X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d7d09656f721437c05bb26d5c715024ff164c0b5..b1b9ffbb5e49d04c058d11702ecd240b1ef8a958:/sdk/cli/bin/crunch-job

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index c2738e224f..2f8623ba66 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -33,6 +33,12 @@ Path to .git directory where the specified commit is found.
 
 Arvados API authorization token to use during the course of the job.
 
+=item --no-clear-tmp
+
+Do not clear per-job/task temporary directories during initial job
+setup. This can speed up development and debugging when running jobs
+locally.
+
 =back
 
 =head1 RUNNING JOBS LOCALLY
@@ -58,7 +64,8 @@ Save a checkpoint and continue.
 =item SIGHUP
 
 Refresh node allocation (i.e., check whether any nodes have been added
-or unallocated). Currently this is a no-op.
+or unallocated) and attributes of the Job record that should affect
+behavior (e.g., cancel job if cancelled_at becomes non-nil).
 
 =back
 
@@ -70,9 +77,10 @@ use POSIX ':sys_wait_h';
 use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK);
 use Arvados;
 use Getopt::Long;
-use Warehouse;
-use Warehouse::Stream;
-use IPC::System::Simple qw(capturex);
+use IPC::Open2;
+use IO::Select;
+use File::Temp;
+use Fcntl ':flock';
 
 $ENV{"TMPDIR"} ||= "/tmp";
 unless (defined $ENV{"CRUNCH_TMP"}) {
@@ -83,6 +91,7 @@ unless (defined $ENV{"CRUNCH_TMP"}) {
   }
 }
 $ENV{"JOB_WORK"} = $ENV{"CRUNCH_TMP"} . "/work";
+$ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";
 $ENV{"CRUNCH_WORK"} = $ENV{"JOB_WORK"}; # deprecated
 mkdir ($ENV{"JOB_WORK"});
 
@@ -90,11 +99,13 @@ my $force_unlock;
 my $git_dir;
 my $jobspec;
 my $job_api_token;
+my $no_clear_tmp;
 my $resume_stash;
 GetOptions('force-unlock' => \$force_unlock,
            'git-dir=s' => \$git_dir,
            'job=s' => \$jobspec,
            'job-api-token=s' => \$job_api_token,
+           'no-clear-tmp' => \$no_clear_tmp,
            'resume-stash=s' => \$resume_stash,
     );
 
@@ -107,10 +118,6 @@ my $job_has_uuid = $jobspec =~ /^[-a-z\d]+$/;
 my $local_job = !$job_has_uuid;
 
 
-$SIG{'HUP'} = sub
-{
-  1;
-};
 $SIG{'USR1'} = sub
 {
   $main::ENV{CRUNCH_DEBUG} = 1;
@@ -122,10 +129,8 @@ $SIG{'USR2'} = sub
 
 
 
-my $arv = Arvados->new;
-my $metastream = Warehouse::Stream->new(whc => new Warehouse);
-$metastream->clear;
-$metastream->write_start('log.txt');
+my $arv = Arvados->new('apiVersion' => 'v1');
+my $metastream;
 
 my $User = $arv->{'users'}->{'current'}->execute;
 
@@ -170,7 +175,8 @@ else
 }
 $job_id = $Job->{'uuid'};
 
-
+my $keep_logfile = $job_id . '.log.txt';
+my $local_logfile = File::Temp->new();
 
