Use a simple 'open' for fetch_block (freeing up an extra filehandle). refs #2325...

[arvados.git] / sdk / cli / bin / crunch-job

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 655bd15242f69ab48f88baf9d5f0a0f20d81e27c..2f8623ba66490f4cf930714473b43a05b4e3215f 100755 (executable)
--- 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.
 
 
 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
 =back
 
 =head1 RUNNING JOBS LOCALLY


@@ -71,9 +77,10 @@ use POSIX ':sys_wait_h';
 use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK);
 use Arvados;
 use Getopt::Long;
 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"}) {
 
 $ENV{"TMPDIR"} ||= "/tmp";
 unless (defined $ENV{"CRUNCH_TMP"}) {


@@ -84,6 +91,7 @@ unless (defined $ENV{"CRUNCH_TMP"}) {
   }
 }
 $ENV{"JOB_WORK"} = $ENV{"CRUNCH_TMP"} . "/work";
   }
 }
 $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"});
 
 $ENV{"CRUNCH_WORK"} = $ENV{"JOB_WORK"}; # deprecated
 mkdir ($ENV{"JOB_WORK"});
 


@@ -91,11 +99,13 @@ my $force_unlock;
 my $git_dir;
 my $jobspec;
 my $job_api_token;
 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,
 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,
     );
 
            'resume-stash=s' => \$resume_stash,
     );
 


@@ -165,11 +175,8 @@ else
 }
 $job_id = $Job->{'uuid'};
 
 }
 $job_id = $Job->{'uuid'};
 

-$metastream = Warehouse::Stream->new(whc => new Warehouse);
-$metastream->clear;
-$metastream->name('.');
-$metastream->write_start($job_id . '.log.txt');
-
+my $keep_logfile = $job_id . '.log.txt';
+my $local_logfile = File::Temp->new();

 
 $Job->{'runtime_constraints'} ||= {};
 $Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0;
 
 $Job->{'runtime_constraints'} ||= {};
 $Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0;


@@ -322,6 +329,12 @@ else
 }
 
 
 }
 
 

+if (!$have_slurm)
+{
+  must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
+}
+
+

 my $build_script;
 
 
 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)
 {
 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};
   $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
 {
 }
 else
 {


@@ -341,22 +368,24 @@ else
   Log (undef, "Install revision ".$Job->{script_version});
   my $nodelist = join(",", @node);
 
   Log (undef, "Install revision ".$Job->{script_version});
   my $nodelist = join(",", @node);
 

-  # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
+  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 $CRUNCH_TMP/src*']);
-    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
 
 
   # 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_SRC_COMMIT"} = $Job->{script_version};
   $ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src";

-  $ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";

 
   my $commit;
   my $git_archive;
 
   my $commit;
   my $git_archive;


@@ -454,6 +482,12 @@ else
   Log (undef, "Install exited $?");
 }
 
   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))
 
 
 foreach (qw (script script_version script_parameters runtime_constraints))


@@ -545,9 +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_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{"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";
 
 
     $ENV{"GZIP"} = "-n";
 


@@ -561,7 +597,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     my $build_script_to_send = "";
     my $command =
        "if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
     my $build_script_to_send = "";
     my $command =
        "if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "

-        ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} "
+        ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "

        ."&& cd $ENV{CRUNCH_TMP} ";
     if ($build_script)
     {
        ."&& cd $ENV{CRUNCH_TMP} ";
     if ($build_script)
     {


@@ -569,11 +605,8 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       $command .=
          "&& perl -";
     }
       $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 .=
     $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);
     my @execargs = ('bash', '-c', $command);
     srun (\@srunargs, \@execargs, undef, $build_script_to_send);
     exit (111);


@@ -725,7 +758,7 @@ if ($job_has_uuid) {
 if ($Job->{'output'})
 {
   eval {
 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,
     $arv->{'collections'}->{'create'}->execute('collection' => {
       'uuid' => $Job->{'output'},
       'manifest_text' => $manifest_text,


@@ -1025,12 +1058,24 @@ sub process_stderr
   } split ("\n", $jobstep[$job]->{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
 {
 
 sub collate_output
 {

-  my $whc = Warehouse->new;

   Log (undef, "collate");
   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)
   {
   my $joboutput;
   for (@jobstep)
   {


@@ -1041,26 +1086,36 @@ sub collate_output
     if ($output !~ /^[0-9a-f]{32}(\+\S+)*$/)
     {
       $output_in_keep ||= $output =~ / [0-9a-f]{32}\S*\+K/;
     if ($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;
     }
     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/;
     {
       $output_in_keep ||= $outblock =~ / [0-9a-f]{32}\S*\+K/;

-      $whc->write_data ($outblock);
+      print $child_in $outblock;

     }
     else
     {
     }
     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;
     }
   }
       $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 $joboutput");
   if ($joboutput)
   {
     Log (undef, "output $joboutput");


@@ -1135,8 +1190,9 @@ sub Log                           # ($jobstep_id, $logmessage)
   }
   print STDERR ((-t STDERR) ? ($datetime." ".$message) : $message);
 
   }
   print STDERR ((-t STDERR) ? ($datetime." ".$message) : $message);
 

-  return if !$metastream;
-  $metastream->write_data ($datetime . " " . $message);
+  if ($metastream) {
+    print $metastream $datetime . " " . $message;
+  }

 }
 
 
 }
 
 


@@ -1165,16 +1221,15 @@ sub cleanup
 sub save_meta
 {
   my $justcheckpoint = shift; # false if this will be the last meta saved
 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 $whc = Warehouse->new;
-  my $loglocator = $whc->store_block ($m->as_string);
-  $arv->{'collections'}->{'create'}->execute('collection' => {
-    'uuid' => $loglocator,
-    'manifest_text' => $m->as_string,
-  });
-  undef $metastream if !$justcheckpoint; # otherwise Log() will try to use it
+  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->update_attributes('log', $loglocator) if $job_has_uuid;
   Log (undef, "log manifest is $loglocator");
   $Job->{'log'} = $loglocator;
   $Job->update_attributes('log', $loglocator) if $job_has_uuid;


@@ -1220,65 +1275,6 @@ sub freeze
 sub thaw
 {
   croak ("Thaw not implemented");
 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;

 }
 
 
 }
 
 


@@ -1338,6 +1334,15 @@ sub ban_node_by_slot {
   Log (undef, "backing off node " . $slot[$slotid]->{node}->{name} . " for 60 seconds");
 }
 
   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
 
 __DATA__
 #!/usr/bin/perl
 


@@ -1360,16 +1365,27 @@ open STDOUT, ">", "$destdir.log";
 open STDERR, ">&STDOUT";
 
 mkdir $destdir;
 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;
 }
 
 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", $install_dir);
 } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {
 if (-e "$destdir/crunch_scripts/install") {
     shell_or_die ("$destdir/crunch_scripts/install", $install_dir);
 } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {