#!/usr/bin/perl # -*- mode: perl; perl-indent-level: 2; indent-tabs-mode: nil; -*- =head1 NAME crunch-job: Execute job steps, save snapshots as requested, collate output. =head1 SYNOPSIS Obtain job details from Arvados, run tasks on compute nodes (typically invoked by scheduler on controller): crunch-job --job x-y-z Obtain job details from command line, run tasks on local machine (typically invoked by application or developer on VM): crunch-job --job '{"script_version":"/path/to/tree","script":"scriptname",...}' =head1 OPTIONS =over =item --force-unlock If the job is already locked, steal the lock and run it anyway. =item --git-dir Path to .git directory where the specified commit is found. =item --job-api-token Arvados API authorization token to use during the course of the job. =item --no-clear-tmp Do not clear per-job/task temporary directories during initial job setup. This can speed up development and debugging when running jobs locally. =back =head1 RUNNING JOBS LOCALLY crunch-job's log messages appear on stderr along with the job tasks' stderr streams. The log is saved in Keep at each checkpoint and when the job finishes. If the job succeeds, the job's output locator is printed on stdout. While the job is running, the following signals are accepted: =over =item control-C, SIGINT, SIGQUIT Save a checkpoint, terminate any job tasks that are running, and stop. =item SIGALRM Save a checkpoint and continue. =item SIGHUP Refresh node allocation (i.e., check whether any nodes have been added or unallocated) and attributes of the Job record that should affect behavior (e.g., cancel job if cancelled_at becomes non-nil). =back =cut 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); use Getopt::Long; use IPC::Open2; use IO::Select; use File::Temp; use Fcntl ':flock'; use File::Path qw( make_path ); use constant EX_TEMPFAIL => 75; $ENV{"TMPDIR"} ||= "/tmp"; unless (defined $ENV{"CRUNCH_TMP"}) { $ENV{"CRUNCH_TMP"} = $ENV{"TMPDIR"} . "/crunch-job"; if ($ENV{"USER"} ne "crunch" && $< != 0) { # use a tmp dir unique for my uid $ENV{"CRUNCH_TMP"} .= "-$<"; } } # Create the tmp directory if it does not exist if ( ! -d $ENV{"CRUNCH_TMP"} ) { make_path $ENV{"CRUNCH_TMP"} or die "Failed to create temporary working directory: " . $ENV{"CRUNCH_TMP"}; } $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 $force_unlock; my $git_dir; my $jobspec; my $job_api_token; my $no_clear_tmp; my $resume_stash; GetOptions('force-unlock' => \$force_unlock, 'git-dir=s' => \$git_dir, 'job=s' => \$jobspec, 'job-api-token=s' => \$job_api_token, 'no-clear-tmp' => \$no_clear_tmp, 'resume-stash=s' => \$resume_stash, ); if (defined $job_api_token) { $ENV{ARVADOS_API_TOKEN} = $job_api_token; } my $have_slurm = exists $ENV{SLURM_JOBID} && exists $ENV{SLURM_NODELIST}; my $job_has_uuid = $jobspec =~ /^[-a-z\d]+$/; my $local_job = !$job_has_uuid; $SIG{'USR1'} = sub { $main::ENV{CRUNCH_DEBUG} = 1; }; $SIG{'USR2'} = sub { $main::ENV{CRUNCH_DEBUG} = 0; }; my $arv = Arvados->new('apiVersion' => 'v1'); my $local_logfile; my $User = $arv->{'users'}->{'current'}->execute; my $Job = {}; my $job_id; my $dbh; my $sth; if ($job_has_uuid) { $Job = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec); if (!$force_unlock) { # If some other crunch-job process has grabbed this job (or we see # other evidence that the job is already underway) we exit # EX_TEMPFAIL so crunch-dispatch (our parent process) doesn't # mark the job as failed. if ($Job->{'is_locked_by_uuid'}) { Log(undef, "Job is locked by " . $Job->{'is_locked_by_uuid'}); exit EX_TEMPFAIL; } if ($Job->{'success'} ne undef) { Log(undef, "Job 'success' flag (" . $Job->{'success'} . ") is not null"); exit EX_TEMPFAIL; } if ($Job->{'running'}) { Log(undef, "Job 'running' flag is already set"); exit EX_TEMPFAIL; } if ($Job->{'started_at'}) { Log(undef, "Job 'started_at' time is already set (" . $Job->{'started_at'} . ")"); exit EX_TEMPFAIL; } } } else { $Job = JSON::decode_json($jobspec); if (!