From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Wed, 2 Jul 2014 14:54:48 +0000 (-0400)
Subject: Use separate $HOME for commands run outside the docker
X-Git-Tag: 1.1.0~2481^2~6
X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/945bebae56ec2fb5faef965cbf55fc8309e8df11?ds=sidebyside

Use separate $HOME for commands run outside the docker
container (e.g. arv-mount) and commands inside the docker container because of
the user id mapping problem.  Converted docker command line to use long form
for readability.
---

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index b0d779bf3c..dd1ba8fbd9 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -622,7 +622,7 @@ 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"} = $ENV{"JOB_WORK"}."/$id.$$";
-    $ENV{"HOME"} = $ENV{"TASK_WORK"};
+    $ENV{"HOME"} = $ENV{"TASK_WORK"}.".home";
     $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep";
     $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
     $ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
@@ -639,7 +639,7 @@ 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} $ENV{TASK_KEEPMOUNT} "
+        ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} ${HOME}"
         ."&& chmod og+wrx $ENV{TASK_WORK}"
 	."&& cd $ENV{CRUNCH_TMP} ";
     if ($build_script)
@@ -652,41 +652,41 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     if ($docker_hash)
     {
       $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$ENV{TASK_WORK}/docker.cid -poll=10000 ";
-      $command .= "$docker_bin run -i -a stdin -a stdout -a stderr --cidfile=$ENV{TASK_WORK}/docker.cid ";
+      $command .= "$docker_bin run --attach=stdout --attach=stderr --user=crunch --cidfile=$ENV{TASK_WORK}/docker.cid ";
       # 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]}') };
-      $command .= "-v \Q$ENV{TASK_WORK}:/tmp/crunch-job:rw\E ";
-      $command .= "-v \Q$ENV{CRUNCH_SRC}:/tmp/crunch-src:ro\E ";
-      $command .= "-v \Q$ENV{TASK_KEEPMOUNT}:/mnt:ro\E ";
-      $command .= "-e \QHOME=/tmp/crunch-job\E ";
+      $command .= "--volume=\Q$ENV{TASK_WORK}:/tmp/crunch-job:rw\E ";
+      $command .= "--volume=\Q$ENV{CRUNCH_SRC}:/tmp/crunch-src:ro\E ";
+      $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E ";
+      $command .= "--env=\QHOME=/home/crunch\E ";
       while (my ($env_key, $env_val) = each %ENV)
       {
         if ($env_key =~ /^(ARVADOS|JOB|TASK)_/) {
           if ($env_key eq "TASK_WORK") {
-            $command .= "-e \QTASK_WORK=/tmp/crunch-job\E ";
+            $command .= "--env=\QTASK_WORK=/tmp/crunch-job\E ";
           }
           elsif ($env_key eq "TASK_KEEPMOUNT") {
-            $command .= "-e \QTASK_KEEPMOUNT=/mnt\E ";
+            $command .= "--env=\QTASK_KEEPMOUNT=/keep\E ";
           }
           elsif ($env_key eq "CRUNCH_SRC") {
-            $command .= "-e \QCRUNCH_SRC=/tmp/crunch-src\E ";
+            $command .= "--env=\QCRUNCH_SRC=/tmp/crunch-src\E ";
           }
           else {
-            $command .= "-e \Q$env_key=$env_val\E ";
+            $command .= "--env=\Q$env_key=$env_val\E ";
           }
         }
       }
       $command .= "\Q$docker_hash\E ";
-      $command .= "stdbuf -o0 -e0 ";
+      $command .= "stdbuf --output=0 --error=0 ";
       $command .= "/tmp/crunch-src/crunch_scripts/" . $Job->{"script"};
     } else {
       # Non-docker run
       $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 ";
-      $command .= "stdbuf -o0 -e0 ";
+      $command .= "stdbuf --output=0 --error=0 ";
       $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
     }