X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/256ceb11e3b67dbe68b955ed09ac0df9f6cda2ba..11374252ee3c26240420bb3aa0d0433fad71731f:/sdk/cli/bin/crunch-job diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job index 3467ec35eb..7205382211 100755 --- a/sdk/cli/bin/crunch-job +++ b/sdk/cli/bin/crunch-job @@ -10,12 +10,14 @@ crunch-job: Execute job steps, save snapshots as requested, collate output. Obtain job details from Arvados, run tasks on compute nodes (typically invoked by scheduler on controller): - crunch-job --job x-y-z + crunch-job --job x-y-z --git-dir /path/to/repo/.git 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",...}' + crunch-job --job '{"script_version":"/path/to/working/tree","script":"scriptname",...}' + + crunch-job --job '{"repository":"https://github.com/curoverse/arvados.git","script_version":"master","script":"scriptname",...}' =head1 OPTIONS @@ -27,7 +29,9 @@ 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. +Path to a .git directory (or a git URL) where the commit given in the +job's C attribute is to be found. If this is I +given, the job's C attribute will be used. =item --job-api-token @@ -39,6 +43,11 @@ Do not clear per-job/task temporary directories during initial job setup. This can speed up development and debugging when running jobs locally. +=item --job + +UUID of the job to run, or a JSON-encoded job resource without a +UUID. If the latter is given, a new job object will be created. + =back =head1 RUNNING JOBS LOCALLY @@ -77,13 +86,14 @@ use POSIX ':sys_wait_h'; use POSIX qw(strftime); use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK); use Arvados; +use Data::Dumper; 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 File::Path qw( make_path remove_tree ); use constant EX_TEMPFAIL => 75; @@ -140,43 +150,26 @@ $SIG{'USR2'} = sub my $arv = Arvados->new('apiVersion' => 'v1'); -my $local_logfile; - -my $User = $arv->{'users'}->{'current'}->execute; my $Job; my $job_id; my $dbh; my $sth; +my @jobstep; + +my $User = api_call("users/current"); + if ($jobspec =~ /^[-a-z\d]+$/) { # $jobspec is an Arvados UUID, not a JSON job specification - $Job = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec); + $Job = api_call("jobs/get", 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->{'state'} ne 'Queued') { - Log(undef, "Job state is " . $Job->{'state'} . ", but I can only start queued jobs."); + # Claim this job, and make sure nobody else does + eval { api_call("jobs/lock", uuid => $Job->{uuid}); }; + if ($@) { + Log(undef, "Error while locking job, exiting ".EX_TEMPFAIL); 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 @@ -191,13 +184,14 @@ else $Job->{'is_locked_by_uuid'} = $User->{'uuid'}; $Job->{'started_at'} = gmtime; + $Job->{'state'} = 'Running'; - $Job = $arv->{'jobs'}->{'create'}->execute('job' => $Job); + $Job = api_call("jobs/create", job => $Job); } $job_id = $Job->{'uuid'}; my $keep_logfile = $job_id . '.log.txt'; -$local_logfile = File::Temp->new(); +log_writer_start($keep_logfile); $Job->{'runtime_constraints'} ||= {}; $Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0; @@ -279,20 +273,11 @@ foreach (@sinfo) @slot = sort { $a->{cpu} <=> $b->{cpu} } @slot; - -my $jobmanager_id; -# Claim this job, and make sure nobody else does -unless ($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('state' => 'Running', - 'tasks_summary' => { 'failed' => 0, - 'todo' => 1, - 'running' => 0, - 'done' => 0 }); - +$Job->update_attributes( + 'tasks_summary' => { 'failed' => 0, + 'todo' => 1, + 'running' => 0, + 'done' => 0 }); Log (undef, "start"); $SIG{'INT'} = sub { $main::please_freeze = 1; }; @@ -314,7 +299,6 @@ $ENV{"CRUNCH_JOB_UUID"} = $job_id; $ENV{"JOB_UUID"} = $job_id; -my @jobstep; my @jobstep_todo = (); my @jobstep_done = (); my @jobstep_tomerge = (); @@ -332,12 +316,12 @@ if (defined $Job->{thawedfromkey}) } else { - my $first_task = $arv->{'job_tasks'}->{'create'}->execute('job_task' => { + my $first_task = api_call("job_tasks/create", job_task => { 'job_uuid' => $Job->{'uuid'}, 'sequence' => 0, 'qsequence' => 0, 'parameters' => {}, - }); + }); push @jobstep, { 'level' => 0, 'failures' => 0, 'arvados_task' => $first_task, @@ -353,140 +337,208 @@ if (!