X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3c90228c2e0466b2e69c08e0ad610dd5d619b4f8..548e0c54db524cb7317850d4dfd8f3ee0b93cdb0:/sdk/cli/bin/crunch-job diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job index c8a1de9c65..39238b0fc6 100755 --- a/sdk/cli/bin/crunch-job +++ b/sdk/cli/bin/crunch-job @@ -126,6 +126,7 @@ my $jobspec; my $job_api_token; my $no_clear_tmp; my $resume_stash; +my $cgroup_root = "/sys/fs/cgroup"; my $docker_bin = "docker.io"; my $docker_run_args = ""; GetOptions('force-unlock' => \$force_unlock, @@ -134,6 +135,7 @@ GetOptions('force-unlock' => \$force_unlock, 'job-api-token=s' => \$job_api_token, 'no-clear-tmp' => \$no_clear_tmp, 'resume-stash=s' => \$resume_stash, + 'cgroup-root=s' => \$cgroup_root, 'docker-bin=s' => \$docker_bin, 'docker-run-args=s' => \$docker_run_args, ); @@ -183,11 +185,12 @@ if (($Job || $local_job)->{docker_image_locator}) { $cmd = [$docker_bin, 'ps', '-q']; } Log(undef, "Sanity check is `@$cmd`"); -srun(["srun", "--nodes=\Q$ENV{SLURM_NNODES}\E", "--ntasks-per-node=1"], - $cmd, - {fork => 1}); -if ($? != 0) { - Log(undef, "Sanity check failed: ".exit_status_s($?)); +my ($exited, $stdout, $stderr) = srun_sync( + ["srun", "--nodes=\Q$ENV{SLURM_NNODES}\E", "--ntasks-per-node=1"], + $cmd, + {label => "sanity check"}); +if ($exited != 0) { + Log(undef, "Sanity check failed: ".exit_status_s($exited)); exit EX_TEMPFAIL; } Log(undef, "Sanity check OK"); @@ -386,28 +389,17 @@ my $nodelist = join(",", @node); my $git_tar_count = 0; if (!defined $no_clear_tmp) { - # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src* - Log (undef, "Clean work dirs"); - - my $cleanpid = fork(); - if ($cleanpid == 0) - { - # Find FUSE mounts under $CRUNCH_TMP and unmount them. - # Then clean up work directories. - # TODO: When #5036 is done and widely deployed, we can limit mount's - # -t option to simply fuse.keep. - srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}], - ['bash', '-ec', '-o', 'pipefail', 'mount -t fuse,fuse.keep | awk "(index(\$3, \"$CRUNCH_TMP\") == 1){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) - { - last if $cleanpid == waitpid (-1, WNOHANG); - freeze_if_want_freeze ($cleanpid); - select (undef, undef, undef, 0.1); - } - if ($?) { - Log(undef, "Clean work dirs: exit ".exit_status_s($?)); + # Find FUSE mounts under $CRUNCH_TMP and unmount them. Then clean + # up work directories crunch_tmp/work, crunch_tmp/opt, + # crunch_tmp/src*. + # + # TODO: When #5036 is done and widely deployed, we can limit mount's + # -t option to simply fuse.keep. + my ($exited, $stdout, $stderr) = srun_sync( + ["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}], + ['bash', '-ec', '-o', 'pipefail', 'mount -t fuse,fuse.keep | awk "(index(\$3, \"$CRUNCH_TMP\") == 1){print \$3}" | xargs -r -n 1 fusermount -u -z; sleep 1; rm -rf $JOB_WORK $CRUNCH_INSTALL $CRUNCH_TMP/task $CRUNCH_TMP/src* $CRUNCH_TMP/*.cid'], + {label => "clean work dirs"}); + if ($exited != 0) { exit(EX_RETRY_UNLOCKED); } } @@ -415,41 +407,44 @@ if (!defined $no_clear_tmp) { # If this job requires a Docker image, install that. my ($docker_locator, $docker_stream, $docker_hash, $docker_limitmem, $dockeruserarg); if ($docker_locator = $Job->{docker_image_locator}) { + Log (undef, "Install docker image $docker_locator"); ($docker_stream, $docker_hash) = find_docker_image($docker_locator); if (!$docker_hash) { croak("No Docker image hash found from locator $docker_locator"); } + Log (undef, "docker image hash is $docker_hash"); $docker_stream =~ s/^\.