[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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[75] | 18 | my $file; |
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| 19 | my $dir; |
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| 20 | my $cmd; |
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| 21 | my $logtrace; |
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[13] | 22 | my $verbose; |
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[75] | 23 | my $job_np = 1; |
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| 24 | my $nodefile = $ENV{OAR_NODE_FILE} || ''; |
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[32] | 25 | my $masterio; |
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[13] | 26 | my $switchio; |
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| 27 | my $help; |
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[75] | 28 | my $oarsh = 'oarsh -q -T'; |
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| 29 | my $sig_transmit; |
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| 30 | my $sig_checkpoint = 'USR2'; |
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[13] | 31 | |
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| 32 | Getopt::Long::GetOptions( |
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[47] | 33 | 'file=s' => \$file, |
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[45] | 34 | 'dir=s' => \$dir, |
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| 35 | 'cmd=s' => \$cmd, |
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[43] | 36 | 'logtrace=s' => \$logtrace, |
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[32] | 37 | 'verbose' => \$verbose, |
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| 38 | 'help' => \$help, |
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| 39 | 'oarsh=s' => \$oarsh, |
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[34] | 40 | 'jobnp=i' => \$job_np, |
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[32] | 41 | 'nodefile=s' => \$nodefile, |
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| 42 | 'masterio=s' => \$masterio, |
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| 43 | 'switchio' => \$switchio, |
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[75] | 44 | 'transmit' => \$sig_transmit, |
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| 45 | 'kill=s' => \$sig_checkpoint, |
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[41] | 46 | ) || pod2usage(-verbose => 0); |
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| 47 | pod2usage(-verbose => 2) if $help; |
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[45] | 48 | pod2usage(-verbose => 2) if not ( |
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[47] | 49 | (-e "$file") |
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[45] | 50 | or (-d "$dir" and $cmd ne '') |
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| 51 | ); |
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[13] | 52 | |
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[43] | 53 | # re-run, keep trace of job already done |
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[38] | 54 | my %state; |
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| 55 | my $log_h = IO::File->new(); |
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[45] | 56 | if (-e "$logtrace") { |
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[43] | 57 | $log_h->open("< $logtrace") |
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| 58 | or die "error: can't read log file: $!"; |
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[38] | 59 | while (<$log_h>) { |
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[45] | 60 | $state{$1} = 'start' if m/^start\s+job\s+([^\s]+)\s/; |
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| 61 | $state{$1} = 'end' if m/^end\s+job\s+([^\s]+)\s/; |
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[41] | 62 | } |
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[38] | 63 | $log_h->close(); |
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| 64 | } |
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[43] | 65 | if ($logtrace) { |
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| 66 | $log_h->open(">> $logtrace") |
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| 67 | or die "error: can't append log file $logtrace: $!"; |
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[40] | 68 | $log_h->autoflush; |
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[38] | 69 | $log_h = unblock $log_h; |
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| 70 | } |
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| 71 | |
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[43] | 72 | # job to run |
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[13] | 73 | my @job = (); |
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[47] | 74 | if (-e "$file") { |
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[45] | 75 | my $job_num = 0; |
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[47] | 76 | open(JOB_LIST, '<', "$file") or die "error: can't open job file $file: $!"; |
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[77] | 77 | while (my $job_cmd = <JOB_LIST>) { |
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| 78 | chomp $job_cmd; |
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| 79 | next if $job_cmd =~ m/^#/; |
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| 80 | next if $job_cmd =~ m/^\s*$/; |
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[45] | 81 | $job_num++; |
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[77] | 82 | my ($job_name) = $job_cmd =~ m/#.*?\bname=(\S+?)\b/i; |
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| 83 | $job_name ||= $job_num; |
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| 84 | push @job, { name => $job_name, cmd => "$job_cmd" }; |
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[45] | 85 | } |
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| 86 | close JOB_LIST; |
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[13] | 87 | } |
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[45] | 88 | else { |
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| 89 | opendir(DIR, $dir) or die "error: can't open folder $dir: $!"; |
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| 90 | while (my $item = readdir(DIR)) { |
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| 91 | next if $item =~ m/^\./; |
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| 92 | next if $item =~ m/:/; |
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| 93 | next if $item =~ m/\.old$/; |
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| 94 | next if $item =~ m/\.sav$/; |
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| 95 | next if $item =~ m/\.bak$/; |
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| 96 | next if $item =~ m/\.no$/; |
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| 97 | next unless (-d "$dir/$item"); |
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| 98 | push @job, { name => $item, cmd => "( cd $dir/$item/; $cmd )" }; |