$have_slurm) my $build_script; +do { + local $/ = undef; + $build_script = ; +}; +my $nodelist = join(",", @node); +if (!defined $no_clear_tmp) { + # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src* + Log (undef, "Clean work dirs"); -$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)); - } + 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 $CRUNCH_TMP/task/*.keep; do /bin/fusermount -z -u $i; done; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_INSTALL $CRUNCH_TMP/task $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, "Cleanup command exited ".exit_status_s($?)); } -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 $?"); - } +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 + # crunch-dispatch -- we will use the given path as a working + # directory instead of resolving script_version to a git commit (or + # doing anything else with git). + $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{'script_version'}; + $ENV{"CRUNCH_SRC"} = $Job->{'script_version'}; +} +else { + # Resolve the given script_version to a git commit sha1. Also, if + # the repository is remote, clone it into our local filesystem: this + # ensures "git archive" will work, and is necessary to reliably + # resolve a symbolic script_version like "master^". + $ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src"; - # Install requested code version - - my @execargs; - my @srunargs = ("srun", - "--nodelist=$nodelist", - "-D", $ENV{'TMPDIR'}, "--job-name=$job_id"); + Log (undef, "Looking for version ".$Job->{script_version}." from repository ".$Job->{repository}); $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}. + # If we're running under crunch-dispatch, it will have already + # pulled the appropriate source tree into its own repository, and + # given us that repo's path as $git_dir. # - # TODO: Accept URLs too, not just local paths. Use git-ls-remote and - # git-archive --remote where appropriate. + # If we're running a "local" job, we might have to fetch content + # from a remote repository. # - # 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'}; - + # (Currently crunch-dispatch gives a local path with --git-dir, but + # we might as well accept URLs there too in case it changes its + # mind.) + my $repo = $git_dir || $Job->{'repository'}; + + # Repository can be remote or local. If remote, we'll need to fetch it + # to a local dir before doing `git log` et al. + my $repo_location; + + if ($repo =~ m{://|^[^/]*:}) { + # $repo is a git url we can clone, like git:// or https:// or + # file:/// or [user@]host:repo.git. Note "user/name@host:foo" is + # not recognized here because distinguishing that from a local + # path is too fragile. If you really need something strange here, + # use the ssh:// form. + $repo_location = 'remote'; + } elsif ($repo =~ m{^\.*/}) { + # $repo is a local path to a git index. We'll also resolve ../foo + # to ../foo/.git if the latter is a directory. To help + # disambiguate local paths from named hosted repositories, this + # form must be given as ./ or ../ if it's a relative path. + if (-d "$repo/.git") { + $repo = "$repo/.git"; + } + $repo_location = 'local'; + } else { + # $repo is none of the above. It must be the name of a hosted + # repository. + my $arv_repo_list = api_call("repositories/list", + 'filters' => [['name','=',$repo]]); + my @repos_found = @{$arv_repo_list->{'items'}}; + my $n_found = $arv_repo_list->{'serverResponse'}->{'items_available'}; + if ($n_found > 0) { + Log(undef, "Repository '$repo' -> " + . join(", ", map { $_->{'uuid'} } @repos_found)); + } + if ($n_found != 1) { + croak("Error: Found $n_found repositories with name '$repo'."); + } + $repo = $repos_found[0]->{'fetch_url'}; + $repo_location = 'remote'; + } + Log(undef, "Using $repo_location repository '$repo'"); $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"; - } + # Resolve given script_version (we'll call that $treeish here) to a + # commit sha1 ($commit). + my $treeish = $Job->{'script_version'}; + my $commit; + if ($repo_location eq 'remote') { + # We minimize excess object-fetching by re-using the same bare + # repository in CRUNCH_TMP/.git for multiple crunch-jobs -- we + # just keep adding remotes to it as needed. + my $local_repo = $ENV{'CRUNCH_TMP'}."/.git"; + my $gitcmd = "git --git-dir=\Q$local_repo\E"; + + # Set up our local repo for caching remote objects, making + # archives, etc. + if (!-d $local_repo) { + make_path($local_repo) or croak("Error: could not create $local_repo"); + } + # This works (exits 0 and doesn't delete fetched objects) even + # if $local_repo is already initialized: + `$gitcmd init --bare`; + if ($?) { + croak("Error: $gitcmd init --bare exited ".exit_status_s($?)); + } - # If this looks like a subversion r#, look for it in git-svn commit messages + # If $treeish looks like a hash (or abbrev hash) we look it up in + # our local cache first, since that's cheaper. (We don't want to + # do that with tags/branches though -- those change over time, so + # they should always be resolved by the remote repo.) + if ($treeish =~ /^[0-9a-f]{7,40}$/s) { + # Hide stderr because it's normal for this to fail: + my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E 2>/dev/null`; + if ($? == 0 && + # Careful not to resolve a branch named abcdeff to commit 1234567: + $sha1 =~ /^$treeish/ && + $sha1 =~ /^([0-9a-f]{40})$/s) { + $commit = $1; + Log(undef, "Commit $commit already present in $local_repo"); + } + } + + if (!defined $commit) { + # If $treeish isn't just a hash or abbrev hash, or isn't here + # yet, we need to fetch the remote to resolve it correctly. + + # First, remove all local heads. This prevents a name that does + # not exist on the remote from resolving to (or colliding with) + # a previously fetched branch or tag (possibly from a different + # remote). + remove_tree("$local_repo/refs/heads", {keep_root => 1}); - 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"); + Log(undef, "Fetching objects from $repo to $local_repo"); + `$gitcmd fetch --no-progress --tags ''\Q$repo\E \Q+refs/heads/*:refs/heads/*\E`; + if ($?) { + croak("Error: `$gitcmd fetch` exited ".exit_status_s($?)); + } } + + # Now that the data is all here, we will use our local repo for + # the rest of our git activities. + $repo = $local_repo; } - # 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"); - } + my $gitcmd = "git --git-dir=\Q$repo\E"; + my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E`; + unless ($? == 0 && $sha1 =~ /^([0-9a-f]{40})$/) { + croak("`$gitcmd rev-list` exited " + .exit_status_s($?) + .", '$treeish' not found. Giving up."); + } + $commit = $1; + Log(undef, "Version $treeish is commit $commit"); + + if ($commit ne $Job->{'script_version'}) { + # Record the real commit id in the database, frozentokey, logs, + # etc. -- instead of an abbreviation or a branch name which can + # become ambiguous or point to a different commit in the future. + if (!$Job->update_attributes('script_version' => $commit)) { + croak("Error: failed to update job's script_version attribute"); } } - 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); + $ENV{"CRUNCH_SRC_COMMIT"} = $commit; + $git_archive = `$gitcmd archive ''\Q$commit\E`; + if ($?) { + croak("Error: $gitcmd archive exited ".exit_status_s($?)); } - else { - croak ("could not figure out commit id for $treeish"); +} + +if (!defined $git_archive) { + Log(undef, "Skip install phase (no git archive)"); + if ($have_slurm) { + Log(undef, "Warning: This probably means workers have no source tree!"); } +} +else { + Log(undef, "Run install script on all workers"); + + my @srunargs = ("srun", + "--nodelist=$nodelist", + "-D", $ENV{'TMPDIR'}, "--job-name=$job_id"); + my @execargs = ("sh", "-c", + "mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -"); - # Note: this section is almost certainly unnecessary if we're - # running tasks in docker containers. my $installpid = fork(); if ($installpid == 0) { @@ -499,7 +551,9 @@ else freeze_if_want_freeze ($installpid); select (undef, undef, undef, 0.1); } - Log (undef, "Install exited $?"); + my $install_exited = $?; + Log (undef, "Install script exited ".exit_status_s($install_exited)); + exit (1) if $install_exited != 0; } if (!$have_slurm) @@ -538,7 +592,8 @@ fi } if ($? != 0) { - croak("Installing Docker image from $docker_locator returned exit code $?"); + croak("Installing Docker image from $docker_locator exited " + .exit_status_s($?)); } } @@ -631,7 +686,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) } $ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name}; $ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu}; - $ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/$id.$$"; + $ENV{"TASK_WORK"} = $ENV{"CRUNCH_TMP"}."/task/$childslotname"; $ENV{"HOME"} = $ENV{"TASK_WORK"}; $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep"; $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated @@ -646,62 +701,86 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++) qw(-n1 -c1 -N1 -D), $ENV{'TMPDIR'}, "--job-name=$job_id.$id.$$", ); - 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) { - $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$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 "; + my $cidfile = "$ENV{CRUNCH_TMP}/$ENV{TASK_UUID}.cid"; + $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$cidfile -poll=10000 "; + $command .= "$docker_bin run --rm=true --attach=stdout --attach=stderr --attach=stdin -i --user=crunch --cidfile=$cidfile --sig-proxy "; + # 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 "; + + # The source tree and $destdir directory (which we have + # installed on the worker host) are available in the container, + # under the same path. + $command .= "--volume=\Q$ENV{CRUNCH_SRC}:$ENV{CRUNCH_SRC}:ro\E "; + $command .= "--volume=\Q$ENV{CRUNCH_INSTALL}:$ENV{CRUNCH_INSTALL}:ro\E "; + + # Currently, we make arv-mount's mount point appear at /keep + # inside the container (instead of using the same path as the + # host like we do with CRUNCH_SRC and CRUNCH_INSTALL). However, + # crunch scripts and utilities must not rely on this. They must + # use $TASK_KEEPMOUNT. $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E "; - $command .= "--env=\QHOME=/home/crunch\E "; + $ENV{TASK_KEEPMOUNT} = "/keep"; + + # 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, $env_val) = each %ENV) { - if ($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=$env_val\E "; - } + if ($env_key =~ /^(ARVADOS|CRUNCH|JOB|TASK)_/) { + $command .= "--env=\Q$env_key=$env_val\E "; } } - $command .= "--env=\QCRUNCH_NODE_SLOTS=$ENV{CRUNCH_NODE_SLOTS}\E "; - $command .= "--env=\QCRUNCH_SRC=/tmp/crunch-src\E "; + $command .= "--env=\QHOME=$ENV{HOME}\E "; $command .= "\Q$docker_hash\E "; $command .= "stdbuf --output=0 --error=0 "; - $command .= "/tmp/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. - Log(undef, "srun() failed on build script"); - die; + die "srun() failed on build script\n"; } close("writer"); if (!defined $childpid) @@ -856,9 +935,8 @@ else { while (my $manifest_line = <$orig_manifest>) { $orig_manifest_text .= $manifest_line; } - my $output = $arv->{'collections'}->{'create'}->execute('collection' => { - 'manifest_text' => $orig_manifest_text, - }); + 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}); @@ -916,10 +994,7 @@ sub reapchildren my $childstatus = $?; my $exitvalue = $childstatus >> 8; - my $exitinfo = sprintf("exit %d signal %d%s", - $exitvalue, - $childstatus & 127, - ($childstatus & 128 ? ' core dump' : '')); + my $exitinfo = "exit ".exit_status_s($childstatus); $Jobstep->{'arvados_task'}->reload; my $task_success = $Jobstep->{'arvados_task'}->{success}; @@ -995,7 +1070,8 @@ sub reapchildren my $newtask_list = []; my $newtask_results; do { - $newtask_results = $arv->{'job_tasks'}->{'list'}->execute( + $newtask_results = api_call( + "job_tasks/list", 'where' => { 'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid} }, @@ -1024,7 +1100,7 @@ sub check_refresh_wanted my @stat = stat $ENV{"CRUNCH_REFRESH_TRIGGER"}; if (@stat && $stat[9] > $latest_refresh) { $latest_refresh = scalar time; - my $Job2 = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec); + my $Job2 = api_call("jobs/get", uuid => $jobspec); for my $attr ('cancelled_at', 'cancelled_by_user_uuid', 'cancelled_by_client_uuid', @@ -1205,7 +1281,7 @@ sub collate_output my ($child_out, $child_in); my $pid = open2($child_out, $child_in, 'arv-put', '--raw', - '--retries', put_retry_count()); + '--retries', retry_count()); my $joboutput; for (@jobstep) { @@ -1240,10 +1316,13 @@ sub collate_output if ($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'"); } } + # TODO: kill $pid instead of waiting, now that we've decided to + # ignore further output. waitpid($pid, 0); return $joboutput; @@ -1291,6 +1370,73 @@ sub fhbits } +# Send log output to Keep via arv-put. +# +# $log_pipe_in and $log_pipe_out are the input and output filehandles to the arv-put pipe. +# $log_pipe_pid is the pid of the arv-put subprocess. +# +# The only functions that should access these variables directly are: +# +# log_writer_start($logfilename) +# Starts an arv-put pipe, reading data on stdin and writing it to +# a $logfilename file in an output collection. +# +# log_writer_send($txt) +# Writes $txt to the output log collection. +# +# log_writer_finish() +# Closes the arv-put pipe and returns the output that it produces. +# +# log_writer_is_active() +# Returns a true value if there is currently a live arv-put +# process, false otherwise. +# +my ($log_pipe_in, $log_pipe_out, $log_pipe_pid); + +sub log_writer_start($) +{ + my $logfilename = shift; + $log_pipe_pid = open2($log_pipe_out, $log_pipe_in, + 'arv-put', '--portable-data-hash', + '--retries', '3', + '--filename', $logfilename, + '-'); +} + +sub log_writer_send($) +{ + my $txt = shift; + print $log_pipe_in $txt; +} + +sub log_writer_finish() +{ + return unless $log_pipe_pid; + + close($log_pipe_in); + my $arv_put_output; + + my $s = IO::Select->new($log_pipe_out); + if ($s->can_read(120)) { + sysread($log_pipe_out, $arv_put_output, 1024); + chomp($arv_put_output); + } else { + Log (undef, "timed out reading from 'arv-put'"); + } + + waitpid($log_pipe_pid, 0); + $log_pipe_pid = $log_pipe_in = $log_pipe_out = undef; + if ($?) { + Log("log_writer_finish: arv-put exited ".exit_status_s($?)) + } + + return $arv_put_output; +} + +sub log_writer_is_active() { + return $log_pipe_pid; +} + sub Log # ($jobstep_id, $logmessage) { if ($_[1] =~ /\n/) { @@ -1304,15 +1450,15 @@ sub Log # ($jobstep_id, $logmessage) $message =~ s{([^ -\176])}{"\\" . sprintf ("%03o", ord($1))}ge; $message .= "\n"; my $datetime; - if ($local_logfile || -t STDERR) { + if (log_writer_is_active() || -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 . " " . $message; + if (log_writer_is_active()) { + log_writer_send($datetime . " " . $message); } } @@ -1324,14 +1470,15 @@ sub croak Log (undef, $message); freeze() if @jobstep_todo; collate_output() if @jobstep_todo; - cleanup() if $Job; - save_meta() if $local_logfile; + cleanup(); + save_meta(); die; } sub cleanup { + return unless $Job; if ($Job->{'state'} eq 'Cancelled') { $Job->update_attributes('finished_at' => scalar gmtime); } else { @@ -1344,16 +1491,9 @@ 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 + return unless log_writer_is_active(); - $local_logfile->flush; - my $retry_count = put_retry_count(); - my $cmd = "arv-put --portable-data-hash --retries $retry_count " . - "--filename ''\Q$keep_logfile\E " . quotemeta($local_logfile->filename); - my $loglocator = `$cmd`; - die "system $cmd failed: $?" if $?; - chomp($loglocator); - - $local_logfile = undef; # the temp file is automatically deleted + my $loglocator = log_writer_finish(); Log (undef, "log manifest is $loglocator"); $Job->{'log'} = $loglocator; $Job->update_attributes('log', $loglocator); @@ -1426,11 +1566,13 @@ sub srun my $opts = shift || {}; my $stdin = shift; my $args = $have_slurm ? [@$srunargs, @$execargs] : $execargs; - print STDERR (join (" ", - map { / / ? "'$_'" : $_ } - (@$args)), - "\n") - if $ENV{CRUNCH_DEBUG}; + + $Data::Dumper::Terse = 1; + $Data::Dumper::Indent = 0; + my $show_cmd = Dumper($args); + $show_cmd =~ s/(TOKEN\\*=)[^\s\']+/${1}[...]/g; + $show_cmd =~ s/\n/ /g; + warn "starting: $show_cmd\n"; if (defined $stdin) { my $child = open STDIN, "-|"; @@ -1473,7 +1615,8 @@ sub find_docker_image { # If not, return undef for both values. my $locator = shift; my ($streamname, $filename); - if (my $image = $arv->{collections}->{get}->execute(uuid => $locator)) { + my $image = api_call("collections/get", uuid => $locator); + if ($image) { foreach my $line (split(/\n/, $image->{manifest_text})) { my @tokens = split(/\s+/, $line); next if (!@tokens); @@ -1494,63 +1637,146 @@ sub find_docker_image { } } -sub put_retry_count { - # Calculate a --retries argument for arv-put that will have it try - # approximately as long as this Job has been running. - my $stoptime = shift || time; - my $starttime = $jobstep[0]->{starttime}; - my $timediff = defined($starttime) ? ($stoptime - $starttime) : 1; - my $retries = 0; - while ($timediff >= 2) { - $retries++; - $timediff /= 2; +sub retry_count { + # Calculate the number of times an operation should be retried, + # assuming exponential backoff, and that we're willing to retry as + # long as tasks have been running. Enforce a minimum of 3 retries. + my ($starttime, $endtime, $timediff, $retries); + if (@jobstep) { + $starttime = $jobstep[0]->{starttime}; + $endtime = $jobstep[-1]->{finishtime}; + } + if (!defined($starttime)) { + $timediff = 0; + } elsif (!defined($endtime)) { + $timediff = time - $starttime; + } else { + $timediff = ($endtime - $starttime) - (time - $endtime); + } + if ($timediff > 0) { + $retries = int(log($timediff) / log(2)); + } else { + $retries = 1; # Use the minimum. } return ($retries > 3) ? $retries : 3; } +sub retry_op { + # Pass in two function references. + # This method will be called with the remaining arguments. + # If it dies, retry it with exponential backoff until it succeeds, + # or until the current retry_count is exhausted. After each failure + # that can be retried, the second function will be called with + # the current try count (0-based), next try time, and error message. + my $operation = shift; + my $retry_callback = shift; + my $retries = retry_count(); + foreach my $try_count (0..