arvados-cli 0.1.20140507111537 → 0.1.20140507113226

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 878dcd432ca0a5a9d5f3a5f8748bd37cbd6e4fc0
-  data.tar.gz: 841aaed95eb94b5656db33d6adb2368620a904b5
+  metadata.gz: 4799416d5cef31a70a4c10ff82561bf85243afc6
+  data.tar.gz: 1700f4b6625d064d47179b184195ad50cd0c8103
 SHA512:
-  metadata.gz: c4812e656ecd450fbfa185ece26b921181753c444cfaf41e833a38217b512bb553691d2d5ed69e91bf5be1dfa87e9bfab0a7d8e9975ea6516f6f09bacda83b22
-  data.tar.gz: b0331563eddfdafe972e2d6da2fd65f135b8d46e7b0bf049bd283ea2a804439ca1762dfce015e1cff5d0ba631a3b822a7c2eb7e9c8cee50b9ea1ab70ca1e8d74
+  metadata.gz: c96958d07008b3ef0b1c6a31f14e48ad8bec9697558373f4cc4a3715b3d65dd5f5a098e139e0d7b1f6a796edea1e233b4a8ef94e28fecb501c7e67a6e7f44a76
+  data.tar.gz: 90ac89a22c4e48f709a1fa19494e127d93431d0289b630cb77f2192ba8e3c45df53689f14fd7f1ab4ccc0895b3e61a99b6de4b0e3f24d692886112b6666ba555

data/bin/crunch-job

@@ -498,7 +498,30 @@ if (!$have_slurm)
   must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
 }
 
-
+# If this job requires a Docker image, install that.
+my $docker_bin = "/usr/bin/docker.io";
+my $docker_image = $Job->{runtime_constraints}->{docker_image} || "";
+if ($docker_image) {
+  my $docker_pid = fork();
+  if ($docker_pid == 0)
+  {
+    srun (["srun", "--nodelist=" . join(' ', @node)],
+          [$docker_bin, 'pull', $docker_image]);
+    exit ($?);
+  }
+  while (1)
+  {
+    last if $docker_pid == waitpid (-1, WNOHANG);
+    freeze_if_want_freeze ($docker_pid);
+    select (undef, undef, undef, 0.1);
+  }
+  # If the Docker image was specified as a hash, pull will fail.
+  # Ignore that error.  We'll see what happens when we try to run later.
+  if (($? != 0) && ($docker_image !~ /^[0-9a-fA-F]{5,}$/))
+  {
+    croak("Installing Docker image $docker_image returned exit code $?");
+  }
+}
 
 foreach (qw (script script_version script_parameters runtime_constraints))
 {
@@ -603,7 +626,6 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       qw(-n1 -c1 -N1 -D), $ENV{'TMPDIR'},
       "--job-name=$job_id.$id.$$",
 	);
-    my @execargs = qw(sh);
     my $build_script_to_send = "";
     my $command =
 	"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
@@ -615,8 +637,27 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       $command .=
 	  "&& perl -";
     }
-    $command .=
-        "&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+    $command .= "&& exec arv-mount --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
+    if ($docker_image)
+    {
+      $command .= "$docker_bin run -i -a stdin -a stdout -a stderr ";
+      # Dynamically configure the container to use the host system as its
+      # DNS server.  Get the host's global addresses from the ip command,
+      # and turn them into docker --dns options using gawk.
+      $command .=
+          q{$(ip -o address show scope global |
+              gawk 'match($4, /^([0-9\.:]+)\//, x){print "--dns", x[1]}') };
+      foreach my $env_key (qw(CRUNCH_SRC CRUNCH_TMP TASK_KEEPMOUNT))
+      {
+        $command .= "-v \Q$ENV{$env_key}:$ENV{$env_key}:rw\E ";
+      }
+      while (my ($env_key, $env_val) = each %ENV)
+      {
+        $command .= "-e \Q$env_key=$env_val\E ";
+      }
+      $command .= "$docker_image ";
+    }
+    $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
     my @execargs = ('bash', '-c', $command);
     srun (\@srunargs, \@execargs, undef, $build_script_to_send);
     exit (111);

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20140507111537
+  version: 0.1.20140507113226
 platform: ruby
 authors:
 - Arvados Authors
@@ -146,7 +146,7 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: '0.8'
-description: This is the Arvados SDK CLI gem, git revision 8fcba3783d9a79bb18a00d339f9b3222f1eccd7f
+description: This is the Arvados SDK CLI gem, git revision 222ce386e36b3d146e718a5d2f64a95fb30996bb
 email: gem-dev@curoverse.com
 executables:
 - arv