=item SIGHUP
Refresh node allocation (i.e., check whether any nodes have been added
-or unallocated). Currently this is a no-op.
+or unallocated) and attributes of the Job record that should affect
+behavior (e.g., cancel job if cancelled_at becomes non-nil).
=back
}
}
$ENV{"JOB_WORK"} = $ENV{"CRUNCH_TMP"} . "/work";
+$ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";
$ENV{"CRUNCH_WORK"} = $ENV{"JOB_WORK"}; # deprecated
mkdir ($ENV{"JOB_WORK"});
my $local_job = !$job_has_uuid;
-$SIG{'HUP'} = sub
-{
- 1;
-};
$SIG{'USR1'} = sub
{
$main::ENV{CRUNCH_DEBUG} = 1;
-my $arv = Arvados->new;
-my $metastream = Warehouse::Stream->new(whc => new Warehouse);
-$metastream->clear;
-$metastream->write_start('log.txt');
+my $arv = Arvados->new('apiVersion' => 'v1');
+my $metastream;
my $User = $arv->{'users'}->{'current'}->execute;
}
$job_id = $Job->{'uuid'};
+$metastream = Warehouse::Stream->new(whc => new Warehouse);
+$metastream->clear;
+$metastream->name('.');
+$metastream->write_start($job_id . '.log.txt');
$Job->{'runtime_constraints'} ||= {};
if ($job_has_uuid)
{
# Claim this job, and make sure nobody else does
-
- $Job->{'is_locked_by_uuid'} = $User->{'uuid'};
- $Job->{'started_at'} = gmtime;
- $Job->{'running'} = 1;
- $Job->{'success'} = undef;
- $Job->{'tasks_summary'} = { 'failed' => 0,
- 'todo' => 1,
- 'running' => 0,
- 'done' => 0 };
- if ($job_has_uuid) {
- unless ($Job->save() && $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) {
- croak("Error while updating / locking job");
- }
+ unless ($Job->update_attributes('is_locked_by_uuid' => $User->{'uuid'}) &&
+ $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) {
+ croak("Error while updating / locking job");
}
+ $Job->update_attributes('started_at' => scalar gmtime,
+ 'running' => 1,
+ 'success' => undef,
+ 'tasks_summary' => { 'failed' => 0,
+ 'todo' => 1,
+ 'running' => 0,
+ 'done' => 0 });
}
$SIG{'TSTP'} = sub { $main::please_freeze = 1; };
$SIG{'ALRM'} = sub { $main::please_info = 1; };
$SIG{'CONT'} = sub { $main::please_continue = 1; };
+$SIG{'HUP'} = sub { $main::please_refresh = 1; };
+
$main::please_freeze = 0;
$main::please_info = 0;
$main::please_continue = 0;
+$main::please_refresh = 0;
my $jobsteps_must_output_keys = 0; # becomes 1 when any task outputs a key
grep { $ENV{$1} = $2 if /^(NOCACHE.*?)=(.*)/ } split ("\n", $$Job{knobs});
my $squeue_checked;
my $squeue_kill_checked;
my $output_in_keep = 0;
+my $latest_refresh = scalar time;
'parameters' => {},
});
push @jobstep, { 'level' => 0,
- 'attempts' => 0,
+ 'failures' => 0,
'arvados_task' => $first_task,
};
push @jobstep_todo, 0;
if ($skip_install)
{
$ENV{"CRUNCH_SRC"} = $Job->{script_version};
+ system("virtualenv", "$ENV{CRUNCH_TMP}/opt") == 0
+ or croak ("virtualenv $ENV{CRUNCH_TMP}/opt failed: exit ".($?>>8));
+ for my $src_path ("$ENV{CRUNCH_SRC}/arvados/sdk/python",
+ "$ENV{CRUNCH_SRC}/sdk/python") {
+ if (-d $src_path) {
+ system ("cd $src_path && \$CRUNCH_TMP/opt/bin/python setup.py install")
+ == 0
+ or croak ("setup.py in $src_path failed: exit ".($?>>8));
+ }
+ }
}
else
{
Log (undef, "Install revision ".$Job->{script_version});
my $nodelist = join(",", @node);
- # Clean out crunch_tmp/work and crunch_tmp/opt
+ # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
my $cleanpid = fork();
if ($cleanpid == 0)
{
srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
- ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt']);
+ ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']);
exit (1);
}
while (1)
$ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version};
$ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src";
- $ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";
my $commit;
my $git_archive;
Log (undef, "Using commit $commit for tree-ish $treeish");
if ($commit ne $treeish) {
$Job->{'script_version'} = $commit;
- !$job_has_uuid or $Job->save() or croak("Error while updating job");
+ !$job_has_uuid or
+ $Job->update_attributes('script_version' => $commit) or
+ croak("Error while updating job");
}
}
}
-my $success;
+$main::success = undef;
{
next;
}
- if ($Jobstep->{attempts} > 2)
- {
- Log ($id, "jobstep $id failed $$Jobstep{attempts} times -- giving up");
- $success = 0;
- last THISROUND;
- }
pipe $reader{$id}, "writer" or croak ($!);
my $flags = fcntl ($reader{$id}, F_GETFL, 0) or croak ($!);
$ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name};
$ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
$ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/".$slot[$childslot]->{cpu};
+ $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}."/keep";
$ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
$ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
+ $ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};
$ENV{"GZIP"} = "-n";
my @execargs = qw(sh);
my $build_script_to_send = "";
my $command =
- "mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} "
+ "if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
+ ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
."&& cd $ENV{CRUNCH_TMP} ";
if ($build_script)
{
}
$ENV{"PYTHONPATH"} =~ s{^}{:} if $ENV{"PYTHONPATH"};
$ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/sdk/python}; # xxx hack
+ $ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/arvados/sdk/python:}; # xxx hack
$ENV{"PYTHONPATH"} =~ s{$}{:/usr/local/arvados/src/sdk/python}; # xxx hack
$command .=
- "&& exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+ "&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
my @execargs = ('bash', '-c', $command);
srun (\@srunargs, \@execargs, undef, $build_script_to_send);
- exit (1);
+ exit (111);
}
close("writer");
if (!defined $childpid)
Log ($id, "job_task ".$Jobstep->{'arvados_task'}->{'uuid'});
Log ($id, "child $childpid started on $childslotname");
- $Jobstep->{attempts} ++;
$Jobstep->{starttime} = time;
$Jobstep->{node} = $childnode->{name};
$Jobstep->{slotindex} = $childslot;
+ reapchildren ();
if (!$gotsome)
{
+ check_refresh_wanted();
check_squeue();
update_progress_stats();
select (undef, undef, undef, 0.1);
readfrompipes ();
if (!reapchildren())
{
+ check_refresh_wanted();
check_squeue();
update_progress_stats();
select (undef, undef, undef, 0.1);
freeze_if_want_freeze();
-if (!defined $success)
+if (!defined $main::success)
{
if (@jobstep_todo &&
$thisround_succeeded == 0 &&
{
my $message = "stop because $thisround_failed tasks failed and none succeeded";
Log (undef, $message);
- $success = 0;
+ $main::success = 0;
}
if (!@jobstep_todo)
{
- $success = 1;
+ $main::success = 1;
}
}
-goto ONELEVEL if !defined $success;
+goto ONELEVEL if !defined $main::success;
release_allocation();
freeze();
-$Job->reload;
-$Job->{'output'} = &collate_output();
-$Job->{'running'} = 0;
-$Job->{'success'} = $Job->{'output'} && $success;
-$Job->{'finished_at'} = gmtime;
-$Job->save if $job_has_uuid;
+if ($job_has_uuid) {
+ $Job->update_attributes('output' => &collate_output(),
+ 'running' => 0,
+ 'success' => $Job->{'output'} && $main::success,
+ 'finished_at' => scalar gmtime)
+}
if ($Job->{'output'})
{
$Job->{'tasks_summary'}->{'todo'} = $todo;
$Job->{'tasks_summary'}->{'done'} = $done;
$Job->{'tasks_summary'}->{'running'} = $running;
- $Job->save if $job_has_uuid;
+ if ($job_has_uuid) {
+ $Job->update_attributes('tasks_summary' => $Job->{'tasks_summary'});