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| 99 | } |
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| 100 | closedir DIR; |
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| 101 | } |
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[13] | 102 | |
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[43] | 103 | # ressources available |
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[34] | 104 | my @ressources = (); |
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[41] | 105 | open(NODE_FILE, '<', "$nodefile") |
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[34] | 106 | or die "can't open $nodefile: $!"; |
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| 107 | while (<NODE_FILE>) { |
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| 108 | chomp; |
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| 109 | next if m/^#/; |
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| 110 | next if m/^\s*$/; |
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[41] | 111 | push @ressources, $_; |
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[34] | 112 | } |
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| 113 | close NODE_FILE; |
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| 114 | |
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| 115 | my $ressource_size = scalar(@ressources); |
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[43] | 116 | die "error: not enought ressources jobnp $job_np > ressources $ressource_size" |
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[41] | 117 | if $job_np > $ressource_size; |
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[34] | 118 | |
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| 119 | my $current_dir = getcwd(); |
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| 120 | |
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[32] | 121 | my $stderr = $ENV{OAR_STDERR} || ''; |
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[13] | 122 | $stderr =~ s/\.stderr$//; |
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[32] | 123 | $stderr = $masterio if $masterio; |
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| 124 | my $stdout = $ENV{OAR_STDOUT} || ''; |
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[13] | 125 | $stdout =~ s/\.stdout$//; |
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[32] | 126 | $stdout = $masterio if $masterio; |
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[13] | 127 | |
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| 128 | my $finished = new Coro::Signal; |
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| 129 | my $job_todo = new Coro::Semaphore 0; |
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[45] | 130 | my $job_name_maxlen; |
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| 131 | for (@job) { |
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| 132 | $job_todo->up; |
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| 133 | $job_name_maxlen = length($_->{name}) if length($_->{name}) > $job_name_maxlen; |
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| 134 | } |
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[13] | 135 | |
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[43] | 136 | # slice of ressources for parallel job |
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[13] | 137 | my $ressources = new Coro::Channel; |
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[34] | 138 | for my $slot (1 .. int($ressource_size / $job_np)) { |
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[41] | 139 | $ressources->put( |
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| 140 | join(',', |
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| 141 | @ressources[ (($slot - 1) * $job_np) .. (($slot * $job_np) - 1) ]) |
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| 142 | ); |
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[13] | 143 | } |
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| 144 | |
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| 145 | my %scheduled = (); |
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| 146 | |
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[43] | 147 | # OAR checkpoint and default signal SIGUSR2 |
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[39] | 148 | my $oar_checkpoint = new Coro::Semaphore 0; |
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[75] | 149 | $SIG{$sig_checkpoint} = sub { |
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[42] | 150 | print "warning: receive checkpoint at " |
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| 151 | . time |
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| 152 | . ", no new job, just finishing running job\n" |
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| 153 | if $verbose; |
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| 154 | $oar_checkpoint->up(); |
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[75] | 155 | kill $sig_checkpoint => keys %scheduled if $sig_transmit; |
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[42] | 156 | }; |
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[39] | 157 | |
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[43] | 158 | # asynchrone start job block |
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[13] | 159 | async { |
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[43] | 160 | JOB: |
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[13] | 161 | for my $job (@job) { |
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[45] | 162 | my $job_name = $job->{name}; |
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| 163 | my $job_cmd = $job->{cmd}; |
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[38] | 164 | |
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[43] | 165 | # job has been already run ? |
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[45] | 166 | if (exists $state{$job_name}) { |
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| 167 | if ($state{$job_name} eq 'start') { |
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| 168 | print "warning: job $job_name was not clearly finished, relaunching...\n" |
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[41] | 169 | if $verbose; |
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| 170 | } |
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[45] | 171 | elsif ($state{$job_name} eq 'end') { |
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| 172 | delete $state{$job_name}; # free memory |
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[41] | 173 | $job_todo->down; |
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[45] | 174 | print "warning: job $job_name already run\n" if $verbose; |
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[41] | 175 | cede; |
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[43] | 176 | next JOB; |
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[41] | 177 | } |
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| 178 | } |
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[40] | 179 | |
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[43] | 180 | # take job ressource |
