[13] | 1 | #!/usr/bin/perl |
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| 2 | # |
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| 3 | # 2011/11/27 gabriel |
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| 4 | |
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| 5 | use strict; |
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| 6 | |
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| 7 | use Getopt::Long(); |
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| 8 | use Pod::Usage; |
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| 9 | use Coro; |
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| 10 | use Coro::Semaphore; |
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| 11 | use Coro::Signal; |
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| 12 | use Coro::Channel; |
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| 13 | use Coro::Handle; |
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| 14 | use IO::File; |
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| 15 | use POSIX qw( WNOHANG WEXITSTATUS ); |
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[32] | 16 | use Cwd qw( getcwd ); |
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[13] | 17 | |
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| 18 | my $file = ''; |
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[38] | 19 | my $logfile = ''; |
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[13] | 20 | my $verbose; |
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[34] | 21 | my $job_np = 1; |
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[32] | 22 | my $nodefile = $ENV{OAR_NODE_FILE} || ''; |
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| 23 | my $masterio; |
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[13] | 24 | my $switchio; |
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| 25 | my $help; |
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| 26 | my $oarsh = 'oarsh -q -T'; |
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| 27 | |
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| 28 | Getopt::Long::GetOptions( |
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[32] | 29 | 'file=s' => \$file, |
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[38] | 30 | 'logfile=s' => \$logfile, |
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[32] | 31 | 'verbose' => \$verbose, |
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| 32 | 'help' => \$help, |
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| 33 | 'oarsh=s' => \$oarsh, |
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[34] | 34 | 'jobnp=i' => \$job_np, |
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[32] | 35 | 'nodefile=s' => \$nodefile, |
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| 36 | 'masterio=s' => \$masterio, |
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| 37 | 'switchio' => \$switchio, |
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[13] | 38 | ) || pod2usage( -verbose => 0 ); |
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| 39 | pod2usage( -verbose => 2 ) if $help; |
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[21] | 40 | pod2usage( -verbose => 2 ) if not -e $file; |
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[13] | 41 | |
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[38] | 42 | my %state; |
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| 43 | my $log_h = IO::File->new(); |
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| 44 | if (-e $logfile) { |
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[40] | 45 | $log_h->open("< $logfile") |
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| 46 | or die "can't read log file: $!"; |
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[38] | 47 | while (<$log_h>) { |
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[40] | 48 | $state{$1} = 'start' if m/^start\s+job\s+(\d+)\s/; |
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| 49 | $state{$1} = 'end' if m/^end\s+job\s+(\d+)\s/; |
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[38] | 50 | } |
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| 51 | $log_h->close(); |
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| 52 | } |
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| 53 | if ($logfile) { |
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| 54 | $log_h->open(">> $logfile") |
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[40] | 55 | or die "can't append log file $logfile: $!"; |
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| 56 | $log_h->autoflush; |
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[38] | 57 | $log_h = unblock $log_h; |
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| 58 | } |
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| 59 | |
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[13] | 60 | my @job = (); |
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[40] | 61 | open( JOB_LIST, '<', "$file" ) or die "can't open job file $file: $!"; |
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[13] | 62 | while (<JOB_LIST>) { |
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| 63 | chomp; |
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| 64 | next if m/^#/; |
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[32] | 65 | next if m/^\s*$/; |
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| 66 | push @job, $_ ; |
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[13] | 67 | } |
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| 68 | close JOB_LIST; |
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| 69 | |
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[34] | 70 | my @ressources = (); |
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| 71 | open( NODE_FILE, '<', "$nodefile" ) |
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| 72 | or die "can't open $nodefile: $!"; |
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| 73 | while (<NODE_FILE>) { |
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| 74 | chomp; |
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| 75 | next if m/^#/; |
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| 76 | next if m/^\s*$/; |
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| 77 | push @ressources, $_ ; |
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| 78 | } |
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| 79 | close NODE_FILE; |
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| 80 | |
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| 81 | my $ressource_size = scalar(@ressources); |
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[35] | 82 | die "not enought ressources jobnp $job_np > ressources $ressource_size" if $job_np > $ressource_size; |
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[34] | 83 | |
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| 84 | my $current_dir = getcwd(); |
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| 85 | |
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[32] | 86 | my $stderr = $ENV{OAR_STDERR} || ''; |
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[13] | 87 | $stderr =~ s/\.stderr$//; |
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[32] | 88 | $stderr = $masterio if $masterio; |
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| 89 | my $stdout = $ENV{OAR_STDOUT} || ''; |
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[13] | 90 | $stdout =~ s/\.stdout$//; |
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[32] | 91 | $stdout = $masterio if $masterio; |
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[13] | 92 | |
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[32] | 93 | |
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[13] | 94 | my $finished = new Coro::Signal; |
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| 95 | my $job_todo = new Coro::Semaphore 0; |
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| 96 | $job_todo->up for (@job); |
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| 97 | |
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| 98 | my $ressources = new Coro::Channel; |
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[34] | 99 | for my $slot (1 .. int($ressource_size / $job_np)) { |
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[35] | 100 | $ressources->put( join(',', @ressources[(($slot - 1) * $job_np) .. (($slot * $job_np) - 1)] ) ); |
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[13] | 101 | } |
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| 102 | |
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[34] | 103 | |
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[13] | 104 | my $job_num = 0; |
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| 105 | my %scheduled = (); |
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| 106 | |
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[39] | 107 | my $oar_checkpoint = new Coro::Semaphore 0; |
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| 108 | $SIG{USR2} = sub { $oar_checkpoint->up }; |
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| 109 | |
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[13] | 110 | async { |
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| 111 | for my $job (@job) { |
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[38] | 112 | $job_num++; |
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| 113 | |
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[40] | 114 | if (exists $state{$job_num}) { |
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| 115 | if ($state{$job_num} eq 'start') { |
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| 116 | print "warning: job $job_num was not finished, relaunching...\n" if $verbose; |
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| 117 | } |
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| 118 | elsif ($state{$job_num} eq 'end') { |
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| 119 | delete $state{$job_num}; |
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| 120 | $job_todo->down; |
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| 121 | print "warning: job $job_num already done\n" if $verbose; |
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| 122 | cede; |
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| 123 | next; |
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| 124 | } |
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| 125 | } |
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| 126 | |
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[36] | 127 | my $job_ressource = $ressources->get; |
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[13] | 128 | |
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[40] | 129 | last if $oar_checkpoint->count() > 0; |
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[39] | 130 | |
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[36] | 131 | my ($node_connect) = split ',', $job_ressource; |
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[13] | 132 | my $fh = IO::File->new(); |
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[34] | 133 | my $job_pid = $fh->open("| $oarsh $node_connect >/dev/null 2>&1") |
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[13] | 134 | or die "don't start subjob: $!"; |
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| 135 | |
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| 136 | $fh->autoflush; |
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| 137 | $fh = unblock $fh; |
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| 138 | |
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[36] | 139 | $scheduled{$job_pid} = { fh => $fh, node_connect => $node_connect, ressource => $job_ressource, num => $job_num }; |
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[13] | 140 | |
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[38] | 141 | $log_h->printf("start job %5i at %s\n", $job_num, time) if $logfile; |
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[36] | 142 | printf "start job %5i / %5i at %s on node %s\n", |
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| 143 | $job_num, $job_pid, time, $job_ressource |
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[13] | 144 | if $verbose; |
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| 145 | |
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| 146 | my ( $job_stdout, $job_stderr ); |
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| 147 | $job_stdout = "> $stdout-$job_num.stdout" if $stdout ne '' and $switchio; |
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| 148 | $job_stderr = "2> $stderr-$job_num.stderr" if $stderr ne '' and $switchio; |
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| 149 | |
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[36] | 150 | my $job_nodefile = "/tmp/oar-parexec-$ENV{LOGNAME}-$job_num"; |
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[34] | 151 | |
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| 152 | if ($job_np > 1) { |
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[36] | 153 | $fh->print("printf \"" |
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| 154 | . join('\n',split(',',$job_ressource,)) |
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| 155 | . "\" > $job_nodefile\n"); |
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[37] | 156 | $fh->print("OAR_NODE_FILE=$job_nodefile\n"); |
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[34] | 157 | $fh->print("OAR_NP=$job_np\n"); |
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[37] | 158 | $fh->print("export OAR_NODE_FILE\n"); |
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[34] | 159 | $fh->print("export OAR_NP\n"); |
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| 160 | $fh->print("unset OAR_MSG_NODEFILE\n"); |
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| 161 | } |
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[32] | 162 | $fh->print("cd $current_dir\n"); |
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[13] | 163 | $fh->print("$job $job_stdout $job_stderr\n"); |
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[34] | 164 | $fh->print("rm -f $job_nodefile\n") if $job_np > 1; |
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[13] | 165 | $fh->print("exit\n"); |
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| 166 | cede; |
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| 167 | } |
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| 168 | } |
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| 169 | |
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| 170 | async { |
