[ARVADOS] updated: 4db7620243da1b74d41a44ef9d1c6a200b6eaae5
git at public.curoverse.com
git at public.curoverse.com
Mon Jun 15 17:41:02 EDT 2015
Summary of changes:
sdk/cli/bin/crunch-job | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
discards 85c53a9973232f020c55e08c0a788186c21477e8 (commit)
via 4db7620243da1b74d41a44ef9d1c6a200b6eaae5 (commit)
This update added new revisions after undoing existing revisions. That is
to say, the old revision is not a strict subset of the new revision. This
situation occurs when you --force push a change and generate a repository
containing something like this:
* -- * -- B -- O -- O -- O (85c53a9973232f020c55e08c0a788186c21477e8)
\
N -- N -- N (4db7620243da1b74d41a44ef9d1c6a200b6eaae5)
When this happens we assume that you've already had alert emails for all
of the O revisions, and so we here report only the revisions in the N
branch from the common base, B.
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 4db7620243da1b74d41a44ef9d1c6a200b6eaae5
Author: Brett Smith <brett at curoverse.com>
Date: Mon Jun 15 13:54:36 2015 -0400
4410: Crunch retries jobs when all SLURM nodes fail.
See the ticket for detailed background discussion and implementation
rationale, especially notes 13 and 14.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index d8ae6e6..f8b7e16 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -98,6 +98,7 @@ use File::Path qw( make_path remove_tree );
use constant TASK_TEMPFAIL => 111;
use constant EX_TEMPFAIL => 75;
+use constant EX_RETRY_UNLOCKED => 93;
$ENV{"TMPDIR"} ||= "/tmp";
unless (defined $ENV{"CRUNCH_TMP"}) {
@@ -721,6 +722,7 @@ ONELEVEL:
my $thisround_succeeded = 0;
my $thisround_failed = 0;
my $thisround_failed_multiple = 0;
+my $working_slot_count = scalar(@slot);
@jobstep_todo = sort { $jobstep[$a]->{level} <=> $jobstep[$b]->{level}
or $a <=> $b } @jobstep_todo;
@@ -986,6 +988,8 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
{
update_progress_stats();
}
+ $working_slot_count = scalar(grep { $_->{node}->{losing_streak} == 0 &&
+ $_->{node}->{hold_count} < 4 } @slot);
if (($thisround_failed_multiple >= 8 && $thisround_succeeded == 0) ||
($thisround_failed_multiple >= 16 && $thisround_failed_multiple > $thisround_succeeded))
{
@@ -1009,10 +1013,8 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
}
# give up if no nodes are succeeding
- if (!grep { $_->{node}->{losing_streak} == 0 &&
- $_->{node}->{hold_count} < 4 } @slot) {
- my $message = "Every node has failed -- giving up on this round";
- Log (undef, $message);
+ if ($working_slot_count < 1) {
+ Log(undef, "Every node has failed -- giving up");
last THISROUND;
}
}
@@ -1048,18 +1050,17 @@ freeze_if_want_freeze();
if (!defined $main::success)
{
- if (@jobstep_todo &&
- $thisround_succeeded == 0 &&
- ($thisround_failed == 0 || $thisround_failed > 4))
- {
+ if (!@jobstep_todo) {
+ $main::success = 1;
+ } elsif ($working_slot_count < 1) {
+ save_meta();
+ exit(EX_RETRY_UNLOCKED);
+ } elsif ($thisround_succeeded == 0 &&
+ ($thisround_failed == 0 || $thisround_failed > 4)) {
my $message = "stop because $thisround_failed tasks failed and none succeeded";
Log (undef, $message);
$main::success = 0;
}
- if (!@jobstep_todo)
- {
- $main::success = 1;
- }
}
goto ONELEVEL if !defined $main::success;
@@ -1556,6 +1557,8 @@ sub fhbits
# Send log output to Keep via arv-put.
#
# $log_pipe_in and $log_pipe_out are the input and output filehandles to the arv-put pipe.
+# $log_pipe_out_buf is a string containing all output read from arv-put so far.
+# $log_pipe_out_select is an IO::Select object around $log_pipe_out.
# $log_pipe_pid is the pid of the arv-put subprocess.
#
# The only functions that should access these variables directly are:
@@ -1564,6 +1567,13 @@ sub fhbits
# Starts an arv-put pipe, reading data on stdin and writing it to
# a $logfilename file in an output collection.
#
+# log_writer_read_output([$timeout])
+# Read output from $log_pipe_out and append it to $log_pipe_out_buf.
+# Passes $timeout to the select() call, with a default of 0.01.
+# Returns the result of the last read() call on $log_pipe_out, or
+# -1 if read() wasn't called because select() timed out.
+# Only other log_writer_* functions should need to call this.
+#
# log_writer_send($txt)
# Writes $txt to the output log collection.
#
@@ -1574,25 +1584,40 @@ sub fhbits
# Returns a true value if there is currently a live arv-put
# process, false otherwise.
#
-my ($log_pipe_in, $log_pipe_out, $log_pipe_pid);
+my ($log_pipe_in, $log_pipe_out, $log_pipe_out_buf, $log_pipe_out_select,
+ $log_pipe_pid);
sub log_writer_start($)
{
my $logfilename = shift;
$log_pipe_pid = open2($log_pipe_out, $log_pipe_in,
'arv-put',
- '--portable-data-hash',
- '--project-uuid', $Job->{owner_uuid},
+ '--stream',
'--retries', '3',
- '--name', $logfilename,
'--filename', $logfilename,
'-');
+ $log_pipe_out_buf = "";
+ $log_pipe_out_select = IO::Select->new($log_pipe_out);
+}
+
+sub log_writer_read_output {
+ my $timeout = shift || 0.01;
+ my $read = -1;
+ while ($read && $log_pipe_out_select->can_read($timeout)) {
+ $read = read($log_pipe_out, $log_pipe_out_buf, 65536,
+ length($log_pipe_out_buf));
+ }
+ if (!defined($read)) {
+ Log(undef, "error reading log manifest from arv-put: $!");
+ }
+ return $read;
}
sub log_writer_send($)
{
my $txt = shift;
print $log_pipe_in $txt;
+ log_writer_read_output();
}
sub log_writer_finish()
@@ -1600,22 +1625,24 @@ sub log_writer_finish()
return unless $log_pipe_pid;
close($log_pipe_in);
- my $arv_put_output;
- my $s = IO::Select->new($log_pipe_out);
- if ($s->can_read(120)) {
- sysread($log_pipe_out, $arv_put_output, 1024);
- chomp($arv_put_output);
- } else {
+ my $read_result = log_writer_read_output(120);
+ if ($read_result == -1) {
Log (undef, "timed out reading from 'arv-put'");
+ } elsif ($read_result != 0) {
+ Log(undef, "failed to read arv-put log manifest to EOF");
}
waitpid($log_pipe_pid, 0);
- $log_pipe_pid = $log_pipe_in = $log_pipe_out = undef;
if ($?) {
- Log("log_writer_finish: arv-put exited ".exit_status_s($?))
+ Log(undef, "log_writer_finish: arv-put exited " . exit_status_s($?))
}
+ close($log_pipe_out);
+ my $arv_put_output = $log_pipe_out_buf;
+ $log_pipe_pid = $log_pipe_in = $log_pipe_out = $log_pipe_out_buf =
+ $log_pipe_out_select = undef;
+
return $arv_put_output;
}
@@ -1679,10 +1706,22 @@ sub save_meta
return if $justcheckpoint; # checkpointing is not relevant post-Warehouse.pm
return unless log_writer_is_active();
- my $loglocator = log_writer_finish();
- Log (undef, "log manifest is $loglocator");
- $Job->{'log'} = $loglocator;
- $Job->update_attributes('log', $loglocator);
+ my $log_manifest = "";
+ if ($Job->{log}) {
+ my $prev_log_coll = api_call("collections/get", uuid => $Job->{log});
+ $log_manifest .= $prev_log_coll->{manifest_text};
+ }
+ $log_manifest .= log_writer_finish();
+
+ my $log_coll = api_call(
+ "collections/create", ensure_unique_name => 1, collection => {
+ manifest_text => $log_manifest,
+ owner_uuid => $Job->{owner_uuid},
+ name => sprintf("Log from %s job %s", $Job->{script}, $Job->{uuid}),
+ });
+ Log(undef, "log manifest is " . $log_coll->{portable_data_hash});
+ $Job->{'log'} = $log_coll->{portable_data_hash};
+ $Job->update_attributes('log', $log_coll->{portable_data_hash});
}
diff --git a/services/api/script/crunch-dispatch.rb b/services/api/script/crunch-dispatch.rb
index 3c1e4c6..439bddb 100755
--- a/services/api/script/crunch-dispatch.rb
+++ b/services/api/script/crunch-dispatch.rb
@@ -54,6 +54,8 @@ class Dispatcher
include ApplicationHelper
EXIT_TEMPFAIL = 75
+ EXIT_RETRY_UNLOCKED = 93
+ RETRY_UNLOCKED_LIMIT = 3
def initialize
@crunch_job_bin = (ENV['CRUNCH_JOB_BIN'] || `which arv-crunch-job`.strip)
@@ -77,6 +79,8 @@ class Dispatcher
@pipe_auth_tokens = {}
@running = {}
@todo = []
+ @todo_job_retries = {}
+ @job_retry_counts = Hash.new(0)
@todo_pipelines = []
end
@@ -86,7 +90,7 @@ class Dispatcher
def refresh_todo
if $options[:jobs]
- @todo = Job.queue.select(&:repository)
+ @todo = @todo_job_retries.values + Job.queue.select(&:repository)
end
if $options[:pipelines]
@todo_pipelines = PipelineInstance.queue
@@ -417,6 +421,10 @@ class Dispatcher
'--job', job.uuid,
'--git-dir', @arvados_internal]
+ if @todo_job_retries.include?(job.uuid)
+ cmd_args << "--force-unlock"
+ end
+
$stderr.puts "dispatch: #{cmd_args.join ' '}"
begin
@@ -452,6 +460,7 @@ class Dispatcher
log_throttle_bytes_skipped: 0,
}
i.close
+ @todo_job_retries.delete(job.uuid)
update_node_status
end
end
@@ -650,18 +659,36 @@ class Dispatcher
# Wait the thread (returns a Process::Status)
exit_status = j_done[:wait_thr].value.exitstatus
+ exit_tempfail = exit_status == EXIT_TEMPFAIL
$stderr.puts "dispatch: child #{pid_done} exit #{exit_status}"
$stderr.puts "dispatch: job #{job_done.uuid} end"
jobrecord = Job.find_by_uuid(job_done.uuid)
- if exit_status != EXIT_TEMPFAIL and jobrecord.state == "Running"
- # crunch-job did not return exit code 75 (see below) and left the job in
- # the "Running" state, which means there was an unhandled error. Fail
- # the job.
- jobrecord.state = "Failed"
- if not jobrecord.save
- $stderr.puts "dispatch: jobrecord.save failed"
+
+ if exit_status == EXIT_RETRY_UNLOCKED
+ # The job failed because all of the nodes allocated to it
+ # failed. Only this crunch-dispatch process can retry the job:
+ # it's already locked, and there's no way to put it back in the
+ # Queued state. Put it in our internal todo list unless the job
+ # has failed this way excessively.
+ @job_retry_counts[jobrecord.uuid] += 1
+ exit_tempfail = @job_retry_counts[jobrecord.uuid] <= RETRY_UNLOCKED_LIMIT
+ if exit_tempfail
+ @todo_job_retries[jobrecord.uuid] = jobrecord
+ else
+ $stderr.puts("dispatch: job #{jobrecord.uuid} exceeded node failure retry limit -- giving up")
+ end
+ end
+
+ if !exit_tempfail
+ @job_retry_counts.delete(jobrecord.uuid)
+ if jobrecord.state == "Running"
+ # Apparently there was an unhandled error. Fail the job.
+ jobrecord.state = "Failed"
+ if not jobrecord.save
+ $stderr.puts "dispatch: jobrecord.save failed"
+ end
end
else
# Don't fail the job if crunch-job didn't even get as far as
@@ -670,6 +697,9 @@ class Dispatcher
# queue. If crunch-job exited after losing a race to another
# crunch-job process, it exits 75 and we should leave the job
# record alone so the winner of the race do its thing.
+ # If crunch-job exited after all of its allocated nodes failed,
+ # it exits 93, and we want to retry it later (see the
+ # EXIT_RETRY_UNLOCKED `if` block).
#
# There is still an unhandled race condition: If our crunch-job
# process is about to lose a race with another crunch-job
@@ -683,7 +713,7 @@ class Dispatcher
# Invalidate the per-job auth token, unless the job is still queued and we
# might want to try it again.
- if jobrecord.state != "Queued"
+ if jobrecord.state != "Queued" and !@todo_job_retries.include?(jobrecord.uuid)
j_done[:job_auth].update_attributes expires_at: Time.now
end
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list