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;
# 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_locator, $docker_hash);
+if ($docker_locator = $Job->{docker_image_locator}) {
+ $docker_hash = find_docker_hash($docker_locator);
+ if (!$docker_hash)
+ {
+ croak("No Docker image hash found from locator $docker_locator");
+ }
+ my $docker_install_script = qq{
+if ! $docker_bin images -q --no-trunc | grep -qxF \Q$docker_hash\E; then
+ arv-get \Q$docker_locator/$docker_hash.tar\E | $docker_bin load
+fi
+};
my $docker_pid = fork();
if ($docker_pid == 0)
{
- srun (["srun", "--nodelist=" . join(' ', @node)],
- [$docker_bin, 'pull', $docker_image]);
+ srun (["srun", "--nodelist=" . join(',', @node)],
+ ["/bin/sh", "-ec", $docker_install_script]);
exit ($?);
}
while (1)
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) && ($docker_image !~ /^[0-9a-fA-F]{5,64}$/))
+ if ($? != 0)
{
- croak("Installing Docker image $docker_image returned exit code $?");
+ croak("Installing Docker image from $docker_locator returned exit code $?");
}
}
"&& perl -";
}
$command .= "&& exec arv-mount --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
- if ($docker_image)
+ if ($docker_hash)
{
- $command .= "$docker_bin run -i -a stdin -a stdout -a stderr ";
+ $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$ENV{TASK_WORK}/docker.cid -poll=10000 ";
+ $command .= "$docker_bin run -i -a stdin -a stdout -a stderr --cidfile=$ENV{TASK_WORK}/docker.cid ";
# Dynamically configure the container to use the host system as its
# DNS server. Get the host's global addresses from the ip command,
# and turn them into docker --dns options using gawk.
}
while (my ($env_key, $env_val) = each %ENV)
{
- $command .= "-e \Q$env_key=$env_val\E ";
+ if ($env_key =~ /^(ARVADOS|JOB|TASK)_/) {
+ $command .= "-e \Q$env_key=$env_val\E ";
+ }
}
- $command .= "\Q$docker_image\E ";
+ $command .= "\Q$docker_hash\E ";
+ } else {
+ $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 "
}
+ $command .= "stdbuf -o0 -e0 ";
$command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
my @execargs = ('bash', '-c', $command);
srun (\@srunargs, \@execargs, undef, $build_script_to_send);
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'},
- 'manifest_text' => $manifest_text,
+ 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 @stripped_manifest_lines = ();
+ my $orig_manifest_text = '';
+ while (my $manifest_line = <$orig_manifest>) {
+ $orig_manifest_text .= $manifest_line;
+ 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(@stripped_manifest_lines, join(" ", @words));
+ }
+ my $stripped_manifest_text = join("", @stripped_manifest_lines);
+ my $output = $arv->{'collections'}->{'create'}->execute('collection' => {
+ 'uuid' => md5_hex($stripped_manifest_text),
+ 'manifest_text' => $orig_manifest_text,
});
+ $Job->update_attributes('output' => $output->{uuid});
if ($Job->{'output_is_persistent'}) {
$arv->{'links'}->{'create'}->execute('link' => {
'tail_kind' => 'arvados#user',
$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;
}
}
}
+sub find_docker_hash {
+ # Given a Keep locator, search for a matching link to find the Docker hash
+ # of the stored image.
+ my $locator = shift;
+ my $links_result = $arv->{links}->{list}->execute(
+ filters => [["head_uuid", "=", $locator],
+ ["link_class", "=", "docker_image_hash"]],
+ limit => 1);
+ my $docker_hash;
+ foreach my $link (@{$links_result->{items}}) {
+ $docker_hash = lc($link->{name});
+ }
+ return $docker_hash;
+}
+
__DATA__
#!/usr/bin/perl
projects / arvados.git / blobdiff