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[36] | 181 | my $job_ressource = $ressources->get; |
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[13] | 182 | |
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[43] | 183 | # no more launch job when OAR checkpointing |
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| 184 | last JOB if $oar_checkpoint->count() > 0; |
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[39] | 185 | |
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[36] | 186 | my ($node_connect) = split ',', $job_ressource; |
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[41] | 187 | my $fh = IO::File->new(); |
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[34] | 188 | my $job_pid = $fh->open("| $oarsh $node_connect >/dev/null 2>&1") |
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[43] | 189 | or die "error: can't start subjob: $!"; |
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[13] | 190 | |
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| 191 | $fh->autoflush; |
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| 192 | $fh = unblock $fh; |
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| 193 | |
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[41] | 194 | $scheduled{$job_pid} = { |
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| 195 | fh => $fh, |
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| 196 | node_connect => $node_connect, |
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| 197 | ressource => $job_ressource, |
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[45] | 198 | name => $job_name |
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[41] | 199 | }; |
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[13] | 200 | |
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[45] | 201 | my $msg = sprintf "start job %${job_name_maxlen}s / %5i at %s on node %s\n", |
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| 202 | $job_name, $job_pid, time, $job_ressource; |
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[43] | 203 | $log_h->print($msg) if $logtrace; |
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[42] | 204 | print($msg) if $verbose; |
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[13] | 205 | |
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[41] | 206 | my ($job_stdout, $job_stderr); |
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[45] | 207 | $job_stdout = "> $stdout-$job_name.stdout" if $stdout ne '' and $switchio; |
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| 208 | $job_stderr = "2> $stderr-$job_name.stderr" if $stderr ne '' and $switchio; |
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[13] | 209 | |
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[45] | 210 | my $job_nodefile = "/tmp/oar-parexec-$ENV{LOGNAME}-$job_name"; |
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[34] | 211 | |
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[43] | 212 | # set job environment, run it and clean |
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[34] | 213 | if ($job_np > 1) { |
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[36] | 214 | $fh->print("printf \"" |
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[41] | 215 | . join('\n', split(',', $job_ressource,)) |
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| 216 | . "\" > $job_nodefile\n"); |
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[37] | 217 | $fh->print("OAR_NODE_FILE=$job_nodefile\n"); |
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[34] | 218 | $fh->print("OAR_NP=$job_np\n"); |
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[37] | 219 | $fh->print("export OAR_NODE_FILE\n"); |
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[34] | 220 | $fh->print("export OAR_NP\n"); |
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| 221 | $fh->print("unset OAR_MSG_NODEFILE\n"); |
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| 222 | } |
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[32] | 223 | $fh->print("cd $current_dir\n"); |
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[45] | 224 | $fh->print("$job_cmd $job_stdout $job_stderr\n"); |
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[34] | 225 | $fh->print("rm -f $job_nodefile\n") if $job_np > 1; |
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[13] | 226 | $fh->print("exit\n"); |
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| 227 | cede; |
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| 228 | } |
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| 229 | } |
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| 230 | |
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[43] | 231 | # asynchrone end job block |
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[13] | 232 | async { |
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| 233 | while () { |
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[41] | 234 | for my $job_pid (keys %scheduled) { |
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[43] | 235 | # non blocking PID test |
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[41] | 236 | if (waitpid($job_pid, WNOHANG)) { |
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[45] | 237 | my $msg = sprintf "end job %${job_name_maxlen}s / %5i at %s on node %s\n", |
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| 238 | $scheduled{$job_pid}->{name}, |
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[42] | 239 | $job_pid, time, $scheduled{$job_pid}->{ressource}; |
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[76] | 240 | |
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| 241 | # Job non finish, just suspend if received checkpoint signal |
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| 242 | $msg =~ s/^end\s+job/suspend job/ |
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| 243 | if $sig_transmit and $oar_checkpoint->count() > 0; |
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| 244 | |
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[43] | 245 | $log_h->print($msg) if $logtrace; |
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[42] | 246 | print($msg) if $verbose; |
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[13] | 247 | close $scheduled{$job_pid}->{fh}; |
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[43] | 248 | # leave ressources for another job |
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[41] | 249 | $ressources->put($scheduled{$job_pid}->{ressource}); |
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[13] | 250 | $job_todo->down; |
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| 251 | delete $scheduled{$job_pid}; |
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| 252 | } |
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| 253 | cede; |
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| 254 | } |
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| 255 | |
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[43] | 256 | # checkpointing ! just finishing running job and quit |
