X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5c1f03ef1ae45d3ac222542d33b3125ce8678d65..dd7bb176c565d0d0718f9b0e59a6d9ee4b8ecbf2:/sdk/cli/bin/crunch-job diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job index eff48a21eb..369bc3e1ae 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 @@ -140,43 +149,31 @@ $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 = retry_op(sub { $arv->{'users'}->{'current'}->execute; }); + if ($jobspec =~ /^[-a-z\d]+$/) { # $jobspec is an Arvados UUID, not a JSON job specification - $Job = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec); + $Job = retry_op(sub { + $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec); + }); if (!$force_unlock) { - # If some other crunch-job process has grabbed this job (or we see - # other evidence that the job is already underway) we exit - # EX_TEMPFAIL so crunch-dispatch (our parent process) doesn't - # mark the job as failed. - if ($Job->{'is_locked_by_uuid'}) { - Log(undef, "Job is locked by " . $Job->{'is_locked_by_uuid'}); - exit EX_TEMPFAIL; - } - if ($Job->{'state'} ne 'Queued') { - Log(undef, "Job state is " . $Job->{'state'} . ", but I can only start queued jobs."); - exit EX_TEMPFAIL; - } - if ($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"); + # Claim this job, and make sure nobody else does + eval { retry_op(sub { + # lock() sets is_locked_by_uuid and changes state to Running. + $arv->{'jobs'}->{'lock'}->execute('uuid' => $Job->{'uuid'}) + }); }; + if ($@) { + Log(undef, "Error while locking job, exiting ".EX_TEMPFAIL); 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 +188,14 @@ else $Job->{'is_locked_by_uuid'} = $User->{'uuid'}; $Job->{'started_at'} = gmtime; + $Job->{'state'} = 'Running'; - $Job = $arv->{'jobs'}->{'create'}->execute('job' => $Job); + $Job = retry_op(sub { $arv->{'jobs'}->{'create'}->execute('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 +277,11 @@ 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 +303,6 @@ $ENV{"CRUNCH_JOB_UUID"} = $job_id; $ENV{"JOB_UUID"} = $job_id; -my @jobstep; my @jobstep_todo = (); my @jobstep_done = (); my @jobstep_tomerge = (); @@ -332,12 +320,14 @@ if (defined $Job->{thawedfromkey}) } else { - my $first_task = $arv->{'job_tasks'}->{'create'}->execute('job_task' => { - 'job_uuid' => $Job->{'uuid'}, - 'sequence' => 0, - 'qsequence' => 0, - 'parameters' => {}, - }); + my $first_task = retry_op(sub { + $arv->{'job_tasks'}->{'create'}->execute('job_task' => { + 'job_uuid' => $Job->{'uuid'}, + 'sequence' => 0, + 'qsequence' => 0, + 'parameters' => {}, + }); + }); push @jobstep, { 'level' => 0, 'failures' => 0, 'arvados_task' => $first_task, @@ -382,17 +372,21 @@ if (!defined $no_clear_tmp) { my $git_archive; if (!defined $git_dir && $Job->{'script_version'} =~ m{^/}) { - # If we're in user-land (i.e., not called from crunch-dispatch) - # script_version can be an absolute directory path, signifying we - # should work straight out of that directory instead of using a git - # commit. + # 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 Log (undef, "Looking for version ".$Job->{script_version}." from repository ".$Job->{repository}); $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version}; @@ -413,13 +407,18 @@ else { # to a local dir before doing `git log` et al. my $repo_location; - if ($repo =~ m{://|\@.*:}) { + if ($repo =~ m{://|^[^/]*:}) { # $repo is a git url we can clone, like git:// or https:// or - # file:/// or git@host:repo.git + # 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{^\.*/}) { # $repo is a local path to a git index. We'll also resolve ../foo - # to ../foo/.git if the latter is a directory. + # to ../foo/.git if the latter is a directory. To help + # disambiguate local paths from named hosted repositories, this + # form must be given as ./ or ../ if it's a relative path. if (-d "$repo/.git") { $repo = "$repo/.git"; } @@ -427,18 +426,20 @@ else { } else { # $repo is none of the above. It must be the name of a hosted # repository. - my $arv_repo_list = $arv->{'repositories'}->{'list'}->execute( - 'filters' => [['name','=',$repo]] - )->{'items'}; - my $n_found = scalar @{$arv_repo_list}; + my $arv_repo_list = retry_op(sub { + $arv->{'repositories'}->{'list'}->execute( + 'filters' => [['name','=',$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 { $_->{'uuid'} } @{$arv_repo_list})); + . join(", ", map { $_->{'uuid'} } @repos_found)); } if ($n_found != 1) { croak("Error: Found $n_found repositories with name '$repo'."); } - $repo = $arv_repo_list->[0]->{'fetch_url'}; + $repo = $repos_found[0]->{'fetch_url'}; $repo_location = 'remote'; } Log(undef, "Using $repo_location repository '$repo'"); @@ -471,11 +472,12 @@ else { # 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 ($treeish =~ /^[0-9a-f]{3,40}$/s) { + 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 && - $sha1 =~ /^$treeish/ && # Don't use commit 123 @ branch abc! + # 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"); @@ -917,8 +919,9 @@ 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 = retry_op(sub { + $arv->{'collections'}->{'create'}->execute( + 'collection' => {'manifest_text' => $orig_manifest_text}); }); Log(undef, "output uuid " . $output->{uuid}); Log(undef, "output hash " . $output->{portable_data_hash}); @@ -1053,13 +1056,15 @@ sub reapchildren my $newtask_list = []; my $newtask_results; do { - $newtask_results = $arv->{'job_tasks'}->{'list'}->execute( - 'where' => { - 'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid} - }, - 'order' => 'qsequence', - 'offset' => scalar(@$newtask_list), - ); + $newtask_results = retry_op(sub { + $arv->{'job_tasks'}->{'list'}->execute( + 'where' => { + 'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid} + }, + 'order' => 'qsequence', + 'offset' => scalar(@$newtask_list), + ); + }); push(@$newtask_list, @{$newtask_results->{items}}); } while (@{$newtask_results->{items}}); foreach my $arvados_task (@$newtask_list) { @@ -1082,7 +1087,9 @@ 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 = retry_op(sub { + $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec); + }); for my $attr ('cancelled_at', 'cancelled_by_user_uuid', 'cancelled_by_client_uuid', @@ -1263,7 +1270,7 @@ sub collate_output my ($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) { @@ -1352,6 +1359,73 @@ 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/) { @@ -1365,15 +1439,15 @@ 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); } } @@ -1385,14 +1459,15 @@ 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 { @@ -1405,16 +1480,9 @@ 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 $cmd exited ".exit_status_s($?) 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); @@ -1534,7 +1602,10 @@ 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 = retry_op(sub { + $arv->{collections}->{get}->execute(uuid => $locator); + }); + if ($image) { foreach my $line (split(/\n/, $image->{manifest_text})) { my @tokens = split(/\s+/, $line); next if (!@tokens); @@ -1555,20 +1626,52 @@ 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 { + # Given a function reference, call it with the remaining arguments. If + # it dies, retry it with exponential backoff until it succeeds, or until + # the current retry_count is exhausted. + my $operation = 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) { + 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 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".