//; my $docker_install_script = qq{ -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 +if $docker_bin images -q --no-trunc --all | grep -xF \Q$docker_hash\E >/dev/null; then + exit 0 +fi +declare -a exit_codes=("\${PIPESTATUS[@]}") +if [ 0 != "\${exit_codes[0]}" ]; then + exit "\${exit_codes[0]}" # `docker images` failed +elif [ 1 != "\${exit_codes[1]}" ]; then + exit "\${exit_codes[1]}" # `grep` encountered an error +else + # Everything worked fine, but grep didn't find the image on this host. + 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 ($? != 0) + + my ($exited, $stdout, $stderr) = srun_sync( + ["srun", "--nodelist=" . join(',', @node)], + ["/bin/bash", "-o", "pipefail", "-ec", $docker_install_script], + {label => "load docker image"}); + if ($exited != 0) { - croak("Installing Docker image from $docker_locator exited " - .exit_status_s($?)); + exit(EX_RETRY_UNLOCKED); } # Determine whether this version of Docker supports memory+swap limits. - srun(["srun", "--nodelist=" . $node[0]], - ["/bin/sh", "-ec", "$docker_bin run --help | grep -qe --memory-swap="], - {fork => 1}); - $docker_limitmem = ($? == 0); + ($exited, $stdout, $stderr) = srun_sync( + ["srun", "--nodes=1"], + [$docker_bin, 'run', '--help'], + {label => "check --memory-swap feature"}); + $docker_limitmem = ($stdout =~ /--memory-swap/); # Find a non-root Docker user to use. # Tries the default user for the container, then 'crunch', then 'nobody', @@ -459,20 +454,22 @@ fi # Docker containers. my @tryusers = ("", "crunch", "nobody"); foreach my $try_user (@tryusers) { + my $label; my $try_user_arg; if ($try_user eq "") { - Log(undef, "Checking if container default user is not UID 0"); + $label = "check whether default user is UID 0"; $try_user_arg = ""; } else { - Log(undef, "Checking if user '$try_user' is not UID 0"); + $label = "check whether user '$try_user' is UID 0"; $try_user_arg = "--user=$try_user"; } - srun(["srun", "--nodelist=" . $node[0]], - ["/bin/sh", "-ec", - "a=`$docker_bin run $docker_run_args $try_user_arg $docker_hash id --user` && " . - " test \$a -ne 0"], - {fork => 1}); - if ($? == 0) { + my ($exited, $stdout, $stderr) = srun_sync( + ["srun", "--nodes=1"], + ["/bin/sh", "-ec", + "$docker_bin run $docker_run_args $try_user_arg $docker_hash id --user"], + {label => $label}); + chomp($stdout); + if ($exited == 0 && $stdout =~ /^\d+$/ && $stdout > 0) { $dockeruserarg = $try_user_arg; if ($try_user eq "") { Log(undef, "Container will run with default user"); @@ -662,11 +659,9 @@ if (!defined $git_archive) { } } else { - my $install_exited; + my $exited; my $install_script_tries_left = 3; for (my $attempts = 0; $attempts < 3; $attempts++) { - Log(undef, "Run install script on all workers"); - my @srunargs = ("srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}, "--job-name=$job_id"); @@ -674,59 +669,21 @@ else { "mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -"); $ENV{"CRUNCH_GIT_ARCHIVE_HASH"} = md5_hex($git_archive); - my ($install_stderr_r, $install_stderr_w); - pipe $install_stderr_r, $install_stderr_w or croak("pipe() failed: $!"); - set_nonblocking($install_stderr_r); - my $installpid = fork(); - if ($installpid == 0) - { - close($install_stderr_r); - fcntl($install_stderr_w, F_SETFL, 0) or croak($!); # no close-on-exec - open(STDOUT, ">&", $install_stderr_w); - open(STDERR, ">&", $install_stderr_w); - srun (\@srunargs, \@execargs, {}, $build_script . $git_archive); - exit (1); - } - close($install_stderr_w); - # Tell freeze_if_want_freeze how to kill the child, otherwise the - # "waitpid(installpid)" loop won't get interrupted by a freeze: - $proc{$installpid} = {}; - my $stderr_buf = ''; - # Track whether anything appears on stderr other than slurm errors - # ("srun: ...") and the "starting: ..." message printed by the - # srun subroutine itself: + my ($stdout, $stderr); + ($exited, $stdout, $stderr) = srun_sync( + \@srunargs, \@execargs, + {label => "run install script on all workers"}, + $build_script . $git_archive); + my $stderr_anything_from_script = 0; - my $match_our_own_errors = '^(srun: error: |starting: \[)'; - while ($installpid != waitpid(-1, WNOHANG)) { - freeze_if_want_freeze ($installpid); - # Wait up to 0.1 seconds for something to appear on stderr, then - # do a non-blocking read. - my $bits = fhbits($install_stderr_r); - select ($bits, undef, $bits, 0.1); - if (0 < sysread ($install_stderr_r, $stderr_buf, 8192, length($stderr_buf))) - { - while ($stderr_buf =~ /^(.*?)\n/) { - my $line = $1; - substr $stderr_buf, 0, 1+length($line), ""; - Log(undef, "stderr $line"); - if ($line !~ /$match_our_own_errors/) { - $stderr_anything_from_script = 1; - } - } - } - } - delete $proc{$installpid}; - $install_exited = $?; - close($install_stderr_r); - if (length($stderr_buf) > 0) { - if ($stderr_buf !~ /$match_our_own_errors/) { + for my $line (split(/\n/, $stderr)) { + if ($line !~ /^(srun: error: |starting: \[)/) { $stderr_anything_from_script = 1; } - Log(undef, "stderr $stderr_buf") } - Log (undef, "Install script exited ".exit_status_s($install_exited)); - last if $install_exited == 0 || $main::please_freeze; + last if $exited == 0 || $main::please_freeze; + # If the install script fails but doesn't print an error message, # the next thing anyone is likely to do is just run it again in # case it was a transient problem like "slurm communication fails @@ -742,7 +699,7 @@ else { unlink($tar_filename); } - if ($install_exited != 0) { + if ($exited != 0) { croak("Giving up"); } } @@ -904,7 +861,11 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) .q{&& MEM=$(awk '($1 == "MemTotal:"){print $2}' /dev/null ; then VOLUMES+=("--volume=$(which crunchrunner):/usr/local/bin/crunchrunner") ; fi } + .q{&& if test -f /etc/ssl/certs/ca-certificates.crt ; then VOLUMES+=("--volume=/etc/ssl/certs/ca-certificates.crt:/etc/arvados/ca-certificates.crt") ; } + .q{elif test -f /etc/pki/tls/certs/ca-bundle.crt ; then VOLUMES+=("--volume=/etc/pki/tls/certs/ca-bundle.crt:/etc/arvados/ca-certificates.crt") ; fi }; $command .= "&& exec arv-mount --read-write --mount-by-pdh=by_pdh --mount-tmp=tmp --crunchstat-interval=10 --allow-other $arv_file_cache \Q$keep_mnt\E --exec "; $ENV{TASK_KEEPMOUNT} = "$keep_mnt/by_pdh"; @@ -914,7 +875,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) { my $containername = "$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}"; my $cidfile = "$ENV{CRUNCH_TMP}/$containername.cid"; - $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$cidfile -poll=10000 "; + $command .= "crunchstat -cgroup-root=\Q$cgroup_root\E -cgroup-parent=docker -cgroup-cid=$cidfile -poll=10000 "; $command .