+ }
Log (undef, "status: $done done, $running running, $todo todo");
$progress_is_dirty = 0;
}
my $elapsed = time - $proc{$pid}->{time};
my $Jobstep = $jobstep[$jobstepid];
- my $exitcode = $?;
- my $exitinfo = "exit $exitcode";
+ my $childstatus = $?;
+ my $exitvalue = $childstatus >> 8;
+ my $exitinfo = sprintf("exit %d signal %d%s",
+ $exitvalue,
+ $childstatus & 127,
+ ($childstatus & 128 ? ' core dump' : ''));
$Jobstep->{'arvados_task'}->reload;
- my $success = $Jobstep->{'arvados_task'}->{success};
+ my $task_success = $Jobstep->{'arvados_task'}->{success};
- Log ($jobstepid, "child $pid on $whatslot $exitinfo success=$success");
+ Log ($jobstepid, "child $pid on $whatslot $exitinfo success=$task_success");
- if (!defined $success) {
+ if (!defined $task_success) {
# task did not indicate one way or the other --> fail
$Jobstep->{'arvados_task'}->{success} = 0;
$Jobstep->{'arvados_task'}->save;
- $success = 0;
+ $task_success = 0;
}
- if (!$success)
+ if (!$task_success)
{
- my $no_incr_attempts;
- $no_incr_attempts = 1 if $Jobstep->{node_fail};
+ my $temporary_fail;
+ $temporary_fail ||= $Jobstep->{node_fail};
+ $temporary_fail ||= ($exitvalue == 111);
++$thisround_failed;
- ++$thisround_failed_multiple if $Jobstep->{attempts} > 1;
+ ++$thisround_failed_multiple if $Jobstep->{'failures'} >= 1;
# Check for signs of a failed or misconfigured node
if (++$slot[$proc{$pid}->{slot}]->{node}->{losing_streak} >=
# Don't count this against jobstep failure thresholds if this
# node is already suspected faulty and srun exited quickly
if ($slot[$proc{$pid}->{slot}]->{node}->{hold_until} &&
- $elapsed < 5 &&
- $Jobstep->{attempts} > 1) {
- Log ($jobstepid, "blaming failure on suspect node " . $slot[$proc{$pid}->{slot}]->{node}->{name} . " instead of incrementing jobstep attempts");
- $no_incr_attempts = 1;
+ $elapsed < 5) {
+ Log ($jobstepid, "blaming failure on suspect node " .
+ $slot[$proc{$pid}->{slot}]->{node}->{name});
+ $temporary_fail ||= 1;
}
ban_node_by_slot($proc{$pid}->{slot});
}
- push @jobstep_todo, $jobstepid;
- Log ($jobstepid, "failure in $elapsed seconds");
+ Log ($jobstepid, sprintf('failure (#%d, %s) after %d seconds',
+ ++$Jobstep->{'failures'},
+ $temporary_fail ? 'temporary ' : 'permanent',
+ $elapsed));
- --$Jobstep->{attempts} if $no_incr_attempts;
+ if (!$temporary_fail || $Jobstep->{'failures'} >= 3) {
+ # Give up on this task, and the whole job
+ $main::success = 0;
+ $main::please_freeze = 1;
+ }
+ else {
+ # Put this task back on the todo queue
+ push @jobstep_todo, $jobstepid;
+ }
$Job->{'tasks_summary'}->{'failed'}++;
}
else
push @jobstep_done, $jobstepid;
Log ($jobstepid, "success in $elapsed seconds");
}
- $Jobstep->{exitcode} = $exitcode;
+ $Jobstep->{exitcode} = $childstatus;
$Jobstep->{finishtime} = time;
- process_stderr ($jobstepid, $success);
+ process_stderr ($jobstepid, $task_success);
Log ($jobstepid, "output " . $Jobstep->{'arvados_task'}->{output});
close $reader{$jobstepid};
foreach my $arvados_task (@{$newtask_list->{'items'}}) {
my $jobstep = {
'level' => $arvados_task->{'sequence'},
- 'attempts' => 0,
+ 'failures' => 0,
'arvados_task' => $arvados_task
};
push @jobstep, $jobstep;
1;
}
+sub check_refresh_wanted
+{
+ my @stat = stat $ENV{"CRUNCH_REFRESH_TRIGGER"};
+ if (@stat && $stat[9] > $latest_refresh) {
+ $latest_refresh = scalar time;
+ if ($job_has_uuid) {
+ my $Job2 = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec);
+ for my $attr ('cancelled_at',
+ 'cancelled_by_user_uuid',
+ 'cancelled_by_client_uuid') {
+ $Job->{$attr} = $Job2->{$attr};
+ }
+ if ($Job->{'cancelled_at'}) {
+ Log (undef, "Job cancelled at " . $Job->{cancelled_at} .