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[42] | 257 | $finished->send if $oar_checkpoint->count() > 0 and scalar(keys(%scheduled)) == 0; |
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[39] | 258 | |
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[42] | 259 | $finished->send if $job_todo->count() == 0; |
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[13] | 260 | cede; |
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| 261 | } |
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| 262 | } |
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| 263 | |
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| 264 | cede; |
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| 265 | |
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[43] | 266 | # all job have been done |
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[13] | 267 | $finished->wait; |
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| 268 | |
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[43] | 269 | # close log trace file |
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| 270 | $log_h->close() if $logtrace; |
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[38] | 271 | |
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[13] | 272 | __END__ |
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| 273 | |
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| 274 | =head1 NAME |
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| 275 | |
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[44] | 276 | oar-parexec - parallel execution of many small job |
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[13] | 277 | |
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| 278 | =head1 SYNOPSIS |
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| 279 | |
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[47] | 280 | oar-parexec --file filecommand \ |
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| 281 | [--logtrace tracefile] [--verbose] \ |
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| 282 | [--jobnp integer] [--nodefile filenode] [--oarsh sssh] \ |
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| 283 | [--switchio] [--masterio basefileio] |
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[46] | 284 | |
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[47] | 285 | oar-parexec --dir foldertoiterate --cmd commandtolaunch \ |
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| 286 | [--logtrace tracefile] [--verbose] \ |
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| 287 | [--jobnp integer] [--nodefile filenode] [--oarsh sssh] \ |
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| 288 | [--switchio] [--masterio basefileio] |
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[46] | 289 | |
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[13] | 290 | oar-parexec --help |
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| 291 | |
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[32] | 292 | =head1 DESCRIPTION |
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| 293 | |
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[44] | 294 | C<oar-parexec> can execute lot of small job in parallel inside a cluster. |
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| 295 | Number of parallel job at one time cannot exceed the number of core define in the node file |
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[32] | 296 | C<oar-parexec> is easier to use inside an OAR job environment |
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[44] | 297 | which define automatically these strategics parameters... |
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| 298 | However, it can be used outside OAR. |
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[32] | 299 | |
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[47] | 300 | Option C<--file> or C<--dir> and C<--cmd> are the only mandatory parameters. |
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[32] | 301 | |
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| 302 | Small job will be launch in the same folder as the master job. |
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[44] | 303 | Two environment variable are defined for each small job |
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[37] | 304 | and only in case of parallel small job (option C<--jobnp> > 1). |
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[32] | 305 | |
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[34] | 306 | OAR_NODE_FILE - file that list node for parallel computing |
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| 307 | OAR_NP - number of processor affected |
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[32] | 308 | |
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[44] | 309 | The file define by OAR_NODE_FILE is created in /tmp |
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| 310 | on the node before launching the small job |
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| 311 | and this file will be delete after job complete. |
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[34] | 312 | C<oar-parexec> is a simple script, |
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| 313 | OAR_NODE_FILE will not be deleted in case of crash of the master job. |
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| 314 | |
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[37] | 315 | OAR define other variable that are equivalent to OAR_NODE_FILE: |
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| 316 | OAR_NODEFILE, OAR_FILE_NODES, OAR_RESOURCE_FILE... |
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| 317 | You can use in your script the OAR original file ressources |
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| 318 | by using these variable if you need it. |
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| 319 | |
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[34] | 320 | |
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[13] | 321 | =head1 OPTIONS |
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| 322 | |
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[32] | 323 | =over 12 |
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[13] | 324 | |
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[47] | 325 | =item B<-f|--file filecommand> |
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[13] | 326 | |
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[32] | 327 | File name which content job list. |
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[45] | 328 | For the JOB_NAME definition, |
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| 329 | the first valid job in the list will have the number 1 and so on... |
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[13] | 330 | |
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[77] | 331 | It's possible to fix the name inside a comment on the job line. |
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| 332 | For example: |
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| 333 | |
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| 334 | $HOME/test/subjob1.sh # name=subjob1 |
