656
|
|
|
|
|
|
|
sub command{ |
657
|
2
|
|
|
2
|
0
|
15
|
my($cmd,$use_threads,$settings)=@_; |
658
|
2
|
|
|
|
|
11
|
my $job=0; |
659
|
2
|
50
|
|
|
|
17
|
if($use_threads){ |
660
|
0
|
|
|
|
|
0
|
$job=threads->new(\&command,$cmd,0,$settings); |
661
|
|
|
|
|
|
|
} else { |
662
|
2
|
|
|
|
|
68
|
logmsg "Running $cmd"; |
663
|
2
|
|
|
|
|
158766
|
system($cmd); |
664
|
2
|
50
|
|
|
|
152
|
die "ERROR with command: $!\n $cmd" if $?; |
665
|
|
|
|
|
|
|
} |
666
|
|
|
|
|
|
|
|
667
|
2
|
|
|
|
|
112
|
return $job; |
668
|
|
|
|
|
|
|
} |
669
|
|
|
|
|
|
|
|
670
|
|
|
|
|
|
|
=pod |
671
|
|
|
|
|
|
|
|
672
|
|
|
|
|
|
|
=over |
673
|
|
|
|
|
|
|
|
674
|
|
|
|
|
|
|
=item test |
675
|
|
|
|
|
|
|
|
676
|
|
|
|
|
|
|
Use this method to perform a test. The test sends |
677
|
|
|
|
|
|
|
ten jobs that print debugging information. |
678
|
|
|
|
|
|
|
|
679
|
|
|
|
|
|
|
You can give an optional hash argument to send other settings as described in new(). |
680
|
|
|
|
|
|
|
|
681
|
|
|
|
|
|
|
perl -MSchedule::SGELK -e '$sge=Schedule::SGELK->new(-numnodes=>2,-numcpus=>8); $sge->test(\%tmpSettings);' |
682
|
|
|
|
|
|
|
|
683
|
|
|
|
|
|
|
=back |
684
|
|
|
|
|
|
|
|
685
|
|
|
|
|
|
|
=cut |
686
|
|
|
|
|
|
|
|
687
|
|
|
|
|
|
|
sub test{ |
688
|
0
|
|
|
0
|
1
|
|
my($self,$tmpSettings)=@_; |
689
|
|
|
|
|
|
|
|
690
|
|
|
|
|
|
|
# get settings |
691
|
0
|
|
|
|
|
|
my %settings=%{ $self->settings }; |
|
0
|
|
|
|
|
|
|
692
|
|
|
|
|
|
|
# read in any temporary settings for this command |
693
|
0
|
0
|
|
|
|
|
$tmpSettings={} if(!defined($tmpSettings)); |
694
|
0
|
|
|
|
|
|
$$tmpSettings{verbose}=1; # make sure it's verbose for debugging |
695
|
0
|
|
|
|
|
|
$settings{$_}=$$tmpSettings{$_} for(keys(%$tmpSettings)); |
696
|
|
|
|
|
|
|
|
697
|
|
|
|
|
|
|
# execute the jobs |
698
|
0
|
|
|
|
|
|
for(1..$self->get("numnodes")){ |
699
|
0
|
|
|
|
|
|
logmsg "Job $_ is being submitted"; |
700
|
0
|
|
|
|
|
|
my $text="Job count\t$_\n"; |
701
|
0
|
|
|
|
|
|
$text.="$_\t$settings{$_}\n" for(keys(%settings)); |
702
|
0
|
|
|
|
|
|
$self->pleaseExecute("echo '$text'|column -t",$tmpSettings); |
703
|
|
|
|
|
|
|
} |
704
|
0
|
|
|
|
|
|
$self->wrapItUp(); |
705
|
0
|
|
|
|
|
|
return 1; |
706
|
|
|
|
|
|
|
} |
707
|
|
|
|
|
|
|
|
708
|
|
|
|
|
|
|
1; |