$retries) { + my $next_try = time + (2 ** $try_count); + my $result = eval { $operation->(@_); }; + if (!$@) { + return $result; + } elsif ($try_count < $retries) { + $retry_callback->($try_count, $next_try, $@); + my $sleep_time = $next_try - time; + sleep($sleep_time) if ($sleep_time > 0); + } + } + # Ensure the error message ends in a newline, so Perl doesn't add + # retry_op's line number to it. + chomp($@); + die($@ . "\n"); +} + +sub api_call { + # Pass in a /-separated API method name, and arguments for it. + # This function will call that method, retrying as needed until + # the current retry_count is exhausted, with a log on the first failure. + my $method_name = shift; + my $log_api_retry = sub { + my ($try_count, $next_try_at, $errmsg) = @_; + $errmsg =~ s/\s*\bat \Q$0\E line \d+\.?\s*//; + $errmsg =~ s/\s/ /g; + $errmsg =~ s/\s+$//; + my $retry_msg; + if ($next_try_at < time) { + $retry_msg = "Retrying."; + } else { + my $next_try_fmt = strftime("%Y-%m-%d %H:%M:%S", $next_try_at); + $retry_msg = "Retrying at $next_try_fmt."; + } + Log(undef, "API method $method_name failed: $errmsg. $retry_msg"); + }; + my $method = $arv; + foreach my $key (split(/\//, $method_name)) { + $method = $method->{$key}; + } + return retry_op(sub { $method->execute(@_); }, $log_api_retry, @_); +} + +sub exit_status_s { + # Given a $?, return a human-readable exit code string like "0" or + # "1" or "0 with signal 1" or "1 with signal 11". + my $exitcode = shift; + my $s = $exitcode >> 8; + if ($exitcode & 0x7f) { + $s .= " with signal " . ($exitcode & 0x7f); + } + if ($exitcode & 0x80) { + $s .= " with core dump"; + } + return $s; +} + __DATA__ #!/usr/bin/perl # checkout-and-build use Fcntl ':flock'; -use File::Path qw( make_path ); +use File::Path qw( make_path remove_tree ); my $destdir = $ENV{"CRUNCH_SRC"}; my $commit = $ENV{"CRUNCH_SRC_COMMIT"}; my $repo = $ENV{"CRUNCH_SRC_URL"}; +my $job_work = $ENV{"JOB_WORK"}; 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): $!"; - } +for my $dir ($destdir, $job_work, $task_work) { + if ($dir) { + make_path $dir; + -e $dir or die "Failed to create temporary directory ($dir): $!"; + } +} + +if ($task_work) { + remove_tree($task_work, {keep_root => 1}); } + open L, ">", "$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`: $!"; - } else { - exit 0; - } + # This version already installed -> nothing to do. + run_argv_and_exit(); } unlink "$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 $?: $!"; - } +if (!@git_archive_data) { + # Nothing to extract -> nothing to install. + run_argv_and_exit(); +} + +open TARX, "|-", "tar", "-C", $destdir, "-xf", "-"; +print TARX @git_archive_data; +if(!close(TARX)) { + die "'tar -C $destdir -xf -' exited $?: $!"; } my $pwd; @@ -1582,11 +1808,16 @@ if ($commit) { close L; -if (@ARGV) { +run_argv_and_exit(); + +sub run_argv_and_exit +{ + if (@ARGV) { exec(@ARGV); die "Cannot exec `@ARGV`: $!"; -} else { + } else { exit 0; + } } sub shell_or_die @@ -1594,8 +1825,13 @@ sub shell_or_die if ($ENV{"DEBUG"}) { print STDERR "@_\n"; } - system (@_) == 0 - or die "@_ failed: $! exit 0x".sprintf("%x",$?); + if (system (@_) != 0) { + my $err = $!; + my $exitstatus = sprintf("exit %d signal %d", $? >> 8, $? & 0x7f); + open STDERR, ">&STDERR_ORIG"; + system ("cat $destdir.log >&2"); + die "@_ failed ($err): $exitstatus"; + } } __DATA__