$resume_stash) { map { croak ("No $_ specified") unless $Job->{$_} } qw(script script_version script_parameters); } $Job->{'is_locked_by_uuid'} = $User->{'uuid'}; $Job->{'started_at'} = gmtime; $Job = $arv->{'jobs'}->{'create'}->execute('job' => $Job); $job_has_uuid = 1; } $job_id = $Job->{'uuid'}; my $keep_logfile = $job_id . '.log.txt'; $local_logfile = File::Temp->new(); $Job->{'runtime_constraints'} ||= {}; $Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0; my $max_ncpus = $Job->{'runtime_constraints'}->{'max_tasks_per_node'}; Log (undef, "check slurm allocation"); my @slot; my @node; # Should use $ENV{SLURM_TASKS_PER_NODE} instead of sinfo? (eg. "4(x3),2,4(x2)") my @sinfo; if (!$have_slurm) { my $localcpus = 0 + `grep -cw ^processor /proc/cpuinfo` || 1; push @sinfo, "$localcpus localhost"; } if (exists $ENV{SLURM_NODELIST}) { push @sinfo, `sinfo -h --format='%c %N' --nodes=\Q$ENV{SLURM_NODELIST}\E`; } foreach (@sinfo) { my ($ncpus, $slurm_nodelist) = split; $ncpus = $max_ncpus if $max_ncpus && $ncpus > $max_ncpus; my @nodelist; while ($slurm_nodelist =~ s/^([^\[,]+?(\[.*?\])?)(,|$)//) { my $nodelist = $1; if ($nodelist =~ /\[((\d+)(-(\d+))?(,(\d+)(-(\d+))?)*)\]/) { my $ranges = $1; foreach (split (",", $ranges)) { my ($a, $b); if (/(\d+)-(\d+)/) { $a = $1; $b = $2; } else { $a = $_; $b = $_; } push @nodelist, map { my $n = $nodelist; $n =~ s/\[[-,\d]+\]/$_/; $n; } ($a..$b); } } else { push @nodelist, $nodelist; } } foreach my $nodename (@nodelist) { Log (undef, "node $nodename - $ncpus slots"); my $node = { name => $nodename, ncpus => $ncpus, losing_streak => 0, hold_until => 0 }; foreach my $cpu (1..$ncpus) { push @slot, { node => $node, cpu => $cpu }; } } push @node, @nodelist; } # Ensure that we get one jobstep running on each allocated node before # we start overloading nodes with concurrent steps @slot = sort { $a->{cpu} <=> $b->{cpu} } @slot; my $jobmanager_id; if ($job_has_uuid) { # Claim this job, and make sure nobody else does unless ($Job->update_attributes('is_locked_by_uuid' => $User->{'uuid'}) && $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) { Log(undef, "Error while updating / locking job, exiting ".EX_TEMPFAIL); exit EX_TEMPFAIL; } $Job->update_attributes('started_at' => scalar gmtime, 'running' => 1, 'success' => undef, 'tasks_summary' => { 'failed' => 0, 'todo' => 1, 'running' => 0, 'done' => 0 }); } Log (undef, "start"); $SIG{'INT'} = sub { $main::please_freeze = 1; }; $SIG{'QUIT'} = sub { $main::please_freeze = 1; }; $SIG{'TERM'} = \&croak; $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}); $ENV{"CRUNCH_JOB_UUID"} = $job_id; $ENV{"JOB_UUID"} = $job_id; my @jobstep; my @jobstep_todo = (); my @jobstep_done = (); my @jobstep_tomerge = (); my $jobstep_tomerge_level = 0; my $squeue_checked; my $squeue_kill_checked; my $output_in_keep = 0; my $latest_refresh = scalar time; if (defined $Job->{thawedfromkey}) { thaw ($Job->{thawedfromkey}); } else { my $first_task = $arv->{'job_tasks'}->{'create'}->execute('job_task' => { 'job_uuid' => $Job->{'uuid'}, 'sequence' => 0, 'qsequence' => 0, 'parameters' => {}, }); push @jobstep, { 'level' => 0, 'failures' => 0, 'arvados_task' => $first_task, }; push @jobstep_todo, 0; } if (!$have_slurm) { must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here."); } my $build_script; $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version}; my $skip_install = ($local_job && $Job->{script_version} =~ m{^/}); if ($skip_install) { if (!defined $no_clear_tmp) { my $clear_tmp_cmd = 'rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*'; system($clear_tmp_cmd) == 0 or croak ("`$clear_tmp_cmd` failed: ".($?>>8)); } $ENV{"CRUNCH_SRC"} = $Job->{script_version}; for my $src_path ("$ENV{CRUNCH_SRC}/arvados/sdk/python") { if (-d $src_path) { system("virtualenv", "$ENV{CRUNCH_TMP}/opt") == 0 or croak ("virtualenv $ENV{CRUNCH_TMP}/opt failed: exit ".