Consume all arguments after arv-mount --exec, and fork subprocess

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

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index b3fef233c651956c2b75e838ac924069d8f3f97e..e3d0c1dc1f40565ed8e4b6f4f82fbb44d0d6519e 100755 (executable)
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -84,6 +84,7 @@ 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"});
 
@@ -119,10 +120,8 @@ $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;
 
@@ -167,6 +166,10 @@ else
 }
 $job_id = $Job->{'uuid'};
 
+$metastream = Warehouse::Stream->new(whc => new Warehouse);
+$metastream->clear;
+$metastream->name('.');
+$metastream->write_start($job_id . '.log.txt');
 
 
 $Job->{'runtime_constraints'} ||= {};
@@ -329,6 +332,16 @@ my $skip_install = ($local_job && $Job->{script_version} =~ m{^/});
 if ($skip_install)
 {
   $ENV{"CRUNCH_SRC"} = $Job->{script_version};
+  system("virtualenv", "$ENV{CRUNCH_TMP}/opt") == 0
+      or croak ("virtualenv $ENV{CRUNCH_TMP}/opt failed: exit ".($?>>8));
+  for my $src_path ("$ENV{CRUNCH_SRC}/arvados/sdk/python",
+                    "$ENV{CRUNCH_SRC}/sdk/python") {
+    if (-d $src_path) {
+      system ("cd $src_path && \$CRUNCH_TMP/opt/bin/python setup.py install")
+          == 0
+          or croak ("setup.py in $src_path failed: exit ".($?>>8));
+    }
+  }
 }
 else
 {
@@ -339,13 +352,13 @@ else
   Log (undef, "Install revision ".$Job->{script_version});
   my $nodelist = join(",", @node);
 
-  # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src
+  # 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']);
+         ['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)
@@ -365,7 +378,6 @@ 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;
@@ -544,8 +556,10 @@ 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_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";
 
@@ -559,7 +573,7 @@ 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; "
-        ."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)
     {
@@ -569,9 +583,10 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     }
     $ENV{"PYTHONPATH"} =~ s{^}{:} if $ENV{"PYTHONPATH"};
     $ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/sdk/python}; # xxx hack
+    $ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/arvados/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);
@@ -1166,9 +1181,14 @@ sub save_meta
   my $m = $metastream;
   $m = $m->copy if $justcheckpoint;
   $m->write_finish;
-  my $loglocator = $m->as_key;
+  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
-  Log (undef, "meta key is $loglocator");
+  Log (undef, "log manifest is $loglocator");
   $Job->{'log'} = $loglocator;
   $Job->update_attributes('log', $loglocator) if $job_has_uuid;
 }
@@ -1344,7 +1364,7 @@ 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;
 }
 
@@ -1363,6 +1383,14 @@ my $pwd;
 chomp ($pwd = `pwd`);
 my $install_dir = $ENV{"CRUNCH_INSTALL"} || "$pwd/opt";
 mkdir $install_dir;
+
+shell_or_die ("virtualenv", $install_dir);
+for my $src_path ("$destdir/arvados/sdk/python", "$destdir/sdk/python") {
+  if (-d $src_path) {
+    shell_or_die ("cd $src_path && $install_dir/bin/python setup.py install");
+  }
+}
+
 if (-e "$destdir/crunch_scripts/install") {
     shell_or_die ("$destdir/crunch_scripts/install", $install_dir);
 } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {