X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/370df5a95b6b143885fa4d96be90c51f25f8ad14..55fc92b5f382b964b65c952f047bc673df582d98:/sdk/cli/bin/crunch-job diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job index 081d745a5b..3539a57a03 100755 --- a/sdk/cli/bin/crunch-job +++ b/sdk/cli/bin/crunch-job @@ -86,6 +86,7 @@ use POSIX ':sys_wait_h'; use POSIX qw(strftime); use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK); use Arvados; +use Cwd qw(realpath); use Data::Dumper; use Digest::MD5 qw(md5_hex); use Getopt::Long; @@ -197,6 +198,16 @@ $Job->{'runtime_constraints'} ||= {}; $Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0; my $max_ncpus = $Job->{'runtime_constraints'}->{'max_tasks_per_node'}; +my $gem_versions = `gem list --quiet arvados-cli 2>/dev/null`; +if ($? == 0) { + $gem_versions =~ s/^arvados-cli \(/ with arvados-cli Gem version(s) /; + chomp($gem_versions); + chop($gem_versions); # Closing parentheses +} else { + $gem_versions = ""; +} +Log(undef, + "running from " . ((-e $0) ? realpath($0) : "stdin") . $gem_versions); Log (undef, "check slurm allocation"); my @slot; @@ -305,7 +316,6 @@ my @jobstep_tomerge = (); my $jobstep_tomerge_level = 0; my $squeue_checked; my $squeue_kill_checked; -my $output_in_keep = 0; my $latest_refresh = scalar time; @@ -335,13 +345,9 @@ if (!$have_slurm) must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here."); } - -my $build_script; -do { - local $/ = undef; - $build_script = ; -}; +my $build_script = handle_readall(\*DATA); 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* @@ -363,8 +369,51 @@ if (!defined $no_clear_tmp) { Log (undef, "Cleanup command exited ".exit_status_s($?)); } +# 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 $docker_locator exited " + .exit_status_s($?)); + } + + 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. + Log(undef, sprintf("Packing Arvados SDK version %s for installation", + $Job->{arvados_sdk_version})); + add_git_archive("git", "--git-dir=$git_dir", "archive", + "--prefix=.arvados.sdk/", + $Job->{arvados_sdk_version}, "sdk"); + } +} -my $git_archive; if (!defined $git_dir && $Job->{'script_version'} =~ m{^/}) { # If script_version looks like an absolute path, *and* the --git-dir # argument was not given -- which implies we were not invoked by @@ -518,12 +567,10 @@ else { } $ENV{"CRUNCH_SRC_COMMIT"} = $commit; - $git_archive = `$gitcmd archive ''\Q$commit\E`; - if ($?) { - croak("Error: $gitcmd archive exited ".exit_status_s($?)); - } + add_git_archive("$gitcmd archive ''\Q$commit\E"); } +my $git_archive = combined_git_archive(); if (!defined $git_archive) { Log(undef, "Skip install phase (no git archive)"); if ($have_slurm) { @@ -551,48 +598,12 @@ else { freeze_if_want_freeze ($installpid); select (undef, undef, undef, 0.1); } - Log (undef, "Install script exited ".exit_status_s($?)); -} - -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 $docker_locator exited " - .exit_status_s($?)); + my $install_exited = $?; + Log (undef, "Install script exited ".exit_status_s($install_exited)); + foreach my $tar_filename (map { tar_filename_n($_); } (1..$git_tar_count)) { + unlink($tar_filename); } + exit (1) if $install_exited != 0; } foreach (qw (script script_version script_parameters runtime_constraints)) @@ -699,17 +710,10 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) 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) { @@ -738,18 +742,32 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E "; $ENV{TASK_KEEPMOUNT} = "/keep"; - # TASK_WORK is a plain docker data volume: it starts out empty, - # is writable, and persists until no containers use it any - # more. We don't use --volumes-from to share it with other - # containers: it is only accessible to this task, and it goes - # away when this task stops. - $command .= "--volume=\Q$ENV{TASK_WORK}\E "; - - # JOB_WORK is also a plain docker data volume for now. TODO: - # Share a single JOB_WORK volume across all task containers on a - # given worker node, and delete it when the job ends (and, in - # case that doesn't work, when the next job starts). - $command .= "--volume=\Q$ENV{JOB_WORK}\E "; + # TASK_WORK is almost exactly like a docker data volume: it + # starts out empty, is writable, and persists until no + # containers use it any more. We don't use --volumes-from to + # share it with other containers: it is only accessible to this + # task, and it goes away when this task stops. + # + # However, a docker data volume is writable only by root unless + # the mount point already happens to exist in the container with + # different permissions. Therefore, we [1] assume /tmp already + # exists in the image and is writable by the crunch user; [2] + # avoid putting TASK_WORK inside CRUNCH_TMP (which won't be + # writable if they are created by docker while setting up the + # other --volumes); and [3] create $TASK_WORK inside the + # container using $build_script. + $command .= "--volume=/tmp "; + $ENV{"TASK_WORK"} = "/tmp/crunch-job-task-work/$childslotname"; + $ENV{"HOME"} = $ENV{"TASK_WORK"}; + $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated + + # TODO: Share a single JOB_WORK volume across all task + # containers on a given worker node, and delete it when the job + # ends (and, in case that doesn't work, when the next job + # starts). + # + # For now, use the same approach as TASK_WORK above. + $ENV{"JOB_WORK"} = "/tmp/crunch-job-work"; while (my ($env_key, $env_val) = each %ENV) { @@ -760,16 +778,16 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) $command .= "--env=\QHOME=$ENV{HOME}\E "; $command .= "\Q$docker_hash\E "; $command .= "stdbuf --output=0 --error=0 "; - $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"}; + $command .= "perl - $ENV{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"}; + $command .= "perl - $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"}; } my @execargs = ('bash', '-c', $command); - srun (\@srunargs, \@execargs, undef, $build_script_to_send); + srun (\@srunargs, \@execargs, undef, $build_script); # exec() failed, we assume nothing happened. die "srun() failed on build script\n"; } @@ -814,7 +832,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) { $main::please_info = 0; freeze(); - collate_output(); + create_output_collection(); save_meta(1); update_progress_stats(); } @@ -876,7 +894,7 @@ while (%proc) $main::please_continue = 0; goto THISROUND; } - $main::please_info = 0, freeze(), collate_output(), save_meta(1) if $main::please_info; + $main::please_info = 0, freeze(), create_output_collection(), save_meta(1) if $main::please_info; readfrompipes (); if (!reapchildren()) { @@ -913,28 +931,14 @@ goto ONELEVEL if !defined $main::success; release_allocation(); freeze(); -my $collated_output = &collate_output(); +my $collated_output = &create_output_collection(); if (!$collated_output) { - Log(undef, "output undef"); + Log (undef, "Failed to write output collection"); } 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 = api_call("collections/create", collection => { - 'manifest_text' => $orig_manifest_text}); - Log(undef, "output uuid " . $output->{uuid}); - Log(undef, "output hash " . $output->{portable_data_hash}); - $Job->update_attributes('output' => $output->{portable_data_hash}); - }; - if ($@) { - Log (undef, "Failed to register output manifest: $@"); - } + Log(undef, "output hash " . $collated_output); + $Job->update_attributes('output' => $collated_output); } Log (undef, "finish"); @@ -1266,14 +1270,24 @@ sub fetch_block return $output_block; } -sub collate_output +# create_output_collections generates a new collection containing the +# output of each successfully completed task, and returns the +# portable_data_hash for the new collection. +# +sub create_output_collection { Log (undef, "collate"); my ($child_out, $child_in); - my $pid = open2($child_out, $child_in, 'arv-put', '--raw', - '--retries', retry_count()); - my $joboutput; + 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"]' + ); + for (@jobstep) { next if (!exists $_->{'arvados_task'}->{'output'} || @@ -1281,17 +1295,10 @@ sub collate_output 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 @@ -1302,15 +1309,14 @@ sub collate_output } $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); - # TODO: Ensure exit status == 0. - } else { - Log (undef, "timed out reading from 'arv-put'"); - } + 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. + } else { + Log (undef, "timed out while creating output collection"); } # TODO: kill $pid instead of waiting, now that we've decided to # ignore further output. @@ -1460,7 +1466,7 @@ sub croak my $message = "@_ at $file line $line\n"; Log (undef, $message); freeze() if @jobstep_todo; - collate_output() if @jobstep_todo; + create_output_collection() if @jobstep_todo; cleanup(); save_meta(); die; @@ -1512,7 +1518,7 @@ sub freeze_if_want_freeze } } freeze(); - collate_output(); + create_output_collection(); cleanup(); save_meta(); exit 1; @@ -1693,7 +1699,7 @@ sub api_call { if ($next_try_at < time) { $retry_msg = "Retrying."; } else { - my $next_try_fmt = strftime("%Y-%m-%d %H:%M:%S", $next_try_at); + my $next_try_fmt = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($next_try_at); $retry_msg = "Retrying at $next_try_fmt."; } Log(undef, "API method $method_name failed: $errmsg. $retry_msg"); @@ -1719,20 +1725,91 @@ sub exit_status_s { return $s; } +sub handle_readall { + # Pass in a glob reference to a file handle. + # Read all its contents and return them as a string. + my $fh_glob_ref = shift; + local $/ = undef; + return <$fh_glob_ref>; +} + +sub tar_filename_n { + my $n = shift; + return sprintf("%s/git.%s.%d.tar", $ENV{CRUNCH_TMP}, $job_id, $n); +} + +sub add_git_archive { + # Pass in a git archive command as a string or list, a la system(). + # This method will save its output to be included in the archive sent to the + # build script. + my $git_input; + $git_tar_count++; + if (!open(GIT_ARCHIVE, ">", tar_filename_n($git_tar_count))) { + croak("Failed to save git archive: $!"); + } + my $git_pid = open2(">&GIT_ARCHIVE", $git_input, @_); + close($git_input); + waitpid($git_pid, 0); + close(GIT_ARCHIVE); + if ($?) { + croak("Failed to save git archive: git exited " . exit_status_s($?)); + } +} + +sub combined_git_archive { + # Combine all saved tar archives into a single archive, then return its + # contents in a string. Return undef if no archives have been saved. + if ($git_tar_count < 1) { + return undef; + } + my $base_tar_name = tar_filename_n(1); + foreach my $tar_to_append (map { tar_filename_n($_); } (2..$git_tar_count)) { + my $tar_exit = system("tar", "-Af", $base_tar_name, $tar_to_append); + if ($tar_exit != 0) { + croak("Error preparing build archive: tar -A exited " . + exit_status_s($tar_exit)); + } + } + if (!open(GIT_TAR, "<", $base_tar_name)) { + croak("Could not open build archive: $!"); + } + my $tar_contents = handle_readall(\*GIT_TAR); + close(GIT_TAR); + return $tar_contents; +} + __DATA__ #!/usr/bin/perl - -# checkout-and-build +# +# This is crunch-job's internal dispatch script. crunch-job running on the API +# server invokes this script on individual compute nodes, or localhost if we're +# running a job locally. It gets called in two modes: +# +# * No arguments: Installation mode. Read a tar archive from the DATA +# file handle; it includes the Crunch script's source code, and +# maybe SDKs as well. Those should be installed in the proper +# locations. This runs outside of any Docker container, so don't try to +# introspect Crunch's runtime environment. +# +# * With arguments: Crunch script run mode. This script should set up the +# environment, then run the command specified in the arguments. This runs +# inside any Docker container. use Fcntl ':flock'; use File::Path qw( make_path remove_tree ); +use POSIX qw(getcwd); + +# 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 $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"}; -for my $dir ($destdir, $task_work) { +for my $dir ($destdir, $job_work, $task_work) { if ($dir) { make_path $dir; -e $dir or die "Failed to create temporary directory ($dir): $!"; @@ -1743,45 +1820,123 @@ if ($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 + # the information they need, but avoids repeating the information for every + # task. + my $Log; + if ($ENV{TASK_SEQUENCE} eq "0") { + $Log = sub { + my $msg = shift; + printf STDERR_ORIG "[Crunch] $msg\n", @_; + }; + } else { + $Log = sub { }; + } + + my $python_src = "$install_dir/python"; + 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", + "--python=python2.7", $venv_dir); + shell_or_die("$venv_dir/bin/pip", "--quiet", "install", $python_src); + $venv_built = 1; + $Log->("Built Python SDK virtualenv"); + } + + my $pkgs; + if ($venv_built) { + $Log->("Running in Python SDK virtualenv"); + $pkgs = `(\Q$venv_dir/bin/pip\E freeze 2>/dev/null | grep arvados) || dpkg-query --show '*arvados*'`; + my $orig_argv = join(" ", map { quotemeta($_); } @ARGV); + @ARGV = ("/bin/sh", "-ec", + ". \Q$venv_dir/bin/activate\E; exec $orig_argv"); + } elsif (-d $python_src) { + $Log->("Warning: virtualenv not found inside Docker container default " + + "\$PATH. Can't install Python SDK."); + } else { + $pkgs = `(pip freeze 2>/dev/null | grep arvados) || dpkg-query --show '*arvados*'`; + } + + if ($pkgs) { + $Log->("Using Arvados SDK:"); + foreach my $line (split /\n/, $pkgs) { + $Log->($line); + } + } else { + $Log->("Arvados SDK packages not found"); + } + + while (my ($sdk_dir, $sdk_envkey) = each(%SDK_ENVVARS)) { + my $sdk_path = "$install_dir/$sdk_dir"; + if (-d $sdk_path) { + if ($ENV{$sdk_envkey}) { + $ENV{$sdk_envkey} = "$sdk_path:" . $ENV{$sdk_envkey}; + } else { + $ENV{$sdk_envkey} = $sdk_path; + } + $Log->("Arvados SDK added to %s", $sdk_envkey); + } + } + + close(STDOUT); + close(STDERR); + open(STDOUT, ">&", STDOUT_ORIG); + open(STDERR, ">&", STDERR_ORIG); + exec(@ARGV); + die "Cannot exec `@ARGV`: $!"; +} +### Installation mode open L, ">", "$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`: $!"; - } else { - exit 0; - } + # This version already installed -> nothing to do. + exit(0); } unlink "$destdir.commit"; -open STDERR_ORIG, ">&STDERR"; -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 $?: $!"; - } +open TARX, "|-", "tar", "-xC", $destdir; +{ + local $/ = undef; + print TARX ; +} +if(!close(TARX)) { + die "'tar -xC $destdir' 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"); +my $sdk_root = "$destdir/.arvados.sdk/sdk"; +if (-d $sdk_root) { + foreach my $sdk_lang (("python", + map { (split /\//, $_, 2)[0]; } keys(%SDK_ENVVARS))) { + if (-d "$sdk_root/$sdk_lang") { + if (!rename("$sdk_root/$sdk_lang", "$install_dir/$sdk_lang")) { + die "Failed to install $sdk_lang SDK: $!"; + } + } } } +my $python_dir = "$install_dir/python"; +if ((-d $python_dir) and can_run("python2.7") and + (system("python2.7", "$python_dir/setup.py", "--quiet", "egg_info") != 0)) { + # egg_info failed, probably when it asked git for a build tag. + # Specify no build tag. + open(my $pysdk_cfg, ">>", "$python_dir/setup.cfg"); + print $pysdk_cfg "\n[egg_info]\ntag_build =\n"; + close($pysdk_cfg); +} + if (-e "$destdir/crunch_scripts/install") { shell_or_die ("$destdir/crunch_scripts/install", $install_dir); } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") { @@ -1799,11 +1954,12 @@ if ($commit) { close L; -if (@ARGV) { - exec(@ARGV); - die "Cannot exec `@ARGV`: $!"; -} else { - exit 0; +sub can_run { + my $command_name = shift; + open(my $which, "-|", "which", $command_name); + while (<$which>) { } + close($which); + return ($? == 0); } sub shell_or_die