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| 171 | while () { |
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| 172 | for my $job_pid ( keys %scheduled ) { |
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| 173 | if ( waitpid( $job_pid, WNOHANG ) ) { |
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[40] | 174 | $log_h->printf("end job %5i at %s\n", |
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| 175 | $scheduled{$job_pid}->{num}, |
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| 176 | time) if $logfile; |
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[36] | 177 | printf "end job %5i / %5i at %s on node %s\n", |
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[13] | 178 | $scheduled{$job_pid}->{num}, |
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[36] | 179 | $job_pid, time, |
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| 180 | $scheduled{$job_pid}->{ressource} |
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[13] | 181 | if $verbose; |
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| 182 | close $scheduled{$job_pid}->{fh}; |
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[36] | 183 | $ressources->put( $scheduled{$job_pid}->{ressource} ); |
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[13] | 184 | $job_todo->down; |
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| 185 | delete $scheduled{$job_pid}; |
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| 186 | } |
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| 187 | cede; |
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| 188 | } |
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| 189 | |
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[40] | 190 | $finished->send if $oar_checkpoint->count > 0 and keys(%scheduled) == 0; |
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[39] | 191 | |
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[13] | 192 | $finished->send if $job_todo->count == 0; |
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| 193 | cede; |
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| 194 | } |
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| 195 | } |
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| 196 | |
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| 197 | cede; |
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| 198 | |
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| 199 | $finished->wait; |
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| 200 | |
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[40] | 201 | $log_h->close() if $logfile; |
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[38] | 202 | |
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[40] | 203 | |
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[13] | 204 | __END__ |
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| 205 | |
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| 206 | =head1 NAME |
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| 207 | |
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| 208 | oar-parexec - parallel execute lot of small job |
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| 209 | |
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| 210 | =head1 SYNOPSIS |
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| 211 | |
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[34] | 212 | oar-parexec --file filecommand [--verbose] [--jobnp integer] [--nodefile filenode] [--masterio basefileio] [--switchio] [--oarsh sssh] |
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[13] | 213 | oar-parexec --help |
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| 214 | |
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[32] | 215 | =head1 DESCRIPTION |
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| 216 | |
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| 217 | C<oar-parexec> execute lot of small job.in parallel inside a cluster. |
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| 218 | Number of parallel job at one time cannot excede core number in the node file. |
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| 219 | C<oar-parexec> is easier to use inside an OAR job environment |
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| 220 | which define automatically theses strategics parameters... |
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| 221 | |
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| 222 | Option C<--file> is the only mandatory one. |
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| 223 | |
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| 224 | Small job will be launch in the same folder as the master job. |
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[34] | 225 | Two environment variable are define for each small job |
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[37] | 226 | and only in case of parallel small job (option C<--jobnp> > 1). |
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[32] | 227 | |
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[34] | 228 | OAR_NODE_FILE - file that list node for parallel computing |
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| 229 | OAR_NP - number of processor affected |
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[32] | 230 | |
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[34] | 231 | The file define by OAR_NODE_FILE is created on the node before launching |
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| 232 | the small job in /tmp and will be delete after... |
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| 233 | C<oar-parexec> is a simple script, |
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| 234 | OAR_NODE_FILE will not be deleted in case of crash of the master job. |
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| 235 | |
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[37] | 236 | OAR define other variable that are equivalent to OAR_NODE_FILE: |
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| 237 | OAR_NODEFILE, OAR_FILE_NODES, OAR_RESOURCE_FILE... |
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| 238 | You can use in your script the OAR original file ressources |
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| 239 | by using these variable if you need it. |
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| 240 | |
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[34] | 241 | |
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[13] | 242 | =head1 OPTIONS |
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| 243 | |
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[32] | 244 | =over 12 |
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[13] | 245 | |
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[32] | 246 | =item B<-f|--file filecommand> |
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[13] | 247 | |
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[32] | 248 | File name which content job list. |
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[13] | 249 | |
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[32] | 250 | =item B<-v|--verbose> |
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[13] | 251 | |
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[34] | 252 | =item B<-j|--jobnp integer> |
