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Revision 1.1 - (download) (as text) (annotate)
Wed Feb 6 22:16:37 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Support lustre work directory.

# Finish a job that has its work directories over on the
# lustre spool directory by copying them back and then
# setting the job to done.

use Data::Dumper;
use Carp;
use strict;
use FIG;
use FIG_Config;
use File::Basename;
use GenomeMeta;
use JobError;
use File::Basename;

@ARGV == 1 or die "Usage: $0 job-dir\n";

my $jobdir = shift;

-d $jobdir or die "$0: job dir $jobdir does not exist\n";

my $job = new Job48($jobdir);
$job or die "cannot create job for $jobdir";

my $hostname = `hostname`;
chomp $hostname;

my $genome = &FIG::file_head("$jobdir/GENOME_ID");
chomp $genome;
$genome =~ /^\d+\.\d+/ or die "$0: Cannnot find genome ID for jobdir $jobdir\n";

my $meta = new GenomeMeta($genome, "$jobdir/meta.xml");

my $genome_dir = "$jobdir/rp/$genome";

$meta->set_metadata("lustre_stage_in.hostname", $hostname);

$meta->add_log_entry($0, "copy lustre spooled job back to $jobdir");

# Find any directories in the jobdir that are symlinked to the lustre spool. Copy
# the contents back here.
opendir(D, $jobdir) or &fatal("cannot opendir $jobdir: $!");
for my $f (readdir(D))
    my $path = "$jobdir/$f";
    next unless -l $path;
    my $targ = readlink($path);
    if (!$targ)
	warn "Error reading symlink $path: $!";

    if ($targ =~ /^$FIG_Config::lustre_spool_dir/)
	warn "Copying back data from $targ to $path\n";
	my $targ_dir = dirname($targ);
	if ($targ_dir eq '' or ! -d $targ_dir)
	    warn "Some error extracting dirname '$targ_dir' from target '$targ'\n";
	my $tar_cmd = "tar -C $targ_dir -c -p -f - $f | tar -C $jobdir -x -p -f -";
	warn "Execute $tar_cmd\n";
	my $rc = system($tar_cmd);
	if ($rc != 0)
	    &fatal("Error $rc running tar cmd $tar_cmd\n");
if (open(D, ">$jobdir/DONE"))
    print D time . "\n";
    warn "Error opening $jobdir/DONE: $!\n";



sub fatal
    my($msg) = @_;

    if ($meta)
	$meta->add_log_entry($0, ['fatal error', $msg]);

    flag_error($genome, $job->id, $jobdir, $meta, "luster_stage_in");

    croak "$0: $msg";

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