($?>>8)); system ("cd $src_path && ./build.sh && \$CRUNCH_TMP/opt/bin/python setup.py install") == 0 or croak ("setup.py in $src_path failed: exit ".($?>>8)); } } } else { do { local $/ = undef; $build_script = ; }; Log (undef, "Install revision ".$Job->{script_version}); my $nodelist = join(",", @node); if (!defined $no_clear_tmp) { # 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 for i in $JOB_WORK/*keep; do /bin/fusermount -z -u $i; done; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']); exit (1); } while (1) { last if $cleanpid == waitpid (-1, WNOHANG); freeze_if_want_freeze ($cleanpid); select (undef, undef, undef, 0.1); } Log (undef, "Clean-work-dir exited $?"); } # Install requested code version my @execargs; my @srunargs = ("srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}, "--job-name=$job_id"); $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version}; $ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src"; my $commit; my $git_archive; my $treeish = $Job->{'script_version'}; # If we're running under crunch-dispatch, it will have pulled the # appropriate source tree into its own repository, and given us that # repo's path as $git_dir. If we're running a "local" job, and a # script_version was specified, it's up to the user to provide the # full path to a local repository in Job->{repository}. # # TODO: Accept URLs too, not just local paths. Use git-ls-remote and # git-archive --remote where appropriate. # # TODO: Accept a locally-hosted Arvados repository by name or # UUID. Use arvados.v1.repositories.list or .get to figure out the # appropriate fetch-url. my $repo = $git_dir || $ENV{'CRUNCH_DEFAULT_GIT_DIR'} || $Job->{'repository'}; $ENV{"CRUNCH_SRC_URL"} = $repo; if (-d "$repo/.git") { # We were given a working directory, but we are only interested in # the index. $repo = "$repo/.git"; } # If this looks like a subversion r#, look for it in git-svn commit messages 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; Log(undef, "git Subversion search exited $?"); if (($? == 0) && ($gitlog =~ /^[a-f0-9]{40}$/)) { $commit = $gitlog; Log(undef, "Using commit $commit for Subversion revision $treeish"); } } # If that didn't work, try asking git to look it up as a tree-ish. if (!defined $commit) { my $found = `git --git-dir=\Q$repo\E rev-list -1 ''\Q$treeish\E`; chomp $found; 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. $Job->{'script_version'} = $commit; !$job_has_uuid or $Job->update_attributes('script_version' => $commit) or croak("Error while updating job"); } } } if (defined $commit) { $ENV{"CRUNCH_SRC_COMMIT"} = $commit; @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) { srun (\@srunargs, \@execargs, {}, $build_script . $git_archive); exit (1); } while (1) { last if $installpid == waitpid (-1, WNOHANG); freeze_if_want_freeze ($installpid); select (undef, undef, undef, 0.1); } Log (undef, "Install exited $?"); } if (!$have_slurm) { # Grab our lock again (we might have deleted and re-created CRUNCH_TMP above) must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here."); } # If this job requires a Docker image, install that. my $docker_bin = "/usr/bin/docker.io"; my ($docker_locator, $docker_stream, $docker_hash); if ($docker_locator = $Job->{docker_image_locator}) { ($docker_stream, $docker_hash) = find_docker_image($docker_locator); if (!$docker_hash) { croak("No Docker image hash found from locator $docker_locator"); } $docker_stream =~ s/^\.