= "$docker_bin run $docker_run_args --name=$containername --attach=stdout --attach=stderr --attach=stdin -i \Q$dockeruserarg\E --cidfile=$cidfile --sig-proxy "; # We only set memory limits if Docker lets us limit both memory and swap. # Memory limits alone have been supported longer, but subprocesses tend @@ -969,6 +930,10 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) # For now, use the same approach as TASK_WORK above. $ENV{"JOB_WORK"} = "/tmp/crunch-job-work"; + # Bind mount the crunchrunner binary and host TLS certificates file into + # the container. + $command .= '"${VOLUMES[@]}" '; + while (my ($env_key, $env_val) = each %ENV) { if ($env_key =~ /^(ARVADOS|CRUNCH|JOB|TASK)_/) { @@ -994,7 +959,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) } } else { # Non-docker run - $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 "; + $command .= "crunchstat -cgroup-root=\Q$cgroup_root\E -poll=10000 "; $command .= $stdbuf; $command .= "perl - $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"}; } @@ -1012,11 +977,12 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) next; } shift @freeslot; - $proc{$childpid} = { jobstep => $id, - time => time, - slot => $childslot, - jobstepname => "$job_id.$id.$childpid", - }; + $proc{$childpid} = { + jobstepidx => $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; @@ -1063,6 +1029,9 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) { update_progress_stats(); } + if (!$gotsome) { + select (undef, undef, undef, 0.1); + } $working_slot_count = scalar(grep { $_->{node}->{fail_count} == 0 && $_->{node}->{hold_count} < 4 } @slot); if (($thisround_failed_multiple >= 8 && $thisround_succeeded == 0) || @@ -1182,36 +1151,31 @@ sub update_progress_stats sub reapchildren { my $children_reaped = 0; + my @successful_task_uuids = (); while((my $pid = waitpid (-1, WNOHANG)) > 0) { my $childstatus = $?; + my $whatslot = ($slot[$proc{$pid}->{slot}]->{node}->{name} . "." . $slot[$proc{$pid}->{slot}]->{cpu}); - my $jobstepid = $proc{$pid}->{jobstep}; - - if (!WIFEXITED($childstatus)) - { - # child did not exit (may be temporarily stopped) - Log ($jobstepid, "child $pid did not actually exit in reapchildren, ignoring for now."); - next; - } + my $jobstepidx = $proc{$pid}->{jobstepidx}; $children_reaped++; my $elapsed = time - $proc{$pid}->{time}; - my $Jobstep = $jobstep[$jobstepid]; + my $Jobstep = $jobstep[$jobstepidx]; my $exitvalue = $childstatus >> 8; my $exitinfo = "exit ".exit_status_s($childstatus); $Jobstep->{'arvados_task'}->reload; my $task_success = $Jobstep->{'arvados_task'}->{success}; - Log ($jobstepid, "child $pid on $whatslot $exitinfo success=$task_success"); + Log ($jobstepidx, "child $pid on $whatslot $exitinfo success=$task_success"); if (!defined $task_success) { # task did not indicate one way or the other --> fail - Log($jobstepid, sprintf( + Log($jobstepidx, sprintf( "ERROR: Task process exited %s, but never updated its task record to indicate success and record its output.", exit_status_s($childstatus))); $Jobstep->{'arvados_task'}->{success} = 0; @@ -1235,85 +1199,91 @@ sub reapchildren # node is already suspected faulty and srun exited quickly if ($slot[$proc{$pid}->{slot}]->{node}->{hold_until} && $elapsed < 5) { - Log ($jobstepid, "blaming failure on suspect node " . + Log ($jobstepidx, "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', - $elapsed)); + Log ($jobstepidx, 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; } # Put this task back on the todo queue - push @jobstep_todo, $jobstepid; + push @jobstep_todo, $jobstepidx; $Job->{'tasks_summary'}->{'failed'}++; } - else + else # task_success { + push @successful_task_uuids, $Jobstep->{'arvados_task'}->{uuid}; ++$thisround_succeeded; $slot[$proc{$pid}->{slot}]->{node}->{losing_streak} = 