X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/eeebd1e25974beff2455c96100532aaa4dae68fb..53b19718f974e7c9014644ce80fa36363ae0b693:/sdk/cli/bin/crunch-job diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job index 2415217a21..c748904105 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) @@ -375,7 +376,7 @@ if (!defined $no_clear_tmp) { # If this job requires a Docker image, install that. my $docker_bin = "/usr/bin/docker.io"; -my ($docker_locator, $docker_stream, $docker_hash); +my ($docker_locator, $docker_stream, $docker_hash, $docker_limitmem); if ($docker_locator = $Job->{docker_image_locator}) { ($docker_stream, $docker_hash) = find_docker_image($docker_locator); if (!$docker_hash) @@ -384,7 +385,7 @@ if ($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 | $docker_bin load fi }; @@ -407,6 +408,12 @@ fi .exit_status_s($?)); } + # 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); + if ($Job->{arvados_sdk_version}) { # The job also specifies an Arvados SDK version. Add the SDKs to the # tar file for the build script to install. @@ -590,19 +597,43 @@ else { my @execargs = ("sh", "-c", "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); } - while (1) - { - last if $installpid == waitpid (-1, WNOHANG); + close($install_stderr_w); + my $stderr_buf = ''; + while ($installpid != waitpid(-1, WNOHANG)) { freeze_if_want_freeze ($installpid); - select (undef, undef, undef, 0.1); + # 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"); + } + } } my $install_exited = $?; + close($install_stderr_r); + if (length($stderr_buf) > 0) { + Log(undef, "stderr $stderr_buf") + } + Log (undef, "Install script exited ".exit_status_s($install_exited)); foreach my $tar_filename (map { tar_filename_n($_); } (1..$git_tar_count)) { unlink($tar_filename); @@ -636,12 +667,44 @@ 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 $initial_tasks_this_level = 0; +foreach my $id (@jobstep_todo) { + $initial_tasks_this_level++ if ($jobstep[$id]->{level} == $level); +} + +# If the number of tasks scheduled at this level #T is smaller than the number +# of slots available #S, only use the first #T slots, or the first slot on +# each node, whichever number is greater. +# +# When we dispatch tasks later, we'll allocate whole-node resources like RAM +# based on these numbers. Using fewer slots makes more resources available +# to each individual task, which should normally be a better strategy when +# there are fewer of them running with less parallelism. +# +# Note that this calculation is not redone if the initial tasks at +# this level queue more tasks at the same level. This may harm +# overall task throughput for that level. +my @freeslot; +if ($initial_tasks_this_level < @node) { + @freeslot = (0..$#node); +} elsif ($initial_tasks_this_level < @slot) { + @freeslot = (0..$initial_tasks_this_level - 1); +} else { + @freeslot = (0..$#slot); +} +my $round_num_freeslots = scalar(@freeslot); +my %round_max_slots = (); +for (my $ii = $#freeslot; $ii >= 0; $ii--) { + my $this_slot = $slot[$freeslot[$ii]]; + my $node_name = $this_slot->{node}->{name}; + $round_max_slots{$node_name} ||= $this_slot->{cpu}; + last if (scalar(keys(%round_max_slots)) >= @node); +} +Log(undef, "start level $level with $round_num_freeslots slots"); my %proc; -my @freeslot = (0..$#slot); my @holdslot; my %reader; my $progress_is_dirty = 1; @@ -650,7 +713,6 @@ my $progress_stats_updated = 0; update_progress_stats(); - THISROUND: for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) { @@ -661,15 +723,15 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) next; } - pipe $reader{$id}, "writer" or croak ($!); - my $flags = fcntl ($reader{$id}, F_GETFL, 0) or croak ($!); - fcntl ($reader{$id}, F_SETFL, $flags | O_NONBLOCK) or croak ($!); + pipe $reader{$id}, "writer" or croak("pipe() failed: $!"); + set_nonblocking($reader{$id}); 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) { @@ -703,7 +765,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) $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{"CRUNCH_NODE_SLOTS"} = $round_max_slots{$ENV{TASK_SLOT_NODE}}; $ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"}; $ENV{"GZIP"} = "-n"; @@ -717,13 +779,26 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) 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} "; + ."&& cd $ENV{CRUNCH_TMP} " + # These environment variables get used explicitly later in + # $command. No tool is expected to read these values directly. + .q{&& MEM=$(awk '($1 == "MemTotal:"){print $2}' @freeslot && $todo_ptr+1 > $#jobstep_todo)) + ($round_num_freeslots > @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) { $main::please_info = 0; @@ -941,7 +1016,7 @@ if (!$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 +1085,7 @@ 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 $Jobstep->{'failures'} >= 1; @@ -1037,7 +1112,6 @@ sub reapchildren if (!$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 +1130,9 @@ 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 +1306,7 @@ 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))|arvados.errors.Keep/) { $jobstep[$job]->{node_fail} = 1; ban_node_by_slot($jobstep[$job]->{slotindex}); } @@ -1252,16 +1328,19 @@ 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 +1350,80 @@ 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 $joboutput; } @@ -1398,8 +1497,11 @@ sub log_writer_start($) { 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, '-'); } @@ -1782,6 +1884,12 @@ sub combined_git_archive { return $tar_contents; } +sub set_nonblocking { + my $fh = shift; + my $flags = fcntl ($fh, F_GETFL, 0) or croak ($!); + fcntl ($fh, F_SETFL, $flags | O_NONBLOCK) or croak ($!); +} + __DATA__ #!/usr/bin/perl # @@ -1803,16 +1911,21 @@ 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"); my $destdir = $ENV{"CRUNCH_SRC"}; -my $commit = $ENV{"CRUNCH_SRC_COMMIT"}; +my $archive_hash = $ENV{"CRUNCH_GIT_ARCHIVE_HASH"}; my $repo = $ENV{"CRUNCH_SRC_URL"}; my $install_dir = $ENV{"CRUNCH_INSTALL"} || (getcwd() . "/opt"); my $job_work = $ENV{"JOB_WORK"}; my $task_work = $ENV{"TASK_WORK"}; +open(STDOUT_ORIG, ">&", STDOUT); +open(STDERR_ORIG, ">&", STDERR); + for my $dir ($destdir, $job_work, $task_work) { if ($dir) { make_path $dir; @@ -1824,11 +1937,6 @@ if ($task_work) { remove_tree($task_work, {keep_root => 1}); } -open(STDOUT_ORIG, ">&", STDOUT); -open(STDERR_ORIG, ">&", STDERR); -open(STDOUT, ">>", "$destdir.log"); -open(STDERR, ">&", STDOUT); - ### Crunch script run mode if (@ARGV) { # We want to do routine logging during task 0 only. This gives the user @@ -1848,9 +1956,9 @@ 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"); } @@ -1889,10 +1997,6 @@ if (@ARGV) { } } - close(STDOUT); - close(STDERR); - open(STDOUT, ">&", STDOUT_ORIG); - open(STDERR, ">&", STDERR_ORIG); exec(@ARGV); die "Cannot exec `@ARGV`: $!"; } @@ -1900,17 +2004,29 @@ if (@ARGV) { ### Installation mode open L, ">", "$destdir.lock" or die "$destdir.lock: $!"; flock L, LOCK_EX; -if (readlink ("$destdir.commit") eq $commit && -d $destdir) { - # This version already installed -> nothing to do. +if (readlink ("$destdir.archive_hash") eq $archive_hash && -d $destdir) { + # This exact git archive (source + arvados sdk) is already installed + # here, so there's no need to reinstall it. + + # We must consume our DATA section, though: otherwise the process + # feeding it to us will get SIGPIPE. + my $buf; + while (read(DATA, $buf, 65536)) { } + exit(0); } -unlink "$destdir.commit"; +unlink "$destdir.archive_hash"; mkdir $destdir; -open TARX, "|-", "tar", "-xC", $destdir; -{ - local $/ = undef; - print TARX ; + +if (!open(TARX, "|-", "tar", "-xC", $destdir)) { + die "Error launching 'tar -xC $destdir': $!"; +} +# If we send too much data to tar in one write (> 4-5 MiB), it stops, and we +# get SIGPIPE. We must feed it data incrementally. +my $tar_input; +while (read(DATA, $tar_input, 65536)) { + print TARX $tar_input; } if(!close(TARX)) { die "'tar -xC $destdir' exited $?: $!"; @@ -1940,19 +2056,24 @@ if ((-d $python_dir) and can_run("python2.7") and close($pysdk_cfg); } +# Hide messages from the install script (unless it fails: shell_or_die +# will show $destdir.log in that case). +open(STDOUT, ">>", "$destdir.log"); +open(STDERR, ">&", STDOUT); + 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) { - unlink "$destdir.commit.new"; - symlink ($commit, "$destdir.commit.new") or die "$destdir.commit.new: $!"; - rename ("$destdir.commit.new", "$destdir.commit") or die "$destdir.commit: $!"; +if ($archive_hash) { + unlink "$destdir.archive_hash.new"; + symlink ($archive_hash, "$destdir.archive_hash.new") or die "$destdir.archive_hash.new: $!"; + rename ("$destdir.archive_hash.new", "$destdir.archive_hash") or die "$destdir.archive_hash: $!"; } close L; @@ -1967,15 +2088,24 @@ 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); + } } }