//; 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_stream/$docker_hash.tar\E | $docker_bin load fi }; my $docker_pid = fork(); if ($docker_pid == 0) { srun (["srun", "--nodelist=" . join(',', @node)], ["/bin/sh", "-ec", $docker_install_script]); exit ($?); } while (1) { last if $docker_pid == waitpid (-1, WNOHANG); freeze_if_want_freeze ($docker_pid); select (undef, undef, undef, 0.1); } if ($? != 0) { croak("Installing Docker image from $docker_locator returned exit code $?"); } } foreach (qw (script script_version script_parameters runtime_constraints)) { Log (undef, "$_ " . (ref($Job->{$_}) ? JSON::encode_json($Job->{$_}) : $Job->{$_})); } foreach (split (/\n/, $Job->{knobs})) { Log (undef, "knob " . $_); } $main::success = undef; ONELEVEL: my $thisround_succeeded = 0; my $thisround_failed = 0; my $thisround_failed_multiple = 0; @jobstep_todo = sort { $jobstep[$a]->{level} <=> $jobstep[$b]->{level} or $a <=> $b } @jobstep_todo; my $level = $jobstep[$jobstep_todo[0]]->{level}; Log (undef, "start level $level"); my %proc; my @freeslot = (0..$#slot); my @holdslot; my %reader; my $progress_is_dirty = 1; my $progress_stats_updated = 0; update_progress_stats(); THISROUND: for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) { my $id = $jobstep_todo[$todo_ptr]; my $Jobstep = $jobstep[$id]; if ($Jobstep->{level} != $level) { next; } pipe $reader{$id}, "writer" or croak ($!); my $flags = fcntl ($reader{$id}, F_GETFL, 0) or croak ($!); fcntl ($reader{$id}, F_SETFL, $flags | O_NONBLOCK) or croak ($!); my $childslot = $freeslot[0]; my $childnode = $slot[$childslot]->{node}; my $childslotname = join (".", $slot[$childslot]->{node}->{name}, $slot[$childslot]->{cpu}); my $childpid = fork(); if ($childpid == 0) { $SIG{'INT'} = 'DEFAULT'; $SIG{'QUIT'} = 'DEFAULT'; $SIG{'TERM'} = 'DEFAULT'; foreach (values (%reader)) { close($_); } fcntl ("writer", F_SETFL, 0) or croak ($!); # no close-on-exec open(STDOUT,">&writer"); open(STDERR,">&writer"); undef $dbh; undef $sth; delete $ENV{"GNUPGHOME"}; $ENV{"TASK_UUID"} = $Jobstep->{'arvados_task'}->{'uuid'}; $ENV{"TASK_QSEQUENCE"} = $id; $ENV{"TASK_SEQUENCE"} = $level; $ENV{"JOB_SCRIPT"} = $Job->{script}; while (my ($param, $value) = each %{$Job->{script_parameters}}) { $param =~ tr/a-z/A-Z/; $ENV{"JOB_PARAMETER_$param"} = $value; } $ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name}; $ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu}; $ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/$id.$$"; $ENV{"HOME"} = $ENV{"TASK_WORK"}; $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"}; $ENV{"GZIP"} = "-n"; my @srunargs = ( "srun", "--nodelist=".$childnode->{name}, qw(-n1 -c1 -N1 -D), $ENV{'TMPDIR'}, "--job-name=$job_id.$id.$$", ); my $build_script_to_send = ""; my $command = "if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; " ."mkdir -p $ENV{CRUNCH_TMP} $ENV{JOB_WORK} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} " ."&& cd $ENV{CRUNCH_TMP} "; if ($build_script) { $build_script_to_send = $build_script; $command .= "&& perl -"; } $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 "; $command .= "$docker_bin run --rm=true --attach=stdout --attach=stderr --user=crunch --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. $command .= q{$(ip -o address show scope global | gawk 'match($4, /^([0-9\.:]+)\//, x){print "--dns", x[1]}') }; $command .= "--volume=\Q$ENV{CRUNCH_SRC}:/tmp/crunch-src:ro\E "; $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E "; $command .= "--env=\QHOME=/home/crunch\E "; while (my ($env_key, $env_val) = each %ENV) { if ($env_key =~ /^(ARVADOS|JOB|TASK)_/) { if ($env_key eq "TASK_WORK") { $command .= "--env=\QTASK_WORK=/tmp/crunch-job\E "; } elsif ($env_key eq "TASK_KEEPMOUNT") { $command .= "--env=\QTASK_KEEPMOUNT=/keep\E "; } else { $command .= "--env=\Q$env_key=$env_val\E "; } } } $command .= "--env=\QCRUNCH_NODE_SLOTS=$ENV{CRUNCH_NODE_SLOTS}\E "; $command .= "--env=\QCRUNCH_SRC=/tmp/crunch-src\E "; $command .= "\Q$docker_hash\E "; $command .= "stdbuf --output=0 --error=0 "; $command .= "/tmp/crunch-src/crunch_scripts/" . $Job->{"script"}; } else { # Non-docker run $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 "; $command .