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| 335 | |
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| 336 | The key C<name> is case insensitive, |
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| 337 | the associated value cannot have a space... |
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| 338 | |
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[47] | 339 | =item B<-d|--dir foldertoiterate> |
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[45] | 340 | |
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| 341 | Command C<--cmd> will be launch in all sub-folder of this master folder. |
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| 342 | Files in this folder will be ignored. |
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[47] | 343 | Sub-folder name which begin with F<.> |
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| 344 | or finish with F<.old>, F<.sav>, F<.bak>, F<.no> will either be ignored... |
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[45] | 345 | |
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| 346 | The JOB_NAME is simply the Sub-folder name. |
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| 347 | |
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| 348 | =item B<-c|--cmd commandtolaunch> |
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| 349 | |
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| 350 | Command (and argument to it) tha will be launch in all sub-folder |
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| 351 | parameter folfer C<--dir> |
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| 352 | |
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[43] | 353 | =item B<-l|--logtrace tracefile> |
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| 354 | |
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| 355 | File which log and trace running job. |
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[44] | 356 | In case of running the same master command (after crash for example), |
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| 357 | only job that are not mark as done will be run again. |
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| 358 | Be careful, job mark as running (start but not finish) will be run again. |
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[45] | 359 | Tracing is base on the JOB_NAME between multiple run. |
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[43] | 360 | |
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| 361 | This option is very usefull in case of crash |
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| 362 | but also for checkpointing and idempotent OAR job. |
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| 363 | |
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[32] | 364 | =item B<-v|--verbose> |
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[13] | 365 | |
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[34] | 366 | =item B<-j|--jobnp integer> |
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[13] | 367 | |
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[34] | 368 | Number of processor to allocated for each small job. |
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| 369 | 1 by default. |
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| 370 | |
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| 371 | =item B<-n|--nodefile filenode> |
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| 372 | |
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[44] | 373 | File name that list all the node where job could be launch. |
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[32] | 374 | By defaut, it's define automatically by OAR via |
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| 375 | environment variable C<OAR_NODE_FILE>. |
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[13] | 376 | |
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[32] | 377 | For example, if you want to use 6 core on your cluster node, |
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| 378 | you need to put 6 times the hostname node in this file, |
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| 379 | one per line... |
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| 380 | It's a very common file in MPI process ! |
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[13] | 381 | |
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[46] | 382 | =item B<-o|-oarsh command> |
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[13] | 383 | |
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[46] | 384 | Command use to launch a shell on a node. |
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| 385 | By default |
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[13] | 386 | |
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[46] | 387 | oarsh -q -T |
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| 388 | |
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| 389 | Change it to C<ssh> if you are not using an OAR cluster... |
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| 390 | |
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[32] | 391 | =item B<-s|--switchio> |
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[21] | 392 | |
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[32] | 393 | Each small job will have it's own output STDOUT and STDERR |
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[45] | 394 | base on master OAR job with C<JOB_NAME> inside |
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[32] | 395 | (or base on C<basefileio> if option C<masterio>). |
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| 396 | Example : |
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[21] | 397 | |
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[45] | 398 | OAR.151524.stdout -> OAR.151524-JOB_NAME.stdout |
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[21] | 399 | |
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[32] | 400 | where 151524 here is the master C<OAR_JOB_ID> |
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[45] | 401 | and C<JOB_NAME> is the small job name. |
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[21] | 402 | |
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[46] | 403 | =item B<-m|--masterio basefileio> |
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[32] | 404 | |
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[46] | 405 | The C<basefileio> will be use in place of environment variable |
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| 406 | C<OAR_STDOUT> and C<OAR_STDERR> (without extension) to build the base name of the small job standart output |
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| 407 | (only use when option C<swithio> is activated). |
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[32] | 408 | |
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[78] | 409 | =item B<-k|--kill signal> |
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| 410 | |