0; $slot[$proc{$pid}->{slot}]->{node}->{hold_until} = 0; $slot[$proc{$pid}->{slot}]->{node}->{fail_count} = 0; - push @jobstep_done, $jobstepid; - Log ($jobstepid, "success in $elapsed seconds"); + push @jobstep_done, $jobstepidx; + Log ($jobstepidx, "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, sprintf("task output (%d bytes): %s", - length($Jobstep->{'arvados_task'}->{output}), - $Jobstep->{'arvados_task'}->{output})); + process_stderr_final ($jobstepidx); + Log ($jobstepidx, sprintf("task output (%d bytes): %s", + length($Jobstep->{'arvados_task'}->{output}), + $Jobstep->{'arvados_task'}->{output})); - close $reader{$jobstepid}; - delete $reader{$jobstepid}; + close $reader{$jobstepidx}; + delete $reader{$jobstepidx}; 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 = api_call( - "job_tasks/list", - '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; } + if (scalar(@successful_task_uuids) > 0) + { + Log (undef, sprintf("%d tasks exited (%d succeeded), checking for new tasks from API server.", $children_reaped, scalar(@successful_task_uuids))); + # Load new tasks + my $newtask_list = []; + my $newtask_results; + do { + $newtask_results = api_call( + "job_tasks/list", + 'filters' => [["created_by_job_task_uuid","in",\@successful_task_uuids]], + 'order' => 'qsequence', + 'offset' => scalar(@$newtask_list), + ); + push(@$newtask_list, @{$newtask_results->{items}}); + } while (@{$newtask_results->{items}}); + Log (undef, sprintf("Got %d new tasks from API server.", scalar(@$newtask_list))); + 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; + } + } + return $children_reaped; } sub check_refresh_wanted { my @stat = stat $ENV{"CRUNCH_REFRESH_TRIGGER"}; - if (@stat && $stat[9] > $latest_refresh) { + if (@stat && + $stat[9] > $latest_refresh && + # ...and we have actually locked the job record... + $job_id eq $Job->{'uuid'}) { $latest_refresh = scalar time; my $Job2 = api_call("jobs/get", uuid => $jobspec); for my $attr ('cancelled_at', @@ -1351,7 +1321,7 @@ sub check_squeue # squeue check interval (15s) this should make the squeue check an # infrequent event. my $silent_procs = 0; - for my $js (map {$jobstep[$_->{jobstep}]} values %proc) + for my $js (map {$jobstep[$_->{jobstepidx}]} values %proc) { if (!exists($js->{stderr_at})) { @@ -1367,7 +1337,7 @@ sub check_squeue # use killem() on procs whose killtime is reached while (my ($pid, $procinfo) = each %proc) { - my $js = $jobstep[$procinfo->{jobstep}]; + my $js = $jobstep[$procinfo->{jobstepidx}]; if (exists $procinfo->{killtime} && $procinfo->{killtime} <= time && $js->{stderr_at} < $last_squeue_check) @@ -1376,7 +1346,7 @@ sub check_squeue if ($js->{stderr_at}) { $sincewhen = " in last " . (time - $js->{stderr_at}) . "s"; } - Log($procinfo->{jobstep}, "killing orphaned srun process $pid (task not in slurm queue, no stderr received$sincewhen)"); + Log($procinfo->{jobstepidx}, "killing orphaned srun process $pid (task not in slurm queue, no stderr received$sincewhen)"); killem ($pid); } } @@ -1413,7 +1383,6 @@ sub check_squeue # Check for child procs >60s old and not mentioned by squeue. while (my ($pid, $procinfo) = each %proc) { - my $js = $jobstep[$procinfo->{jobstep}]; if ($procinfo->{time} < time - 60 && $procinfo->{jobstepname} && !exists $ok{$procinfo->{jobstepname}} @@ -1427,7 +1396,7 @@ sub check_squeue # error/delay has caused the task to die without notifying srun, # and we'll kill srun ourselves. $procinfo->{killtime} = time + 30; - Log($procinfo->{jobstep}, "notice: task is not in slurm queue but srun process $pid has not exited"); + Log($procinfo->{jobstepidx}, "notice: task is not in slurm queue but srun process $pid has not exited"); } } } @@ -1448,11 +1417,16 @@ sub readfrompipes my $gotsome = 0; my %fd_job; my $sel = IO::Select->new(); - foreach my $job (keys %reader) + foreach my $jobstepidx (keys %reader) { - my $fd = $reader{$job}; + my $fd = $reader{$jobstepidx}; $sel->add($fd); - $fd_job{$fd} = $job; + $fd_job{$fd} = $jobstepidx; + + if (my $stdout_fd = $jobstep[$jobstepidx]->{stdout_r}) { + $sel->add($stdout_fd); + $fd_job{$stdout_fd} = $jobstepidx; + } } # select on all reader fds with 0.1s timeout my @ready_fds = $sel->can_read(0.1); @@ -1461,66 +1435,79 @@ sub readfrompipes my $buf; if (0 < sysread ($fd, $buf, 65536)) { + $gotsome = 1; print STDERR $buf if $ENV{CRUNCH_DEBUG}; - my $job = $fd_job{$fd}; - $jobstep[$job]->{stderr_at} = time; - $jobstep[$job]->{stderr} .= $buf; + + my $jobstepidx = $fd_job{$fd}; + if ($jobstep[$jobstepidx]->{stdout_r} == $fd) { + $jobstep[$jobstepidx]->{stdout_captured} .= $buf; + next; + } + + $jobstep[$jobstepidx]->{stderr_at} = time; + $jobstep[$jobstepidx]->{stderr} .= $buf; # Consume everything up to the last \n - preprocess_stderr ($job); + preprocess_stderr ($jobstepidx); - if (length ($jobstep[$job]->{stderr}) > 16384) + if (length ($jobstep[$jobstepidx]->{stderr}) > 16384) { # If we get a lot of stderr without a newline, chop off the # front to avoid letting our buffer grow indefinitely. - substr ($jobstep[$job]->{stderr}, - 0, length($jobstep[$job]->{stderr}) - 8192) = ""; + substr ($jobstep[$jobstepidx]->{stderr}, + 0, length($jobstep[$jobstepidx]->{stderr}) - 8192) = ""; } - $gotsome = 1; } } return $gotsome; } +# Consume all full lines of stderr for a jobstep. Everything after the +# last newline will remain in $jobstep[$jobstepidx]->{stderr} after +# returning. sub preprocess_stderr { - my $job = shift; + my $jobstepidx = shift; + # slotindex is only defined for children running Arvados job tasks. + # Be prepared to handle the undef case (for setup srun calls, etc.). + my $job_slot_index = $jobstep[$jobstepidx]->{slotindex}; - while ($jobstep[$job]->{stderr} =~ /^(.*?)\n/) { + while ($jobstep[$jobstepidx]->{stderr} =~ /^(.*?)\n/) { my $line = $1; - substr $jobstep[$job]->{stderr}, 0, 1+length($line), ""; - Log ($job, "stderr $line"); + substr $jobstep[$jobstepidx]->{stderr}, 0, 1+length($line), ""; + Log ($jobstepidx, "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/) { - my $job_slot_index = $jobstep[$job]->{slotindex}; - $slot[$job_slot_index]->{node}->{fail_count}++; - $jobstep[$job]->{tempfail} = 1; - ban_node_by_slot($job_slot_index); + elsif ($line =~ /srun: error: (Node failure on|Aborting, .*\bio error\b)/) { + $jobstep[$jobstepidx]->{tempfail} = 1; + if (defined($job_slot_index)) { + $slot[$job_slot_index]->{node}->{fail_count}++; + ban_node_by_slot($job_slot_index); + } } elsif ($line =~ /srun: error: (Unable to create job step|.*: Communication connection failure)/) { - $jobstep[$job]->{tempfail} = 1; - ban_node_by_slot($jobstep[$job]->{slotindex}); + $jobstep[$jobstepidx]->{tempfail} = 1; + ban_node_by_slot($job_slot_index) if (defined($job_slot_index)); } - elsif ($line =~ /arvados\.errors\.Keep/) { - $jobstep[$job]->{tempfail} = 1; + elsif ($line =~ /\bKeep(Read|Write|Request)Error:/) { + $jobstep[$jobstepidx]->{tempfail} = 1; } } } -sub process_stderr +sub process_stderr_final { - my $job = shift; - my $task_success = shift; - preprocess_stderr ($job); + my $jobstepidx = shift; + preprocess_stderr ($jobstepidx); map { - Log ($job, "stderr $_"); - } split ("\n", $jobstep[$job]->{stderr}); + Log ($jobstepidx, "stderr $_"); + } split ("\n", $jobstep[$jobstepidx]->{stderr}); + $jobstep[$jobstepidx]->{stderr} = ''; } sub fetch_block @@ -1658,7 +1645,7 @@ sub killem } if (!exists $proc{$_}->{"sent_$sig"}) { - Log ($proc{$_}->{jobstep}, "sending 2x signal $sig to pid $_"); + Log ($proc{$_}->{jobstepidx}, "sending 2x signal $sig to pid $_"); kill $sig, $_; select (undef, undef, undef, 0.1); if ($sig == 2) @@ -1782,16 +1769,21 @@ sub log_writer_is_active() { return $log_pipe_pid; } -sub Log # ($jobstep_id, $logmessage) +sub Log # ($jobstepidx, $logmessage) { - if ($_[1] =~ /\n/) { + my ($jobstepidx, $logmessage) = @_; + if ($logmessage =~ /\n/) { for my $line (split (/\n/, $_[1])) { - Log ($_[0], $line); + Log ($jobstepidx, $line); } return; } my $fh = select STDERR; $|=1; select $fh; - my $message = sprintf ("%s %d %s %s", $job_id, $$, @_); + my $task_qseq = ''; + if (defined($jobstepidx) && exists($jobstep[$jobstepidx]->{arvados_task})) { + $task_qseq = $jobstepidx; + } + my $message = sprintf ("%s %d %s %s", $job_id, $$, $task_qseq, $logmessage); $message =~ s{([^ -\176])}{"\\" . sprintf ("%03o", ord($1))}ge; $message .= "\n"; my $datetime; @@ -1915,6 +1907,88 @@ sub freezeunquote } +sub srun_sync +{ + my $srunargs = shift; + my $execargs = shift; + my $opts = shift || {}; + my $stdin = shift; + + my $label = exists $opts->{label} ? $opts->{label} : "@$execargs"; + Log (undef, "$label: start"); + + my ($stderr_r, $stderr_w); + pipe $stderr_r, $stderr_w or croak("pipe() failed: $!"); + + my ($stdout_r, $stdout_w); + pipe $stdout_r, $stdout_w or croak("pipe() failed: $!"); + + my $srunpid = fork(); + if ($srunpid == 0) + { + close($stderr_r); + close($stdout_r); + fcntl($stderr_w, F_SETFL, 0) or croak($!); # no close-on-exec + fcntl($stdout_w, F_SETFL, 0) or croak($!); + open(STDERR, ">&", $stderr_w); + open(STDOUT, ">&", $stdout_w); + srun ($srunargs, $execargs, $opts, $stdin); + exit (1); + } + close($stderr_w); + close($stdout_w); + + set_nonblocking($stderr_r); + set_nonblocking($stdout_r); + + # Add entries to @jobstep and %proc so check_squeue() and + # freeze_if_want_freeze() can treat it like a job task process. + push @jobstep, { + stderr => '', + stderr_at => 0, + stderr_captured => '', + stdout_r => $stdout_r, + stdout_captured => '', + }; + my $jobstepidx = $#jobstep; + $proc{$srunpid} = { + jobstepidx => $jobstepidx, + }; + $reader{$jobstepidx} = $stderr_r; + + while ($srunpid != waitpid ($srunpid, WNOHANG)) { + my $busy = readfrompipes(); + if (!$busy || ($latest_refresh + 2 < scalar time)) { + check_refresh_wanted(); + check_squeue(); + } + if (!$busy) { + select(undef, undef, undef, 0.1); + } + killem(keys %proc) if $main::please_freeze; + } + my $exited = $?; + + 1 while readfrompipes(); + process_stderr_final ($jobstepidx); + + Log (undef, "$label: exit ".exit_status_s($exited)); + + close($stdout_r); + close($stderr_r); + delete $proc{$srunpid}; + delete $reader{$jobstepidx}; + + my $j = pop @jobstep; + # If the srun showed signs of tempfail, ensure the caller treats that as a + # failure case. + if ($main::please_freeze || $j->{tempfail}) { + $exited ||= 255; + } + return ($exited, $j->{stdout_captured}, $j->{stderr_captured}); +} + + sub srun { my $srunargs = shift;