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Revision 1.1 - (view) (download) (as text)
| 1 : | olson | 1.1 | |
| 2 : | # | ||
| 3 : | # Finish a job that has its work directories over on the | ||
| 4 : | # lustre spool directory by copying them back and then | ||
| 5 : | # setting the job to done. | ||
| 6 : | # | ||
| 7 : | |||
| 8 : | use Data::Dumper; | ||
| 9 : | use Carp; | ||
| 10 : | use strict; | ||
| 11 : | use FIG; | ||
| 12 : | use FIG_Config; | ||
| 13 : | use File::Basename; | ||
| 14 : | use GenomeMeta; | ||
| 15 : | use JobError; | ||
| 16 : | use File::Basename; | ||
| 17 : | |||
| 18 : | @ARGV == 1 or die "Usage: $0 job-dir\n"; | ||
| 19 : | |||
| 20 : | my $jobdir = shift; | ||
| 21 : | |||
| 22 : | -d $jobdir or die "$0: job dir $jobdir does not exist\n"; | ||
| 23 : | |||
| 24 : | my $job = new Job48($jobdir); | ||
| 25 : | $job or die "cannot create job for $jobdir"; | ||
| 26 : | |||
| 27 : | my $hostname = `hostname`; | ||
| 28 : | chomp $hostname; | ||
| 29 : | |||
| 30 : | my $genome = &FIG::file_head("$jobdir/GENOME_ID"); | ||
| 31 : | chomp $genome; | ||
| 32 : | $genome =~ /^\d+\.\d+/ or die "$0: Cannnot find genome ID for jobdir $jobdir\n"; | ||
| 33 : | |||
| 34 : | my $meta = new GenomeMeta($genome, "$jobdir/meta.xml"); | ||
| 35 : | |||
| 36 : | my $genome_dir = "$jobdir/rp/$genome"; | ||
| 37 : | |||
| 38 : | $meta->set_metadata("lustre_stage_in.hostname", $hostname); | ||
| 39 : | |||
| 40 : | $meta->add_log_entry($0, "copy lustre spooled job back to $jobdir"); | ||
| 41 : | |||
| 42 : | # | ||
| 43 : | # Find any directories in the jobdir that are symlinked to the lustre spool. Copy | ||
| 44 : | # the contents back here. | ||
| 45 : | # | ||
| 46 : | opendir(D, $jobdir) or &fatal("cannot opendir $jobdir: $!"); | ||
| 47 : | for my $f (readdir(D)) | ||
| 48 : | { | ||
| 49 : | my $path = "$jobdir/$f"; | ||
| 50 : | next unless -l $path; | ||
| 51 : | my $targ = readlink($path); | ||
| 52 : | if (!$targ) | ||
| 53 : | { | ||
| 54 : | warn "Error reading symlink $path: $!"; | ||
| 55 : | next | ||
| 56 : | } | ||
| 57 : | |||
| 58 : | if ($targ =~ /^$FIG_Config::lustre_spool_dir/) | ||
| 59 : | { | ||
| 60 : | warn "Copying back data from $targ to $path\n"; | ||
| 61 : | unlink($path); | ||
| 62 : | my $targ_dir = dirname($targ); | ||
| 63 : | if ($targ_dir eq '' or ! -d $targ_dir) | ||
| 64 : | { | ||
| 65 : | warn "Some error extracting dirname '$targ_dir' from target '$targ'\n"; | ||
| 66 : | next; | ||
| 67 : | } | ||
| 68 : | my $tar_cmd = "tar -C $targ_dir -c -p -f - $f | tar -C $jobdir -x -p -f -"; | ||
| 69 : | warn "Execute $tar_cmd\n"; | ||
| 70 : | my $rc = system($tar_cmd); | ||
| 71 : | if ($rc != 0) | ||
| 72 : | { | ||
| 73 : | &fatal("Error $rc running tar cmd $tar_cmd\n"); | ||
| 74 : | } | ||
| 75 : | } | ||
| 76 : | } | ||
| 77 : | |||
| 78 : | if (open(D, ">$jobdir/DONE")) | ||
| 79 : | { | ||
| 80 : | print D time . "\n"; | ||
| 81 : | close(D); | ||
| 82 : | } | ||
| 83 : | else | ||
| 84 : | { | ||
| 85 : | warn "Error opening $jobdir/DONE: $!\n"; | ||
| 86 : | } | ||
| 87 : | |||
| 88 : | unlink("$jobdir/ACTIVE"); | ||
| 89 : | |||
| 90 : | exit(0); | ||
| 91 : | |||
| 92 : | sub fatal | ||
| 93 : | { | ||
| 94 : | my($msg) = @_; | ||
| 95 : | |||
| 96 : | if ($meta) | ||
| 97 : | { | ||
| 98 : | $meta->add_log_entry($0, ['fatal error', $msg]); | ||
| 99 : | } | ||
| 100 : | |||
| 101 : | flag_error($genome, $job->id, $jobdir, $meta, "luster_stage_in"); | ||
| 102 : | |||
| 103 : | croak "$0: $msg"; | ||
| 104 : | } | ||
| 105 : |
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