X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3957f3dbb398a1039c8ebb12a008bf9a7f17a4f0..03e8ba641e0161f15d96351e2432805977fd9d57:/sdk/cli/bin/crunch-job diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job index 554a1431ee..b74d7af427 100755 --- a/sdk/cli/bin/crunch-job +++ b/sdk/cli/bin/crunch-job @@ -96,6 +96,7 @@ use File::Temp; use Fcntl ':flock'; use File::Path qw( make_path remove_tree ); +use constant TASK_TEMPFAIL => 111; use constant EX_TEMPFAIL => 75; $ENV{"TMPDIR"} ||= "/tmp"; @@ -361,7 +362,7 @@ if (!defined $no_clear_tmp) { # TODO: When #5036 is done and widely deployed, we can get rid of the # regular expression and just unmount everything with type fuse.keep. srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}], - ['bash', '-ec', 'mount -t fuse,fuse.keep | awk \'($3 ~ /\ykeep\y/){print $3}\' | xargs -r -n 1 fusermount -u -z; sleep 1; rm -rf $JOB_WORK $CRUNCH_INSTALL $CRUNCH_TMP/task $CRUNCH_TMP/src*']); + ['bash', '-ec', 'mount -t fuse,fuse.keep | awk \'($3 ~ /\ykeep\y/){print $3}\' | xargs -r -n 1 fusermount -u -z; sleep 1; rm -rf $JOB_WORK $CRUNCH_INSTALL $CRUNCH_TMP/task $CRUNCH_TMP/src* $CRUNCH_TMP/*.cid']); exit (1); } while (1) @@ -384,7 +385,7 @@ if ($docker_locator = $Job->{docker_image_locator}) { } $docker_stream =~ s/^\.//; my $docker_install_script = qq{ -if ! $docker_bin images -q --no-trunc | grep -qxF \Q$docker_hash\E; then +if ! $docker_bin images -q --no-trunc --all | grep -qxF \Q$docker_hash\E; then arv-get \Q$docker_locator$docker_stream/$docker_hash.tar\E | $docker_bin load fi }; @@ -670,6 +671,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) my $childslotname = join (".", $slot[$childslot]->{node}->{name}, $slot[$childslot]->{cpu}); + my $childpid = fork(); if ($childpid == 0) { @@ -721,7 +723,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) $command .= "&& exec arv-mount --by-id --allow-other $ENV{TASK_KEEPMOUNT} --exec "; if ($docker_hash) { - my $cidfile = "$ENV{CRUNCH_TMP}/$ENV{TASK_UUID}.cid"; + my $cidfile = "$ENV{CRUNCH_TMP}/$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}.cid"; $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$cidfile -poll=10000 "; $command .= "$docker_bin run --rm=true --attach=stdout --attach=stderr --attach=stdin -i --user=crunch --cidfile=$cidfile --sig-proxy "; @@ -831,7 +833,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) || (@slot > @freeslot && $todo_ptr+1 > $#jobstep_todo)) { - last THISROUND if $main::please_freeze; + last THISROUND if $main::please_freeze || defined($main::success); if ($main::please_info) { $main::please_info = 0; @@ -941,7 +943,7 @@ if (!$collated_output) { Log (undef, "Failed to write output collection"); } else { - Log(undef, "output hash " . $collated_output); + Log(undef, "job output $collated_output"); $Job->update_attributes('output' => $collated_output); } @@ -1010,7 +1012,7 @@ sub reapchildren { my $temporary_fail; $temporary_fail ||= $Jobstep->{node_fail}; - $temporary_fail ||= ($exitvalue == 111); + $temporary_fail ||= ($exitvalue == TASK_TEMPFAIL); ++$thisround_failed; ++$thisround_failed_multiple if $Jobstep->{'failures'} >= 1; @@ -1037,7 +1039,6 @@ sub reapchildren if (!$temporary_fail || $Jobstep->{'failures'} >= 3) { # Give up on this task, and the whole job $main::success = 0; - $main::please_freeze = 1; } # Put this task back on the todo queue push @jobstep_todo, $jobstepid; @@ -1056,7 +1057,9 @@ sub reapchildren $Jobstep->{'arvados_task'}->{finished_at} = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($Jobstep->{finishtime}); $Jobstep->{'arvados_task'}->save; process_stderr ($jobstepid, $task_success); - Log ($jobstepid, "output " . $Jobstep->{'arvados_task'}->{output}); + Log ($jobstepid, sprintf("task output (%d bytes): %s", + length($Jobstep->{'arvados_task'}->{output}), + $Jobstep->{'arvados_task'}->{output})); close $reader{$jobstepid}; delete $reader{$jobstepid}; @@ -1230,7 +1233,7 @@ sub preprocess_stderr # whoa. $main::please_freeze = 1; } - elsif ($line =~ /srun: error: (Node failure on|Unable to create job step) /) { + elsif ($line =~ /srun: error: (Node failure on|Unable to create job step|.*: Communication connection failure)/) { $jobstep[$job]->{node_fail} = 1; ban_node_by_slot($jobstep[$job]->{slotindex}); } @@ -1252,16 +1255,19 @@ sub process_stderr sub fetch_block { my $hash = shift; - my ($keep, $child_out, $output_block); - - my $cmd = "arv-get \Q$hash\E"; - open($keep, '-|', $cmd) or die "fetch_block: $cmd: $!"; - $output_block = ''; + my $keep; + if (!open($keep, "-|", "arv-get", "--retries", retry_count(), $hash)) { + Log(undef, "fetch_block run error from arv-get $hash: $!"); + return undef; + } + my $output_block = ""; while (1) { my $buf; my $bytes = sysread($keep, $buf, 1024 * 1024); if (!defined $bytes) { - die "reading from arv-get: $!"; + Log(undef, "fetch_block read error from arv-get: $!"); + $output_block = undef; + last; } elsif ($bytes == 0) { # sysread returns 0 at the end of the pipe. last; @@ -1271,60 +1277,80 @@ sub fetch_block } } close $keep; + if ($?) { + Log(undef, "fetch_block arv-get exited " . exit_status_s($?)); + $output_block = undef; + } return $output_block; } -# create_output_collections generates a new collection containing the -# output of each successfully completed task, and returns the -# portable_data_hash for the new collection. -# +# Create a collection by concatenating the output of all tasks (each +# task's output is either a manifest fragment, a locator for a +# manifest fragment stored in Keep, or nothing at all). Return the +# portable_data_hash of the new collection. sub create_output_collection { Log (undef, "collate"); my ($child_out, $child_in); - my $pid = open2($child_out, $child_in, 'python', '-c', - 'import arvados; ' . - 'import sys; ' . - 'print arvados.api()' . - '.collections()' . - '.create(body={"manifest_text":sys.stdin.read()})' . - '.execute()["portable_data_hash"]' - ); - + my $pid = open2($child_out, $child_in, 'python', '-c', q{ +import arvados +import sys +print (arvados.api("v1").collections(). + create(body={"manifest_text": sys.stdin.read()}). + execute(num_retries=int(sys.argv[1]))["portable_data_hash"]) +}, retry_count()); + + my $task_idx = -1; + my $manifest_size = 0; for (@jobstep) { - next if (!exists $_->{'arvados_task'}->{'output'} || - !$_->{'arvados_task'}->{'success'}); + ++$task_idx; my $output = $_->{'arvados_task'}->{output}; - if ($output !~ /^[0-9a-f]{32}(\+\S+)*$/) - { - print $child_in $output; - } - elsif (defined (my $outblock = fetch_block ($output))) - { - print $child_in $outblock; + next if (!defined($output)); + my $next_write; + if ($output =~ /^[0-9a-f]{32}(\+\S+)*$/) { + $next_write = fetch_block($output); + } else { + $next_write = $output; } - else - { - Log (undef, "XXX fetch_block($output) failed XXX"); + if (defined($next_write)) { + if (!defined(syswrite($child_in, $next_write))) { + # There's been an error writing. Stop the loop. + # We'll log details about the exit code later. + last; + } else { + $manifest_size += length($next_write); + } + } else { + my $uuid = $_->{'arvados_task'}->{'uuid'}; + Log (undef, "Error retrieving '$output' output by task $task_idx ($uuid)"); $main::success = 0; } } - $child_in->close; + close($child_in); + Log(undef, "collated output manifest text to send to API server is $manifest_size bytes with access tokens"); my $joboutput; my $s = IO::Select->new($child_out); if ($s->can_read(120)) { - sysread($child_out, $joboutput, 64 * 1024 * 1024); - chomp($joboutput); - # TODO: Ensure exit status == 0. + sysread($child_out, $joboutput, 1024 * 1024); + waitpid($pid, 0); + if ($?) { + Log(undef, "output collection creation exited " . exit_status_s($?)); + $joboutput = undef; + } else { + chomp($joboutput); + } } else { Log (undef, "timed out while creating output collection"); + foreach my $signal (2, 2, 2, 15, 15, 9) { + kill($signal, $pid); + last if waitpid($pid, WNOHANG) == -1; + sleep(1); + } } - # TODO: kill $pid instead of waiting, now that we've decided to - # ignore further output. - waitpid($pid, 0); + close($child_out); return $joboutput; } @@ -1398,8 +1424,11 @@ sub log_writer_start($) { my $logfilename = shift; $log_pipe_pid = open2($log_pipe_out, $log_pipe_in, - 'arv-put', '--portable-data-hash', + 'arv-put', + '--portable-data-hash', + '--project-uuid', $Job->{owner_uuid}, '--retries', '3', + '--name', $logfilename, '--filename', $logfilename, '-'); } @@ -1803,6 +1832,8 @@ use Fcntl ':flock'; use File::Path qw( make_path remove_tree ); use POSIX qw(getcwd); +use constant TASK_TEMPFAIL => 111; + # Map SDK subdirectories to the path environments they belong to. my %SDK_ENVVARS = ("perl/lib" => "PERLLIB", "ruby/lib" => "RUBYLIB"); @@ -1848,9 +1879,9 @@ if (@ARGV) { my $venv_dir = "$job_work/.arvados.venv"; my $venv_built = -e "$venv_dir/bin/activate"; if ((!$venv_built) and (-d $python_src) and can_run("virtualenv")) { - shell_or_die("virtualenv", "--quiet", "--system-site-packages", + shell_or_die(undef, "virtualenv", "--quiet", "--system-site-packages", "--python=python2.7", $venv_dir); - shell_or_die("$venv_dir/bin/pip", "--quiet", "install", "-I", $python_src); + shell_or_die(TASK_TEMPFAIL, "$venv_dir/bin/pip", "--quiet", "install", "-I", $python_src); $venv_built = 1; $Log->("Built Python SDK virtualenv"); } @@ -1946,12 +1977,12 @@ if ((-d $python_dir) and can_run("python2.7") and } if (-e "$destdir/crunch_scripts/install") { - shell_or_die ("$destdir/crunch_scripts/install", $install_dir); + shell_or_die (undef, "$destdir/crunch_scripts/install", $install_dir); } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") { # Old version - shell_or_die ("./tests/autotests.sh", $install_dir); + shell_or_die (undef, "./tests/autotests.sh", $install_dir); } elsif (-e "./install.sh") { - shell_or_die ("./install.sh", $install_dir); + shell_or_die (undef, "./install.sh", $install_dir); } if ($commit) { @@ -1972,15 +2003,24 @@ sub can_run { sub shell_or_die { + my $exitcode = shift; + if ($ENV{"DEBUG"}) { print STDERR "@_\n"; } if (system (@_) != 0) { my $err = $!; - my $exitstatus = sprintf("exit %d signal %d", $? >> 8, $? & 0x7f); + my $code = $?; + my $exitstatus = sprintf("exit %d signal %d", $code >> 8, $code & 0x7f); open STDERR, ">&STDERR_ORIG"; system ("cat $destdir.log >&2"); - die "@_ failed ($err): $exitstatus"; + warn "@_ failed ($err): $exitstatus"; + if (defined($exitcode)) { + exit $exitcode; + } + else { + exit (($code >> 8) || 1); + } } }