add usr/local/arvados/src pythonpath

[arvados.git] / services / crunch / crunch-job

diff --git a/services/crunch/crunch-job b/services/crunch/crunch-job
index 8c50ba6eaf5ab710537db8f5496077f0f90ec245..171a4003e5f93bd0ee4e285eda8989dfad95cef4 100755 (executable)
--- a/services/crunch/crunch-job
+++ b/services/crunch/crunch-job
@@ -76,8 +76,13 @@ use IPC::System::Simple qw(capturex);
 
 $ENV{"TMPDIR"} ||= "/tmp";
 $ENV{"CRUNCH_TMP"} = $ENV{"TMPDIR"} . "/crunch-job";
-$ENV{"CRUNCH_WORK"} = $ENV{"CRUNCH_TMP"} . "/work";
-mkdir ($ENV{"CRUNCH_TMP"});
+if ($ENV{"USER"} ne "crunch" && $< != 0) {
+  # use a tmp dir unique for my uid
+  $ENV{"CRUNCH_TMP"} .= "-$<";
+}
+$ENV{"JOB_WORK"} = $ENV{"CRUNCH_TMP"} . "/work";
+$ENV{"CRUNCH_TMP"} = $ENV{"JOB_WORK"}; # deprecated
+mkdir ($ENV{"JOB_WORK"});
 
 my $force_unlock;
 my $git_dir;
@@ -130,8 +135,8 @@ if ($job_has_uuid)
 {
   $Job = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec);
   if (!$force_unlock) {
-    if ($Job->{'is_locked_by'}) {
-      croak("Job is locked: " . $Job->{'is_locked_by'});
+    if ($Job->{'is_locked_by_uuid'}) {
+      croak("Job is locked: " . $Job->{'is_locked_by_uuid'});
     }
     if ($Job->{'success'} ne undef) {
       croak("Job 'success' flag (" . $Job->{'success'} . ") is not null");
@@ -154,7 +159,7 @@ else
     qw(script script_version script_parameters);
   }
 
-  $Job->{'is_locked_by'} = $User->{'uuid'};
+  $Job->{'is_locked_by_uuid'} = $User->{'uuid'};
   $Job->{'started_at'} = gmtime;
 
   $Job = $arv->{'jobs'}->{'create'}->execute('job' => $Job);
@@ -251,7 +256,7 @@ if ($job_has_uuid)
 {
   # Claim this job, and make sure nobody else does
 
-  $Job->{'is_locked_by'} = $User->{'uuid'};
+  $Job->{'is_locked_by_uuid'} = $User->{'uuid'};
   $Job->{'started_at'} = gmtime;
   $Job->{'running'} = 1;
   $Job->{'success'} = undef;
@@ -260,7 +265,7 @@ if ($job_has_uuid)
                               'running' => 0,
                               'done' => 0 };
   if ($job_has_uuid) {
-    unless ($Job->save() && $Job->{'is_locked_by'} == $User->{'uuid'}) {
+    unless ($Job->save() && $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) {
       croak("Error while updating / locking job");
     }
   }
@@ -340,7 +345,7 @@ else
   if ($cleanpid == 0)
   {
     srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
-         ['bash', '-c', 'if mount | grep -q $CRUNCH_WORK/; then sudo /bin/umount $CRUNCH_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $CRUNCH_WORK $CRUNCH_TMP/opt']);
+         ['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)
@@ -544,7 +549,8 @@ 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_TMPDIR"} = $ENV{"CRUNCH_WORK"}.$slot[$childslot]->{cpu};
+    $ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/".$slot[$childslot]->{cpu};
+    $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
     $ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
 
     $ENV{"GZIP"} = "-n";
@@ -558,7 +564,7 @@ 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{CRUNCH_WORK} $ENV{CRUNCH_TMP} "
+       "mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} "
        ."&& cd $ENV{CRUNCH_TMP} ";
     if ($build_script)
     {
@@ -566,7 +572,9 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       $command .=
          "&& perl -";
     }
-    $ENV{"PYTHONPATH"} = "$ENV{CRUNCH_SRC}/sdk/python"; # xxx hack
+    $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"};
     my @execargs = ('bash', '-c', $command);
@@ -829,7 +837,7 @@ sub reapchildren
   # Load new tasks
   my $newtask_list = $arv->{'job_tasks'}->{'list'}->execute(
     'where' => {
-      'created_by_job_task' => $Jobstep->{'arvados_task'}->{uuid}
+      'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid}
     },
     'order' => 'qsequence'
   );