 $Job->{'runtime_constraints'} ||= {};
 $Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0;
@@ -257,20 +263,17 @@ my $jobmanager_id;
 if ($job_has_uuid)
 {
   # Claim this job, and make sure nobody else does
-
-  $Job->{'is_locked_by_uuid'} = $User->{'uuid'};
-  $Job->{'started_at'} = gmtime;
-  $Job->{'running'} = 1;
-  $Job->{'success'} = undef;
-  $Job->{'tasks_summary'} = { 'failed' => 0,
-                              'todo' => 1,
-                              'running' => 0,
-                              'done' => 0 };
-  if ($job_has_uuid) {
-    unless ($Job->save() && $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) {
-      croak("Error while updating / locking job");
-    }
+  unless ($Job->update_attributes('is_locked_by_uuid' => $User->{'uuid'}) &&
+          $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) {
+    croak("Error while updating / locking job");
   }
+  $Job->update_attributes('started_at' => scalar gmtime,
+                          'running' => 1,
+                          'success' => undef,
+                          'tasks_summary' => { 'failed' => 0,
+                                               'todo' => 1,
+                                               'running' => 0,
+                                               'done' => 0 });
 }
 
 
@@ -281,9 +284,12 @@ $SIG{'TERM'} = \&croak;
 $SIG{'TSTP'} = sub { $main::please_freeze = 1; };
 $SIG{'ALRM'} = sub { $main::please_info = 1; };
 $SIG{'CONT'} = sub { $main::please_continue = 1; };
+$SIG{'HUP'} = sub { $main::please_refresh = 1; };
+
 $main::please_freeze = 0;
 $main::please_info = 0;
 $main::please_continue = 0;
+$main::please_refresh = 0;
 my $jobsteps_must_output_keys = 0;	# becomes 1 when any task outputs a key
 
 grep { $ENV{$1} = $2 if /^(NOCACHE.*?)=(.*)/ } split ("\n", $$Job{knobs});
@@ -299,6 +305,7 @@ my $jobstep_tomerge_level = 0;
 my $squeue_checked;
 my $squeue_kill_checked;
 my $output_in_keep = 0;
+my $latest_refresh = scalar time;
 
 
 
@@ -322,6 +329,12 @@ else
 }
 
 
+if (!$have_slurm)
+{
+  must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
+}
+
+
 my $build_script;
 
 
@@ -330,7 +343,21 @@ $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));
+    }
+  }
 }
 else
 {
@@ -341,22 +368,24 @@ else
   Log (undef, "Install revision ".$Job->{script_version});
   my $nodelist = join(",", @node);
 
-  # Clean out crunch_tmp/work and crunch_tmp/opt
+  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 sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt']);
-    exit (1);
-  }
-  while (1)
-  {
-    last if $cleanpid == waitpid (-1, WNOHANG);
-    freeze_if_want_freeze ($cleanpid);
-    select (undef, undef, undef, 0.1);
+    my $cleanpid = fork();
+    if ($cleanpid == 0)
+    {
+      srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
+	    ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; 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 $?");
   }
-  Log (undef, "Clean-work-dir exited $?");
 
   # Install requested code version
 
@@ -367,7 +396,6 @@ else
 
   $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version};
   $ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src";
-  $ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";
 
   my $commit;
   my $git_archive;
@@ -421,7 +449,9 @@ else
 	Log (undef, "Using commit $commit for tree-ish $treeish");
         if ($commit ne $treeish) {
           $Job->{'script_version'} = $commit;
-          !$job_has_uuid or $Job->save() or croak("Error while updating job");
+          !$job_has_uuid or
+              $Job->update_attributes('script_version' => $commit) or
+              croak("Error while updating job");
         }
       }
     }
@@ -452,6 +482,12 @@ else
   Log (undef, "Install exited $?");
 }
 
+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.");
+}
+
 
 
 foreach (qw (script script_version script_parameters runtime_constraints))
@@ -543,9 +579,11 @@ 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"} = $ENV{"JOB_WORK"}."/".$slot[$childslot]->{cpu};
+    $ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/$id.$$";
+    $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}."/keep";
     $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
     $ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
+    $ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};
 
     $ENV{"GZIP"} = "-n";
 