= "stdbuf --output=0 --error=0 "; $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"}; } my @execargs = ('bash', '-c', $command); srun (\@srunargs, \@execargs, undef, $build_script_to_send); # exec() failed, we assume nothing happened. Log(undef, "srun() failed on build script"); die; } close("writer"); if (!defined $childpid) { close $reader{$id}; delete $reader{$id}; next; } shift @freeslot; $proc{$childpid} = { jobstep => $id, time => time, slot => $childslot, jobstepname => "$job_id.$id.$childpid", }; croak ("assert failed: \$slot[$childslot]->{'pid'} exists") if exists $slot[$childslot]->{pid}; $slot[$childslot]->{pid} = $childpid; Log ($id, "job_task ".$Jobstep->{'arvados_task'}->{'uuid'}); Log ($id, "child $childpid started on $childslotname"); $Jobstep->{starttime} = time; $Jobstep->{node} = $childnode->{name}; $Jobstep->{slotindex} = $childslot; 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; $progress_is_dirty = 1; while (!@freeslot || (@slot > @freeslot && $todo_ptr+1 > $#jobstep_todo)) { last THISROUND if $main::please_freeze; if ($main::please_info) { $main::please_info = 0; freeze(); collate_output(); save_meta(1); update_progress_stats(); } my $gotsome = readfrompipes () + reapchildren (); if (!$gotsome) { check_refresh_wanted(); check_squeue(); update_progress_stats(); select (undef, undef, undef, 0.1); } elsif (time - $progress_stats_updated >= 30) { update_progress_stats(); } if (($thisround_failed_multiple >= 8 && $thisround_succeeded == 0) || ($thisround_failed_multiple >= 16 && $thisround_failed_multiple > $thisround_succeeded)) { my $message = "Repeated failure rate too high ($thisround_failed_multiple/" .($thisround_failed+$thisround_succeeded) .") -- giving up on this round"; Log (undef, $message); last THISROUND; } # move slots from freeslot to holdslot (or back to freeslot) if necessary for (my $i=$#freeslot; $i>=0; $i--) { if ($slot[$freeslot[$i]]->{node}->{hold_until} > scalar time) { push @holdslot, (splice @freeslot, $i, 1); } } for (my $i=$#holdslot; $i>=0; $i--) { if ($slot[$holdslot[$i]]->{node}->{hold_until} <= scalar time) { push @freeslot, (splice @holdslot, $i, 1); } } # 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); last THISROUND; } } } push @freeslot, splice @holdslot; map { $slot[$freeslot[$_]]->{node}->{losing_streak} = 0 } (0..$#freeslot); Log (undef, "wait for last ".(scalar keys %proc)." children to finish"); while (%proc) { if ($main::please_continue) { $main::please_continue = 0; goto THISROUND; } $main::please_info = 0, freeze(), collate_output(), save_meta(1) if $main::please_info; readfrompipes (); if (!reapchildren()) { check_refresh_wanted(); check_squeue(); update_progress_stats(); select (undef, undef, undef, 0.1); killem (keys %proc) if $main::please_freeze; } } update_progress_stats(); freeze_if_want_freeze(); if (!defined $main::success) { if (@jobstep_todo && $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; 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"); } else { eval { open(my $orig_manifest, '-|', 'arv-get', $collated_output) or die "failed to get collated manifest: $!"; my $orig_manifest_text = ''; while (my $manifest_line = <$orig_manifest>) { $orig_manifest_text .= $manifest_line; } my $output = $arv->{'collections'}->{'create'}->execute('collection' => { 'manifest_text' => $orig_manifest_text, }); 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: $@"); } } Log (undef, "finish"); save_meta(); exit ($Job->{'success'} ? 1 : 0); sub update_progress_stats { $progress_stats_updated = time; return if !$progress_is_dirty; my ($todo, $done, $running) = (scalar @jobstep_todo, scalar @jobstep_done, scalar @slot - scalar @freeslot - scalar @holdslot); $Job->{'tasks_summary'} ||= {}; $Job->{'tasks_summary'}->{'todo'} = $todo; $Job->{'tasks_summary'}->{'done'} = $done; $Job->{'tasks_summary'}->{'running'} = $running; 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; } sub reapchildren { my $pid = waitpid (-1, WNOHANG); return 0 if $pid <= 0; my $whatslot = ($slot[$proc{$pid}->{slot}]->{node}->{name} . "." . $slot[$proc{$pid}->{slot}]->{cpu}); my $jobstepid = $proc{$pid}->{jobstep}; my $elapsed = time - $proc{$pid}->{time}; my $Jobstep = $jobstep[$jobstepid]; 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 $task_success = $Jobstep->{'arvados_task'}->{success}; Log ($jobstepid, "child $pid on $whatslot $exitinfo success=$task_success"); if (!defined $task_success) { # task did not indicate one way or the other --> fail $Jobstep->{'arvados_task'}->{success} = 0; $Jobstep->{'arvados_task'}->save; $task_success = 0; } if (!