+ " by user " . $Job->{cancelled_by_user_uuid});
+ $main::success = 0;
+ $main::please_freeze = 1;
+ }
+ }
+ }
+}
sub check_squeue
{
sub process_stderr
{
my $job = shift;
- my $success = shift;
+ my $task_success = shift;
preprocess_stderr ($job);
map {
{
my $errstr = $whc->errstr;
$whc->write_data ("XXX fetch_block($output) failed: $errstr XXX\n");
- $success = 0;
+ $main::success = 0;
}
}
$joboutput = $whc->write_finish if !defined $joboutput;
if ($joboutput)
{
Log (undef, "output $joboutput");
- $Job->{'output'} = $joboutput;
- $Job->save if $job_has_uuid;
+ $Job->update_attributes('output' => $joboutput) if $job_has_uuid;
}
else
{
sub cleanup
{
return if !$job_has_uuid;
- $Job->reload;
- $Job->{'running'} = 0;
- $Job->{'success'} = 0;
- $Job->{'finished_at'} = gmtime;
- $Job->save;
+ $Job->update_attributes('running' => 0,
+ 'success' => 0,
+ 'finished_at' => scalar gmtime);
}
my $m = $metastream;
$m = $m->copy if $justcheckpoint;
$m->write_finish;
- my $loglocator = $m->as_key;
+ my $whc = Warehouse->new;
+ my $loglocator = $whc->store_block ($m->as_string);
+ $arv->{'collections'}->{'create'}->execute('collection' => {
+ 'uuid' => $loglocator,
+ 'manifest_text' => $m->as_string,
+ });
undef $metastream if !$justcheckpoint; # otherwise Log() will try to use it
- Log (undef, "meta key is $loglocator");
+ Log (undef, "log manifest is $loglocator");
$Job->{'log'} = $loglocator;
- $Job->save if $job_has_uuid;
+ $Job->update_attributes('log', $loglocator) if $job_has_uuid;
}
my ($k, $v) = split ("=", $_, 2);
$Jobstep->{$k} = freezeunquote ($v) if $k;
}
- $Jobstep->{attempts} = 0;
+ $Jobstep->{'failures'} = 0;
push @jobstep, $Jobstep;
if ($Jobstep->{exitcode} eq "0")
open L, ">", "$destdir.lock" or die "$destdir.lock: $!";
flock L, LOCK_EX;
-if (readlink ("$destdir.commit") eq $commit) {
+if (readlink ("$destdir.commit") eq $commit && -d $destdir) {
exit 0;
}
chomp ($pwd = `pwd`);
my $install_dir = $ENV{"CRUNCH_INSTALL"} || "$pwd/opt";
mkdir $install_dir;
+
+shell_or_die ("virtualenv", $install_dir);
+for my $src_path ("$destdir/arvados/sdk/python", "$destdir/sdk/python") {
+ if (-d $src_path) {
+ shell_or_die ("cd $src_path && $install_dir/bin/python setup.py install");
+ }
+}
+
if (-e "$destdir/crunch_scripts/install") {
shell_or_die ("$destdir/crunch_scripts/install", $install_dir);
} elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {
projects / arvados.git / blobdiff