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[13] | 253 | |
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[34] | 254 | Number of processor to allocated for each small job. |
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| 255 | 1 by default. |
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| 256 | |
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| 257 | =item B<-n|--nodefile filenode> |
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| 258 | |
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[32] | 259 | File name that list all the node to launch job. |
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| 260 | By defaut, it's define automatically by OAR via |
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| 261 | environment variable C<OAR_NODE_FILE>. |
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[13] | 262 | |
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[32] | 263 | For example, if you want to use 6 core on your cluster node, |
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| 264 | you need to put 6 times the hostname node in this file, |
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| 265 | one per line... |
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| 266 | It's a very common file in MPI process ! |
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[13] | 267 | |
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[32] | 268 | =item B<-m|--masterio basefileio> |
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[13] | 269 | |
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[32] | 270 | The C<basefileio> will be use in place of environment variable |
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| 271 | C<OAR_STDOUT> and C<OAR_STDERR> (without extension) to build the base name of the small job standart output |
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[37] | 272 | (only use when option C<swithio> is activated). |
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[13] | 273 | |
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[32] | 274 | =item B<-s|--switchio> |
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[21] | 275 | |
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[32] | 276 | Each small job will have it's own output STDOUT and STDERR |
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| 277 | base on master OAR job with C<JOB_NUM> inside |
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| 278 | (or base on C<basefileio> if option C<masterio>). |
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| 279 | Example : |
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[21] | 280 | |
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[32] | 281 | OAR.151524.stdout -> OAR.151524-JOB_NUM.stdout |
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[21] | 282 | |
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[32] | 283 | where 151524 here is the master C<OAR_JOB_ID> |
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| 284 | and C<JOB_NUM> is the small job nnumber. |
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[21] | 285 | |
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[32] | 286 | =item B<-o|-oarsh command> |
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| 287 | |
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| 288 | Command use to launch a shell on a node. |
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| 289 | By default |
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| 290 | |
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| 291 | oarsh -q -T |
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| 292 | |
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| 293 | =item B<-h|--help> |
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| 294 | |
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| 295 | =back |
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| 296 | |
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| 297 | |
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| 298 | =head1 EXAMPLE |
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| 299 | |
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[21] | 300 | Content for the job file (option C<--file>) could have: |
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| 301 | |
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[13] | 302 | - empty line |
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| 303 | - comment line begin with # |
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| 304 | - valid shell command |
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| 305 | |
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| 306 | Example where F<$HOME/test/subjob1.sh> is a shell script (executable). |
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| 307 | |
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| 308 | $HOME/test/subjob1.sh |
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| 309 | $HOME/test/subjob2.sh |
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| 310 | $HOME/test/subjob3.sh |
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| 311 | $HOME/test/subjob4.sh |
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[32] | 312 | ... |
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[13] | 313 | $HOME/test/subjob38.sh |
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| 314 | $HOME/test/subjob39.sh |
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| 315 | $HOME/test/subjob40.sh |
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| 316 | |
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| 317 | These jobs could be launch by |
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| 318 | |
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| 319 | oarsub -n test -l /core=6,walltime=00:35:00 "oar-parexec -f ./subjob.list.txt" |
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| 320 | |
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[28] | 321 | |
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[21] | 322 | =head1 SEE ALSO |
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| 323 | |
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| 324 | oar-dispatch, mpilauncher |
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| 325 | |
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| 326 | |
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[13] | 327 | =head1 AUTHORS |
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| 328 | |
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[21] | 329 | Written by Gabriel Moreau, Grenoble - France |
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[13] | 330 | |
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[21] | 331 | |
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| 332 | =head1 LICENSE AND COPYRIGHT |
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| 333 | |
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| 334 | GPL version 2 or later and Perl equivalent |
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| 335 | |
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[28] | 336 | Copyright (C) 2011 Gabriel Moreau / LEGI - CNRS UMR 5519 - France |
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[21] | 337 | |
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