$task_success) { my $temporary_fail; $temporary_fail ||= $Jobstep->{node_fail}; $temporary_fail ||= ($exitvalue == 111); ++$thisround_failed; ++$thisround_failed_multiple if $Jobstep->{'failures'} >= 1; # Check for signs of a failed or misconfigured node if (++$slot[$proc{$pid}->{slot}]->{node}->{losing_streak} >= 2+$slot[$proc{$pid}->{slot}]->{node}->{ncpus}) { # 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) { Log ($jobstepid, "blaming failure on suspect node " . $slot[$proc{$pid}->{slot}]->{node}->{name}); $temporary_fail ||= 1; } ban_node_by_slot($proc{$pid}->{slot}); } Log ($jobstepid, sprintf('failure (#%d, %s) after %d seconds', ++$Jobstep->{'failures'}, $temporary_fail ? 'temporary ' : 'permanent', $elapsed)); 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 { ++$thisround_succeeded; $slot[$proc{$pid}->{slot}]->{node}->{losing_streak} = 0; $slot[$proc{$pid}->{slot}]->{node}->{hold_until} = 0; push @jobstep_done, $jobstepid; Log ($jobstepid, "success in $elapsed seconds"); } $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}); close $reader{$jobstepid}; delete $reader{$jobstepid}; delete $slot[$proc{$pid}->{slot}]->{pid}; push @freeslot, $proc{$pid}->{slot}; delete $proc{$pid}; if ($task_success) { # Load new tasks my $newtask_list = []; my $newtask_results; do { $newtask_results = $arv->{'job_tasks'}->{'list'}->execute( 'where' => { 'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid} }, 'order' => 'qsequence', 'offset' => scalar(@$newtask_list), ); push(@$newtask_list, @{$newtask_results->{items}}); } while (@{$newtask_results->{items}}); foreach my $arvados_task (@$newtask_list) { my $jobstep = { 'level' => $arvados_task->{'sequence'}, 'failures' => 0, 'arvados_task' => $arvados_task }; push @jobstep, $jobstep; push @jobstep_todo, $#jobstep; } } $progress_is_dirty = 1; 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 { # return if the kill list was checked <4 seconds ago if (defined $squeue_kill_checked && $squeue_kill_checked > time - 4) { return; } $squeue_kill_checked = time; # use killem() on procs whose killtime is reached for (keys %proc) { if (exists $proc{$_}->{killtime} && $proc{$_}->{killtime} <= time) { killem ($_); } } # return if the squeue was checked <60 seconds ago if (defined $squeue_checked && $squeue_checked > time - 60) { return; } $squeue_checked = time; if (!$have_slurm) { # here is an opportunity to check for mysterious problems with local procs return; } # get a list of steps still running my @squeue = `squeue -s -h -o '%i %j' && echo ok`; chop @squeue; if ($squeue[-1] ne "ok") { return; } pop @squeue; # which of my jobsteps are running, according to squeue? my %ok; foreach (@squeue) { if (/^(\d+)\.(\d+) (\S+)/) { if ($1 eq $ENV{SLURM_JOBID}) { $ok{$3} = 1; } } } # which of my active child procs (>60s old) were not mentioned by squeue? foreach (keys %proc) { if ($proc{$_}->{time} < time - 60 && !exists $ok{$proc{$_}->{jobstepname}} && !exists $proc{$_}->{killtime}) { # kill this proc if it hasn't exited in 30 seconds $proc{$_}->{killtime} = time + 30; } } } sub release_allocation { if ($have_slurm) { Log (undef, "release job allocation"); system "scancel $ENV{SLURM_JOBID}"; } } sub readfrompipes { my $gotsome = 0; foreach my $job (keys %reader) { my $buf; while (0 < sysread ($reader{$job}, $buf, 8192)) { print STDERR $buf if $ENV{CRUNCH_DEBUG}; $jobstep[$job]->{stderr} .