@@ -558,7 +596,8 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     my @execargs = qw(sh);
     my $build_script_to_send = "";
     my $command =
-	"mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} "
+	"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
+        ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
 	."&& cd $ENV{CRUNCH_TMP} ";
     if ($build_script)
     {
@@ -566,11 +605,8 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       $command .=
 	  "&& perl -";
     }
-    $ENV{"PYTHONPATH"} =~ s{^}{:} if $ENV{"PYTHONPATH"};
-    $ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/sdk/python}; # xxx hack
-    $ENV{"PYTHONPATH"} =~ s{$}{:/usr/local/arvados/src/sdk/python}; # xxx hack
     $command .=
-        "&& exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+        "&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
     my @execargs = ('bash', '-c', $command);
     srun (\@srunargs, \@execargs, undef, $build_script_to_send);
     exit (111);
@@ -622,6 +658,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
 	+ reapchildren ();
     if (!$gotsome)
     {
+      check_refresh_wanted();
       check_squeue();
       update_progress_stats();
       select (undef, undef, undef, 0.1);
@@ -678,6 +715,7 @@ while (%proc)
   readfrompipes ();
   if (!reapchildren())
   {
+    check_refresh_wanted();
     check_squeue();
     update_progress_stats();
     select (undef, undef, undef, 0.1);
@@ -710,17 +748,17 @@ goto ONELEVEL if !defined $main::success;
 
 release_allocation();
 freeze();
-$Job->reload;
-$Job->{'output'} = &collate_output();
-$Job->{'running'} = 0;
-$Job->{'success'} = $Job->{'output'} && $main::success;
-$Job->{'finished_at'} = gmtime;
-$Job->save if $job_has_uuid;
+if ($job_has_uuid) {
+  $Job->update_attributes('output' => &collate_output(),
+                          'running' => 0,
+                          'success' => $Job->{'output'} && $main::success,
+                          'finished_at' => scalar gmtime)
+}
 
 if ($Job->{'output'})
 {
   eval {
-    my $manifest_text = capturex("whget", $Job->{'output'});
+    my $manifest_text = `arv keep get \Q$Job->{'output'}\E`;
     $arv->{'collections'}->{'create'}->execute('collection' => {
       'uuid' => $Job->{'output'},
       'manifest_text' => $manifest_text,
@@ -749,7 +787,9 @@ sub update_progress_stats
   $Job->{'tasks_summary'}->{'todo'} = $todo;
   $Job->{'tasks_summary'}->{'done'} = $done;
   $Job->{'tasks_summary'}->{'running'} = $running;
-  $Job->save if $job_has_uuid;
+  if ($job_has_uuid) {
+    $Job->update_attributes('tasks_summary' => $Job->{'tasks_summary'});
+  }
   Log (undef, "status: $done done, $running running, $todo todo");
   $progress_is_dirty = 0;
 }
@@ -865,6 +905,27 @@ sub reapchildren
   1;
 }
 
+sub check_refresh_wanted
+{
+  my @stat = stat $ENV{"CRUNCH_REFRESH_TRIGGER"};
+  if (@stat && $stat[9] > $latest_refresh) {
+    $latest_refresh = scalar time;
+    if ($job_has_uuid) {
+      my $Job2 = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec);
+      for my $attr ('cancelled_at',
+                    'cancelled_by_user_uuid',
+                    'cancelled_by_client_uuid') {
+        $Job->{$attr} = $Job2->{$attr};
+      }
+      if ($Job->{'cancelled_at'}) {
+        Log (undef, "Job cancelled at " . $Job->{cancelled_at} .
+             " by user " . $Job->{cancelled_by_user_uuid});
+        $main::success = 0;
+        $main::please_freeze = 1;
+      }
+    }
+  }
+}
 
 sub check_squeue
 {
@@ -997,12 +1058,24 @@ sub process_stderr
   } split ("\n", $jobstep[$job]->{stderr});
 }
 
