X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1966eff7c92733225cd9fe1a4121ae0b8f1153d3..72d24b26cac507988ba6583064451b81d1854d78:/sdk/cli/bin/crunch-job diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job index 4b6632c45a..70f379e53f 100755 --- a/sdk/cli/bin/crunch-job +++ b/sdk/cli/bin/crunch-job @@ -74,6 +74,7 @@ behavior (e.g., cancel job if cancelled_at becomes non-nil). use strict; use POSIX ':sys_wait_h'; +use POSIX qw(strftime); use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK); use Arvados; use Digest::MD5 qw(md5_hex); @@ -447,9 +448,10 @@ else if ($treeish =~ m{^\d{1,4}$}) { my $gitlog = `git --git-dir=\Q$repo\E log --pretty="format:%H" --grep="git-svn-id:.*\@"\Q$treeish\E" " master`; chomp $gitlog; - if ($gitlog =~ /^[a-f0-9]{40}$/) { + Log(undef, "git Subversion search exited $?"); + if (($? == 0) && ($gitlog =~ /^[a-f0-9]{40}$/)) { $commit = $gitlog; - Log (undef, "Using commit $commit for script_version $treeish"); + Log(undef, "Using commit $commit for Subversion revision $treeish"); } } @@ -458,21 +460,19 @@ else if (!defined $commit) { my $found = `git --git-dir=\Q$repo\E rev-list -1 ''\Q$treeish\E`; chomp $found; - if ($found =~ /^[0-9a-f]{40}$/s) { + Log(undef, "git rev-list exited $? with result '$found'"); + if (($? == 0) && ($found =~ /^[0-9a-f]{40}$/s)) { $commit = $found; + Log(undef, "Using commit $commit for tree-ish $treeish"); if ($commit ne $treeish) { # Make sure we record the real commit id in the database, # frozentokey, logs, etc. -- instead of an abbreviation or a # branch name which can become ambiguous or point to a # different commit in the future. - $ENV{"CRUNCH_SRC_COMMIT"} = $commit; - Log (undef, "Using commit $commit for tree-ish $treeish"); - if ($commit ne $treeish) { - $Job->{'script_version'} = $commit; - !$job_has_uuid or - $Job->update_attributes('script_version' => $commit) or - croak("Error while updating job"); - } + $Job->{'script_version'} = $commit; + !$job_has_uuid or + $Job->update_attributes('script_version' => $commit) or + croak("Error while updating job"); } } } @@ -482,11 +482,14 @@ else @execargs = ("sh", "-c", "mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -"); $git_archive = `git --git-dir=\Q$repo\E archive ''\Q$commit\E`; + croak("git archive failed: exit " . ($? >> 8)) if ($? != 0); } else { croak ("could not figure out commit id for $treeish"); } + # Note: this section is almost certainly unnecessary if we're + # running tasks in docker containers. my $installpid = fork(); if ($installpid == 0) { @@ -649,7 +652,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) my $build_script_to_send = ""; my $command = "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}" + ."mkdir -p $ENV{CRUNCH_TMP} $ENV{JOB_WORK} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} " ."&& cd $ENV{CRUNCH_TMP} "; if ($build_script) { @@ -657,7 +660,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) $command .= "&& perl -"; } - $command .= "&& exec arv-mount --allow-other $ENV{TASK_KEEPMOUNT} --exec "; + $command .= "&& exec arv-mount --by-id --allow-other $ENV{TASK_KEEPMOUNT} --exec "; if ($docker_hash) { $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$ENV{TASK_WORK}/docker.cid -poll=10000 "; @@ -727,6 +730,9 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) delete $Jobstep->{stderr}; delete $Jobstep->{finishtime}; + $Jobstep->{'arvados_task'}->{started_at} = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($Jobstep->{starttime}); + $Jobstep->{'arvados_task'}->save; + splice @jobstep_todo, $todo_ptr, 1; --$todo_ptr; @@ -842,12 +848,6 @@ release_allocation(); freeze(); my $collated_output = &collate_output(); -if ($job_has_uuid) { - $Job->update_attributes('running' => 0, - 'success' => $collated_output && $main::success, - 'finished_at' => scalar gmtime) -} - if (!