= $buf; preprocess_stderr ($job); if (length ($jobstep[$job]->{stderr}) > 16384) { substr ($jobstep[$job]->{stderr}, 0, 8192) = ""; } $gotsome = 1; } } return $gotsome; } sub preprocess_stderr { my $job = shift; while ($jobstep[$job]->{stderr} =~ /^(.*?)\n/) { my $line = $1; substr $jobstep[$job]->{stderr}, 0, 1+length($line), ""; Log ($job, "stderr $line"); if ($line =~ /srun: error: (SLURM job $ENV{SLURM_JOB_ID} has expired|Unable to confirm allocation for job $ENV{SLURM_JOB_ID})/) { # whoa. $main::please_freeze = 1; } elsif ($line =~ /srun: error: (Node failure on|Unable to create job step) /) { $jobstep[$job]->{node_fail} = 1; ban_node_by_slot($jobstep[$job]->{slotindex}); } } } sub process_stderr { my $job = shift; my $task_success = shift; preprocess_stderr ($job); map { Log ($job, "stderr $_"); } split ("\n", $jobstep[$job]->{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 = ''; while (1) { my $buf; my $bytes = sysread($keep, $buf, 1024 * 1024); if (!defined $bytes) { die "reading from arv-get: $!"; } elsif ($bytes == 0) { # sysread returns 0 at the end of the pipe. last; } else { # some bytes were read into buf. $output_block .= $buf; } } close $keep; return $output_block; } sub collate_output { Log (undef, "collate"); my ($child_out, $child_in); my $pid = open2($child_out, $child_in, 'arv-put', '--raw'); my $joboutput; for (@jobstep) { next if (!exists $_->{'arvados_task'}->{'output'} || !$_->{'arvados_task'}->{'success'}); my $output = $_->{'arvados_task'}->{output}; if ($output !~ /^[0-9a-f]{32}(\+\S+)*$/) { $output_in_keep ||= $output =~ / [0-9a-f]{32}\S*\+K/; print $child_in $output; } elsif (@jobstep == 1) { $joboutput = $output; last; } elsif (defined (my $outblock = fetch_block ($output))) { $output_in_keep ||= $outblock =~ / [0-9a-f]{32}\S*\+K/; print $child_in $outblock; } else { Log (undef, "XXX fetch_block($output) failed XXX"); $main::success = 0; } } $child_in->close; if (!defined $joboutput) { my $s = IO::Select->new($child_out); if ($s->can_read(120)) { sysread($child_out, $joboutput, 64 * 1024 * 1024); chomp($joboutput); } else { Log (undef, "timed out reading from 'arv-put'"); } } waitpid($pid, 0); return $joboutput; } sub killem { foreach (@_) { my $sig = 2; # SIGINT first if (exists $proc{$_}->{"sent_$sig"} && time - $proc{$_}->{"sent_$sig"} > 4) { $sig = 15; # SIGTERM if SIGINT doesn't work } if (exists $proc{$_}->{"sent_$sig"} && time - $proc{$_}->{"sent_$sig"} > 4) { $sig = 9; # SIGKILL if SIGTERM doesn't work } if (!exists $proc{$_}->{"sent_$sig"}) { Log ($proc{$_}->{jobstep}, "sending 2x signal $sig to pid $_"); kill $sig, $_; select (undef, undef, undef, 0.1); if ($sig == 2) { kill $sig, $_; # srun wants two SIGINT to really interrupt } $proc{$_}->{"sent_$sig"} = time; $proc{$_}->{"killedafter"} = time - $proc{$_}->{"time"}; } } } sub fhbits { my($bits); for (@_) { vec($bits,fileno($_),1) = 1; } $bits; } sub Log # ($jobstep_id, $logmessage) { if ($_[1] =~ /\n/) { for my $line (split (/\n/, $_[1])) { Log ($_[0], $line); } return; } my $fh = select STDERR; $|=1; select $fh; my $message = sprintf ("%s %d %s %s", $job_id, $$, @_); $message =~ s{([^ -\176])}{"\\" . sprintf ("%03o", ord($1))}ge; $message .= "\n"; my $datetime; if ($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) : $message); if ($local_logfile) { print $local_logfile $datetime . " " . $message; } } sub croak { my ($package, $file, $line) = caller; my $message = "@_ at $file line $line\n"; Log (undef, $message); freeze() if @jobstep_todo; collate_output() if @jobstep_todo; cleanup(); save_meta() if $local_logfile; die; } sub cleanup { return if !