use POSIX ':sys_wait_h';
use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK);
use Arvados;
+use Digest::MD5 qw(md5_hex);
use Getopt::Long;
use IPC::Open2;
use IO::Select;
my $arv = Arvados->new('apiVersion' => 'v1');
-my $metastream;
+my $local_logfile;
my $User = $arv->{'users'}->{'current'}->execute;
$job_id = $Job->{'uuid'};
my $keep_logfile = $job_id . '.log.txt';
-my $local_logfile = File::Temp->new();
+$local_logfile = File::Temp->new();
$Job->{'runtime_constraints'} ||= {};
$Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0;
must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
}
-
+# If this job requires a Docker image, install that.
+my $docker_bin = "/usr/bin/docker.io";
+my $docker_image = $Job->{runtime_constraints}->{docker_image} || "";
+if ($docker_image) {
+ my $docker_pid = fork();
+ if ($docker_pid == 0)
+ {
+ srun (["srun", "--nodelist=" . join(' ', @node)],
+ [$docker_bin, 'pull', $docker_image]);
+ exit ($?);
+ }
+ while (1)
+ {
+ last if $docker_pid == waitpid (-1, WNOHANG);
+ freeze_if_want_freeze ($docker_pid);
+ select (undef, undef, undef, 0.1);
+ }
+ # If the Docker image was specified as a hash, pull will fail.
+ # Ignore that error. We'll see what happens when we try to run later.
+ if (($? != 0) && ($docker_image !~ /^[0-9a-fA-F]{5,64}$/))
+ {
+ croak("Installing Docker image $docker_image returned exit code $?");
+ }
+}
foreach (qw (script script_version script_parameters runtime_constraints))
{
qw(-n1 -c1 -N1 -D), $ENV{'TMPDIR'},
"--job-name=$job_id.$id.$$",
);
- my @execargs = qw(sh);
my $build_script_to_send = "";
my $command =
"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
$command .=
"&& perl -";
}
- $command .=
- "&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+ $command .= "&& exec arv-mount --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
+ if ($docker_image)
+ {
+ $command .= "$docker_bin run -i -a stdin -a stdout -a stderr ";
+ # Dynamically configure the container to use the host system as its
+ # DNS server. Get the host's global addresses from the ip command,
+ # and turn them into docker --dns options using gawk.
+ $command .=
+ q{$(ip -o address show scope global |
+ gawk 'match($4, /^([0-9\.:]+)\//, x){print "--dns", x[1]}') };
+ foreach my $env_key (qw(CRUNCH_SRC CRUNCH_TMP TASK_KEEPMOUNT))
+ {
+ $command .= "-v \Q$ENV{$env_key}:$ENV{$env_key}:rw\E ";
+ }
+ while (my ($env_key, $env_val) = each %ENV)
+ {
+ $command .= "-e \Q$env_key=$env_val\E ";
+ }
+ $command .= "\Q$docker_image\E ";
+ }
+ $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
my @execargs = ('bash', '-c', $command);
srun (\@srunargs, \@execargs, undef, $build_script_to_send);
exit (111);
release_allocation();
freeze();
+my $collated_output = &collate_output();
+
if ($job_has_uuid) {
- $Job->update_attributes('output' => &collate_output(),
- 'running' => 0,
- 'success' => $Job->{'output'} && $main::success,
+ $Job->update_attributes('running' => 0,
+ 'success' => $collated_output && $main::success,
'finished_at' => scalar gmtime)
}
-if ($Job->{'output'})
+if ($collated_output)
{
eval {
- my $manifest_text = `arv keep get ''\Q$Job->{'output'}\E`;
- $arv->{'collections'}->{'create'}->execute('collection' => {
- 'uuid' => $Job->{'output'},
+ open(my $orig_manifest, '-|', 'arv', 'keep', 'get', $collated_output)
+ or die "failed to get collated manifest: $!";
+ # Read the original manifest, and strip permission hints from it,
+ # so we can put the result in a Collection.
+ my @manifest_lines = ();
+ while (my $manifest_line = <$orig_manifest>) {
+ my @words = split(/ /, $manifest_line, -1);
+ foreach my $ii (0..$#words) {
+ if ($words[$ii] =~ /^[0-9a-f]{32}\+/) {
+ $words[$ii] =~ s/\+A[0-9a-f]{40}@[0-9a-f]{8}\b//;
+ }
+ }
+ push(@manifest_lines, join(" ", @words));
+ }
+ my $manifest_text = join("", @manifest_lines);
+ my $output = $arv->{'collections'}->{'create'}->execute('collection' => {
+ 'uuid' => md5_hex($manifest_text),
'manifest_text' => $manifest_text,
});
+ $Job->update_attributes('output' => $output->{uuid});
if ($Job->{'output_is_persistent'}) {
$arv->{'links'}->{'create'}->execute('link' => {
'tail_kind' => 'arvados#user',
delete $proc{$pid};
# Load new tasks
- my $newtask_list = $arv->{'job_tasks'}->{'list'}->execute(
- 'where' => {
- 'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid}
- },
- 'order' => 'qsequence'
- );
- foreach my $arvados_task (@{$newtask_list->{'items'}}) {
+ my $newtask_list = [];
+ my $newtask_results;
+ do {
+ $newtask_results = $arv->{'job_tasks'}->{'list'}->execute(
+ 'where' => {
+ 'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid}
+ },
+ 'order' => 'qsequence',
+ 'offset' => scalar(@$newtask_list),
+ );
+ push(@$newtask_list, @{$newtask_results->{items}});
+ } while (@{$newtask_results->{items}});
+ foreach my $arvados_task (@$newtask_list) {
my $jobstep = {
'level' => $arvados_task->{'sequence'},
'failures' => 0,
$message =~ s{([^ -\176])}{"\\" . sprintf ("%03o", ord($1))}ge;
$message .= "\n";
my $datetime;
- if ($metastream || -t STDERR) {
+ if ($local_logfile || -t STDERR) {
my @gmtime = gmtime;
$datetime = sprintf ("%04d-%02d-%02d_%02d:%02d:%02d",
$gmtime[5]+1900, $gmtime[4]+1, @gmtime[3,2,1,0]);
}
print STDERR ((-t STDERR) ? ($datetime." ".$message) : $message);
- if ($metastream) {
- print $metastream $datetime . " " . $message;
+ if ($local_logfile) {
+ print $local_logfile $datetime . " " . $message;
}
}
freeze() if @jobstep_todo;
collate_output() if @jobstep_todo;
cleanup();
- save_meta() if $metastream;
+ save_meta() if $local_logfile;
die;
}
. quotemeta($local_logfile->filename);
my $loglocator = `$cmd`;
die "system $cmd failed: $?" if $?;
+ chomp($loglocator);
$local_logfile = undef; # the temp file is automatically deleted
Log (undef, "log manifest is $loglocator");
projects / arvados.git / blobdiff