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| 411 | Signal to listen and make a clean stop of the current C<oar-parexec> process. |
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| 412 | By default, use USR2 signal (see C<kill -l>> for a list of possible signal). |
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| 413 | |
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| 414 | =item B<-t|--transmit> |
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| 415 | |
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| 416 | Resend catch signal to sub-job when receiving it. |
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| 417 | By default, no signal is transmis to child process. |
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| 418 | |
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| 419 | It's only valuable if use for long sub-job than can |
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| 420 | in return make themselves a clean restart. |
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| 421 | |
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| 422 | |
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[32] | 423 | =item B<-h|--help> |
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| 424 | |
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| 425 | =back |
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| 426 | |
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| 427 | |
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| 428 | =head1 EXAMPLE |
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| 429 | |
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[44] | 430 | =head2 Simple list of sequential job |
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| 431 | |
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[47] | 432 | Content for the job file command (option C<--file>) could have: |
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[21] | 433 | |
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[13] | 434 | - empty line |
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| 435 | - comment line begin with # |
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| 436 | - valid shell command |
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| 437 | |
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| 438 | Example where F<$HOME/test/subjob1.sh> is a shell script (executable). |
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| 439 | |
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[77] | 440 | $HOME/test/subjob01.sh # name=subjob01 |
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| 441 | $HOME/test/subjob02.sh # name=subjob02 |
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| 442 | $HOME/test/subjob03.sh # name=subjob03 |
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| 443 | $HOME/test/subjob04.sh # name=subjob04 |
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[32] | 444 | ... |
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[77] | 445 | $HOME/test/subjob38.sh # name=subjob38 |
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| 446 | $HOME/test/subjob39.sh # name=subjob39 |
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| 447 | $HOME/test/subjob40.sh # name=subjob40 |
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[13] | 448 | |
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[44] | 449 | These jobs could be launch by: |
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[13] | 450 | |
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[49] | 451 | oarsub -n test -l /core=6,walltime=04:00:00 \ |
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| 452 | "oar-parexec -f ./subjob.list.txt" |
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[13] | 453 | |
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[47] | 454 | =head2 Folder job |
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| 455 | |
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| 456 | In a folder F<subjob.d>, create sub-folder with your data inside : F<test1>, <test2>... |
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| 457 | The same command will be executed in every sub-folder. |
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| 458 | C<oar-parexec> change the current directory to the sub-folder before launching it. |
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| 459 | |
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| 460 | A very simple job could be: |
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| 461 | |
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[49] | 462 | oarsub -n test -l /core=6,walltime=04:00:00 \ |
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| 463 | "oar-parexec -d ./subjob.d -c 'sleep 10; env'" |
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[47] | 464 | |
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| 465 | The command C<env> will be excuted in all folder F<test1>, F<test2>... after a 10s pause. |
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| 466 | |
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| 467 | Sometime, it's simpler to use file list command, |
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| 468 | sometime, jobs by folder with the same command run is more relevant. |
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| 469 | |
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[44] | 470 | =head2 Parallel job |
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[28] | 471 | |
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[44] | 472 | You need to put the number of core each small job need with option C<--jobnp>. |
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| 473 | If your job is build on OpenMP or MPI, |
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| 474 | you can use OAR_NP and OAR_NODE_FILE variables to configure them. |
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| 475 | On OAR cluster, you need to use C<oarsh> or a wrapper like C<oar-envsh> |
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| 476 | for connexion between node instead of C<ssh>. |
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| 477 | |
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| 478 | Example with parallel small job on 2 core: |
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| 479 | |
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[49] | 480 | oarsub -n test -l /core=6,walltime=04:00:00 \ |
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| 481 | "oar-parexec -j 2 -f ./subjob.list.txt" |
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[44] | 482 | |
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| 483 | =head2 Tracing and master crash |
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| 484 | |
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| 485 | If the master node crash after hours of calculus, everything is lost ? |
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| 486 | No, with option C<--logtrace>, |
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| 487 | it's possible to remember older result |
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| 488 | and not re-run these job the second and next time. |
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| 489 | |
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[49] | 490 | oarsub -n test -l /core=6,walltime=04:00:00 \ |
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| 491 | "oar-parexec -f ./subjob.list.txt -l ./subjob.list.log" |
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[44] | 492 | |
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| 493 | After a crash or an C<oardel> command, |
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| 494 | you can then re-run the same command that will end to execute the jobs in the list |
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| 495 | |
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[49] | 496 | oarsub -n test -l /core=6,walltime=04:00:00 \ |
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| 497 | "oar-parexec -f ./subjob.list.txt -l ./subjob.list.log" |
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[44] | 498 | |
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| 499 | C<logtrace> file are just plain file. |
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| 500 | We use the extension '.log' because these files are automatically |
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| 501 | eliminate from our backup system! |
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| 502 | |
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| 503 | =head2 Checkpointing and Idempotent |
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| 504 | |
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| 505 | C<oar-parexec> is compatible with the OAR checkpointing. |
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| 506 | Il you have 2000 small jobs that need 55h to be done on 6 cores, |
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| 507 | you can cut this in small parts. |
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| 508 | |
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| 509 | For this example, we suppose that each small job need about 10min... |
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| 510 | So, we send a checkpoint 12min before the end of the process |
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| 511 | to let C<oar-parexec> finish the jobs started. |
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| 512 | After being checkpointed, C<oar-parexec> do not start any new small job. |
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| 513 | |
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[49] | 514 | oarsub -t idempotent -n test \ |
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| 515 | -l /core=6,walltime=04:00:00 \ |
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| 516 | --checkpoint 720 \ |
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[44] | 517 | "oar-parexec -f ./subjob.list.txt -l ./subjob.list.log" |
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| 518 | |
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| 519 | After 3h48min, the OAR job will begin to stop launching new small job. |
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| 520 | When all running small job are finished, it's exit. |
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| 521 | But as the OAR job is type C<idempotent>, |
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| 522 | OAR will re-submit it as long as all small job are not executed... |
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| 523 | |
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| 524 | This way, we let other users a chance to use the cluster! |
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| 525 | |
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| 526 | In this last exemple, we use moldable OAR job with idempotent |
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| 527 | to reserve many core for a small time or a few cores for a long time: |
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| 528 | |
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| 529 | oarsub -t idempotent -n test \ |
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| 530 | -l /core=50,walltime=01:05:00 \ |
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| 531 | -l /core=6,walltime=04:00:00 \ |
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| 532 | --checkpoint 720 \ |
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| 533 | "oar-parexec -f ./subjob.list.txt -l ./subjob.list.log" |
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| 534 | |
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[78] | 535 | =head2 Signal, recurse and long job |
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[44] | 536 | |
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[78] | 537 | By default, OAR use signal USR2 for checkpointing. |
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| 538 | It's possible to change this with option C<--kill>>. |
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| 539 | |
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| 540 | When use with long small job, checkpointing could be too long... |
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| 541 | Option C<--transmit> could be use to checkpoint small job! |
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| 542 | These will then stop cleanly and will be restarted next time. |
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| 543 | |
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| 544 | In the C<logtrace> file, small job will have the status suspend. |
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| 545 | They will be launch with the same command next OAR run. |
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| 546 | |
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[21] | 547 | =head1 SEE ALSO |
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| 548 | |
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[44] | 549 | oar-dispatch, mpilauncher, |
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| 550 | orsh, oar-envsh, ssh |
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[21] | 551 | |
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| 552 | |
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[13] | 553 | =head1 AUTHORS |
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| 554 | |
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[21] | 555 | Written by Gabriel Moreau, Grenoble - France |
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[13] | 556 | |
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[21] | 557 | |
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| 558 | =head1 LICENSE AND COPYRIGHT |
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| 559 | |
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| 560 | GPL version 2 or later and Perl equivalent |
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| 561 | |
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[28] | 562 | Copyright (C) 2011 Gabriel Moreau / LEGI - CNRS UMR 5519 - France |
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[21] | 563 | |
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