$job_has_uuid; $Job->update_attributes('running' => 0, 'success' => 0, 'finished_at' => scalar gmtime); } sub save_meta { my $justcheckpoint = shift; # false if this will be the last meta saved return if $justcheckpoint; # checkpointing is not relevant post-Warehouse.pm $local_logfile->flush; my $cmd = "arv-put --portable-data-hash --filename ''\Q$keep_logfile\E " . quotemeta($local_logfile->filename); my $loglocator = `$cmd`; die "system $cmd failed: $?" if $?; chomp($loglocator); $local_logfile = undef; # the temp file is automatically deleted Log (undef, "log manifest is $loglocator"); $Job->{'log'} = $loglocator; $Job->update_attributes('log', $loglocator) if $job_has_uuid; } sub freeze_if_want_freeze { if ($main::please_freeze) { release_allocation(); if (@_) { # kill some srun procs before freeze+stop map { $proc{$_} = {} } @_; while (%proc) { killem (keys %proc); select (undef, undef, undef, 0.1); my $died; while (($died = waitpid (-1, WNOHANG)) > 0) { delete $proc{$died}; } } } freeze(); collate_output(); cleanup(); save_meta(); exit 0; } } sub freeze { Log (undef, "Freeze not implemented"); return; } sub thaw { croak ("Thaw not implemented"); } sub freezequote { my $s = shift; $s =~ s/\\/\\\\/g; $s =~ s/\n/\\n/g; return $s; } sub freezeunquote { my $s = shift; $s =~ s{\\(.)}{$1 eq "n" ? "\n" : $1}ge; return $s; } sub srun { my $srunargs = shift; my $execargs = shift; my $opts = shift || {}; my $stdin = shift; my $args = $have_slurm ? [@$srunargs, @$execargs] : $execargs; print STDERR (join (" ", map { / / ? "'$_'" : $_ } (@$args)), "\n") if $ENV{CRUNCH_DEBUG}; if (defined $stdin) { my $child = open STDIN, "-|"; defined $child or die "no fork: $!"; if ($child == 0) { print $stdin or die $!; close STDOUT or die $!; exit 0; } } return system (@$args) if $opts->{fork}; exec @$args; warn "ENV size is ".length(join(" ",%ENV)); die "exec failed: $!: @$args"; } sub ban_node_by_slot { # Don't start any new jobsteps on this node for 60 seconds my $slotid = shift; $slot[$slotid]->{node}->{hold_until} = 60 + scalar time; $slot[$slotid]->{node}->{hold_count}++; Log (undef, "backing off node " . $slot[$slotid]->{node}->{name} . " for 60 seconds"); } sub must_lock_now { my ($lockfile, $error_message) = @_; open L, ">", $lockfile or croak("$lockfile: $!"); if (!flock L, LOCK_EX|LOCK_NB) { croak("Can't lock $lockfile: $error_message\n"); } } sub find_docker_image { # Given a Keep locator, check to see if it contains a 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)) { 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(/:/, $filedata, 3))[2]; } } } } if (defined($filename) and ($filename =~ /^([0-9A-Fa-f]{64})\.tar$/)) { return ($streamname, $1); } else { return (undef, undef); } } __DATA__ #!/usr/bin/perl # 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) { if (@ARGV) { exec(@ARGV); die "Cannot exec `@ARGV`: $!"; } else { exit 0; } } unlink "$destdir.commit"; open STDOUT, ">", "$destdir.log"; open STDERR, ">&STDOUT"; mkdir $destdir; my @git_archive_data = ; if (@git_archive_data) { open TARX, "|-", "tar", "-C", $destdir, "-xf", "-"; print TARX @git_archive_data; if(!close(TARX)) { die "'tar -C $destdir -xf -' exited $?: $!"; } } my $pwd; chomp ($pwd = `pwd`); my $install_dir = $ENV{"CRUNCH_INSTALL"} || "$pwd/opt"; mkdir $install_dir; for my $src_path ("$destdir/arvados/sdk/python") { if (-d $src_path) { shell_or_die ("virtualenv", $install_dir); shell_or_die ("cd $src_path && ./build.sh && $install_dir/bin/python setup.py install"); } } if (-e "$destdir/crunch_scripts/install") { shell_or_die ("$destdir/crunch_scripts/install", $install_dir); } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") { # Old version shell_or_die ("./tests/autotests.sh", $install_dir); } elsif (-e "./install.sh") { shell_or_die ("./install.sh", $install_dir); } if ($commit) { unlink "$destdir.commit.new"; symlink ($commit, "$destdir.commit.new") or die "$destdir.commit.new: $!"; rename ("$destdir.commit.new", "$destdir.commit") or die "$destdir.commit: $!"; } close L; if (@ARGV) { exec(@ARGV); die "Cannot exec `@ARGV`: $!"; } else { exit 0; } sub shell_or_die { if ($ENV{"DEBUG"}) { print STDERR "@_\n"; } system (@_) == 0 or die "@_ failed: $! exit 0x".sprintf("%x",$?); } __DATA__