+sub fetch_block
+{
+  my $hash = shift;
+  my ($child_out, $output_block);
+
+  my $cmd = "arv keep get \Q$hash\E";
+  open($keep, '-|', $cmd) or die "fetch_block: $cmd: $!"
+  sysread($keep, $output_block, 64 * 1024 * 1024);
+  close $keep;
+  return $output_block;
+}
 
 sub collate_output
 {
-  my $whc = Warehouse->new;
   Log (undef, "collate");
-  $whc->write_start (1);
+
+  my ($child_out, $child_in);
+  my $pid = open2($child_out, $child_in, 'arv', 'keep', 'put', '--raw');
   my $joboutput;
   for (@jobstep)
   {
@@ -1013,31 +1086,40 @@ sub collate_output
     if ($output !~ /^[0-9a-f]{32}(\+\S+)*$/)
     {
       $output_in_keep ||= $output =~ / [0-9a-f]{32}\S*\+K/;
-      $whc->write_data ($output);
+      print $child_in $output;
     }
     elsif (@jobstep == 1)
     {
       $joboutput = $output;
-      $whc->write_finish;
+      last;
     }
-    elsif (defined (my $outblock = $whc->fetch_block ($output)))
+    elsif (defined (my $outblock = fetch_block ($output)))
     {
       $output_in_keep ||= $outblock =~ / [0-9a-f]{32}\S*\+K/;
-      $whc->write_data ($outblock);
+      print $child_in $outblock;
     }
     else
     {
-      my $errstr = $whc->errstr;
-      $whc->write_data ("XXX fetch_block($output) failed: $errstr XXX\n");
+      Log (undef, "XXX fetch_block($output) failed XXX");
       $main::success = 0;
     }
   }
-  $joboutput = $whc->write_finish if !defined $joboutput;
+  $child_in->close;
+
+  if (!defined $joboutput) {
+    my $s = IO::Select->new($child_out);
+    if ($s->can_read(120)) {
+      sysread($child_out, $joboutput, 64 * 1024 * 1024);
+    } else {
+      Log (undef, "timed out reading from 'arv keep put'");
+    }
+  }
+  waitpid($pid, 0);
+
   if ($joboutput)
   {
     Log (undef, "output $joboutput");
-    $Job->{'output'} = $joboutput;
-    $Job->save if $job_has_uuid;
+    $Job->update_attributes('output' => $joboutput) if $job_has_uuid;
   }
   else
   {
@@ -1108,8 +1190,9 @@ sub Log				# ($jobstep_id, $logmessage)
   }
   print STDERR ((-t STDERR) ? ($datetime." ".$message) : $message);
 
-  return if !$metastream;
-  $metastream->write_data ($datetime . " " . $message);
+  if ($metastream) {
+    print $metastream $datetime . " " . $message;
+  }
 }
 
 
@@ -1129,25 +1212,27 @@ sub croak
 sub cleanup
 {
   return if !$job_has_uuid;
-  $Job->reload;
-  $Job->{'running'} = 0;
-  $Job->{'success'} = 0;
-  $Job->{'finished_at'} = gmtime;
-  $Job->save;
+  $Job->update_attributes('running' => 0,
+                          'success' => 0,
+                          'finished_at' => scalar gmtime);
 }
 
 
 sub save_meta
 {
   my $justcheckpoint = shift; # false if this will be the last meta saved
-  my $m = $metastream;
-  $m = $m->copy if $justcheckpoint;
-  $m->write_finish;
-  my $loglocator = $m->as_key;
-  undef $metastream if !$justcheckpoint; # otherwise Log() will try to use it
-  Log (undef, "meta key is $loglocator");
+  return if $justcheckpoint;  # checkpointing is not relevant post-Warehouse.pm
+
+  $local_logfile->flush;
+  my $cmd = "arv keep put --filename \Q$keep_logfile\E "
+      . quotemeta($local_logfile->filename);
+  my $loglocator = `$cmd`;
+  die "system $cmd failed: $?" if $?;
+
+  $local_logfile = undef;   # the temp file is automatically deleted
+  Log (undef, "log manifest is $loglocator");
   $Job->{'log'} = $loglocator;
-  $Job->save if $job_has_uuid;
+  $Job->update_attributes('log', $loglocator) if $job_has_uuid;
 }
 