$collated_output) { Log(undef, "output undef"); } @@ -855,37 +855,16 @@ else { eval { open(my $orig_manifest, '-|', 'arv-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, }); - Log(undef, "output " . $output->{uuid}); - $Job->update_attributes('output' => $output->{uuid}) if $job_has_uuid; - if ($Job->{'output_is_persistent'}) { - $arv->{'links'}->{'create'}->execute('link' => { - 'tail_kind' => 'arvados#user', - 'tail_uuid' => $User->{'uuid'}, - 'head_kind' => 'arvados#collection', - 'head_uuid' => $Job->{'output'}, - 'link_class' => 'resources', - 'name' => 'wants', - }); - } + Log(undef, "output uuid " . $output->{uuid}); + Log(undef, "output hash " . $output->{portable_data_hash}); + $Job->update_attributes('output' => $output->{portable_data_hash}) if $job_has_uuid; }; if ($@) { Log (undef, "Failed to register output manifest: $@"); @@ -895,6 +874,13 @@ else { Log (undef, "finish"); save_meta(); + +if ($job_has_uuid) { + $Job->update_attributes('running' => 0, + 'success' => $collated_output && $main::success, + 'finished_at' => scalar gmtime) +} + exit ($Job->{'success'} ? 1 : 0); @@ -998,6 +984,8 @@ sub reapchildren } $Jobstep->{exitcode} = $childstatus; $Jobstep->{finishtime} = time; + $Jobstep->{'arvados_task'}->{finished_at} = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($Jobstep->{finishtime}); + $Jobstep->{'arvados_task'}->save; process_stderr ($jobstepid, $task_success); Log ($jobstepid, "output " . $Jobstep->{'arvados_task'}->{output}); @@ -1219,7 +1207,8 @@ sub collate_output Log (undef, "collate"); my ($child_out, $child_in); - my $pid = open2($child_out, $child_in, 'arv-put', '--raw'); + my $pid = open2($child_out, $child_in, 'arv-put', '--raw', + '--retries', put_retry_count()); my $joboutput; for (@jobstep) { @@ -1359,8 +1348,9 @@ sub save_meta return if $justcheckpoint; # checkpointing is not relevant post-Warehouse.pm $local_logfile->flush; - my $cmd = "arv-put --filename ''\Q$keep_logfile\E " - . quotemeta($local_logfile->filename); + my $retry_count = put_retry_count(); + my $cmd = "arv-put --portable-data-hash --retries $retry_count " . + "--filename ''\Q$keep_logfile\E " . quotemeta($local_logfile->filename); my $loglocator = `$cmd`; die "system $cmd failed: $?" if $?; chomp($loglocator); @@ -1484,14 +1474,40 @@ sub find_docker_image { # If so, return its stream name and Docker hash. # If not, return undef for both values. my $locator = shift; + my ($streamname, $filename); if (my $image = $arv->{collections}->{get}->execute(uuid => $locator)) { - my @file_list = @{$image->{files}}; - if ((scalar(@file_list) == 1) && - ($file_list[0][1] =~ /^([0-9A-Fa-f]{64})\.tar$/)) { - return ($file_list[0][0], $1); + foreach my $line (split(/\n/, $image->{manifest_text})) { + my @tokens = split(/\s+/, $line); + next if (!@tokens); + $streamname = shift(@tokens); + foreach my $filedata (grep(/^\d+:\d+:/, @tokens)) { + if (defined($filename)) { + return (undef, undef); # More than one file in the Collection. + } else { + $filename = (split(/:/, $filedata, 3))[2]; + } + } } } - return (undef, undef); + if (defined($filename) and ($filename =~ /^([0-9A-Fa-f]{64})\.tar$/)) { + return ($streamname, $1); + } else { + return (undef, undef); + } +} + +sub put_retry_count { + # Calculate a --retries argument for arv-put that will have it try + # approximately as long as this Job has been running. + my $stoptime = shift || time; + my $starttime = $jobstep[0]->{starttime}; + my $timediff = defined($starttime) ? ($stoptime - $starttime) : 1; + my $retries = 0; + while ($timediff >= 2) { + $retries++; + $timediff /= 2; + } + return ($retries > 3) ? $retries : 3; } __DATA__ @@ -1500,15 +1516,29 @@ __DATA__ # checkout-and-build use Fcntl ':flock'; +use File::Path qw( make_path ); my $destdir = $ENV{"CRUNCH_SRC"}; my $commit = $ENV{"CRUNCH_SRC_COMMIT"}; my $repo = $ENV{"CRUNCH_SRC_URL"}; +my $task_work = $ENV{"TASK_WORK"}; + +for my $dir ($destdir, $task_work) { + if ($dir) { + make_path $dir; + -e $dir or die "Failed to create temporary directory ($dir): $!"; + } +} open L, ">", "$destdir.lock" or die "$destdir.lock: $!"; flock L, LOCK_EX; if (readlink ("$destdir.commit") eq $commit && -d $destdir) { - exit 0; + if (@ARGV) { + exec(@ARGV); + die "Cannot exec `@ARGV`: $!"; + } else { + exit 0; + } } unlink "$destdir.commit"; @@ -1554,7 +1584,12 @@ if ($commit) { close L; -exit 0; +if (@ARGV) { + exec(@ARGV); + die "Cannot exec `@ARGV`: $!"; +} else { + exit 0; +} sub shell_or_die {