 
@@ -1190,65 +1275,6 @@ sub freeze
 sub thaw
 {
   croak ("Thaw not implemented");
-
-  my $whc;
-  my $key = shift;
-  Log (undef, "thaw from $key");
-
-  @jobstep = ();
-  @jobstep_done = ();
-  @jobstep_todo = ();
-  @jobstep_tomerge = ();
-  $jobstep_tomerge_level = 0;
-  my $frozenjob = {};
-
-  my $stream = new Warehouse::Stream ( whc => $whc,
-				       hash => [split (",", $key)] );
-  $stream->rewind;
-  while (my $dataref = $stream->read_until (undef, "\n\n"))
-  {
-    if ($$dataref =~ /^job /)
-    {
-      foreach (split ("\n", $$dataref))
-      {
-	my ($k, $v) = split ("=", $_, 2);
-	$frozenjob->{$k} = freezeunquote ($v);
-      }
-      next;
-    }
-
-    if ($$dataref =~ /^merge (\d+) (.*)/)
-    {
-      $jobstep_tomerge_level = $1;
-      @jobstep_tomerge
-	  = map { freezeunquote ($_) } split ("\n", freezeunquote($2));
-      next;
-    }
-
-    my $Jobstep = { };
-    foreach (split ("\n", $$dataref))
-    {
-      my ($k, $v) = split ("=", $_, 2);
-      $Jobstep->{$k} = freezeunquote ($v) if $k;
-    }
-    $Jobstep->{'failures'} = 0;
-    push @jobstep, $Jobstep;
-
-    if ($Jobstep->{exitcode} eq "0")
-    {
-      push @jobstep_done, $#jobstep;
-    }
-    else
-    {
-      push @jobstep_todo, $#jobstep;
-    }
-  }
-
-  foreach (qw (script script_version script_parameters))
-  {
-    $Job->{$_} = $frozenjob->{$_};
-  }
-  $Job->save if $job_has_uuid;
 }
 
 
@@ -1308,6 +1334,15 @@ sub ban_node_by_slot {
   Log (undef, "backing off node " . $slot[$slotid]->{node}->{name} . " for 60 seconds");
 }
 
+sub must_lock_now
+{
+  my ($lockfile, $error_message) = @_;
+  open L, ">", $lockfile or croak("$lockfile: $!");
+  if (!flock L, LOCK_EX|LOCK_NB) {
+    croak("Can't lock $lockfile: $error_message\n");
+  }
+}
+
 __DATA__
 #!/usr/bin/perl
 
@@ -1321,7 +1356,7 @@ my $repo = $ENV{"CRUNCH_SRC_URL"};
 
 open L, ">", "$destdir.lock" or die "$destdir.lock: $!";
 flock L, LOCK_EX;
-if (readlink ("$destdir.commit") eq $commit) {
+if (readlink ("$destdir.commit") eq $commit && -d $destdir) {
     exit 0;
 }
 
@@ -1330,16 +1365,27 @@ open STDOUT, ">", "$destdir.log";
 open STDERR, ">&STDOUT";
 
 mkdir $destdir;
-open TARX, "|-", "tar", "-C", $destdir, "-xf", "-";
-print TARX <DATA>;
-if(!close(TARX)) {
-  die "'tar -C $destdir -xf -' exited $?: $!";
+my @git_archive_data = <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 $?: $!";
+  }
 }
 
 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 && $install_dir/bin/python setup.py install");
+  }
+}
+
 if (-e "$destdir/crunch_scripts/install") {
     shell_or_die ("$destdir/crunch_scripts/install", $install_dir);
 } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {