X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a1dc811844d2dc76bea5ebfdc2f571a12cb41b49..fcbb743e3de63e93280f2fbeedea49f98430d26f:/sdk/cli/bin/crunch-job

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 70ba04fcab..5eb2f902f9 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -127,6 +127,7 @@ my $job_api_token;
 my $no_clear_tmp;
 my $resume_stash;
 my $docker_bin = "docker.io";
+my $docker_run_args = "";
 GetOptions('force-unlock' => \$force_unlock,
            'git-dir=s' => \$git_dir,
            'job=s' => \$jobspec,
@@ -134,6 +135,7 @@ GetOptions('force-unlock' => \$force_unlock,
            'no-clear-tmp' => \$no_clear_tmp,
            'resume-stash=s' => \$resume_stash,
            'docker-bin=s' => \$docker_bin,
+           'docker-run-args=s' => \$docker_run_args,
     );
 
 if (defined $job_api_token) {
@@ -467,7 +469,7 @@ fi
     }
     srun(["srun", "--nodelist=" . $node[0]],
          ["/bin/sh", "-ec",
-          "a=`$docker_bin run $try_user_arg $docker_hash id --user` && " .
+          "a=`$docker_bin run $docker_run_args $try_user_arg $docker_hash id --user` && " .
           " test \$a -ne 0"],
          {fork => 1});
     if ($? == 0) {
@@ -870,11 +872,12 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     $ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
     $ENV{"TASK_WORK"} = $ENV{"CRUNCH_TMP"}."/task/$childslotname";
     $ENV{"HOME"} = $ENV{"TASK_WORK"};
-    $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep";
     $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
     $ENV{"CRUNCH_NODE_SLOTS"} = $round_max_slots{$ENV{TASK_SLOT_NODE}};
     $ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};
 
+    my $keep_mnt = $ENV{"TASK_WORK"}.".keep";
+
     $ENV{"GZIP"} = "-n";
 
     my @srunargs = (
@@ -886,23 +889,32 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
 
     my $stdbuf = " stdbuf --output=0 --error=0 ";
 
+    my $arv_file_cache = "";
+    if (defined($Job->{'runtime_constraints'}->{'keep_cache_mb_per_task'})) {
+      $arv_file_cache = "--file-cache=" . ($Job->{'runtime_constraints'}->{'keep_cache_mb_per_task'} * 1024 * 1024);
+    }
+
     my $command =
-	"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
-        ."mkdir -p $ENV{CRUNCH_TMP} $ENV{JOB_WORK} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
-	."&& cd $ENV{CRUNCH_TMP} "
+	"if [ -e \Q$ENV{TASK_WORK}\E ]; then rm -rf \Q$ENV{TASK_WORK}\E; fi; "
+        ."mkdir -p \Q$ENV{CRUNCH_TMP}\E \Q$ENV{JOB_WORK}\E \Q$ENV{TASK_WORK}\E \Q$keep_mnt\E "
+	."&& cd \Q$ENV{CRUNCH_TMP}\E "
         # These environment variables get used explicitly later in
         # $command.  No tool is expected to read these values directly.
         .q{&& MEM=$(awk '($1 == "MemTotal:"){print $2}' </proc/meminfo) }
         .q{&& SWAP=$(awk '($1 == "SwapTotal:"){print $2}' </proc/meminfo) }
         ."&& MEMLIMIT=\$(( (\$MEM * 95) / ($ENV{CRUNCH_NODE_SLOTS} * 100) )) "
         ."&& let SWAPLIMIT=\$MEMLIMIT+\$SWAP ";
-    $command .= "&& exec arv-mount --by-pdh --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
+
+    $command .= "&& exec arv-mount --read-write --mount-by-pdh=by_pdh --mount-tmp=tmp --crunchstat-interval=10 --allow-other $arv_file_cache \Q$keep_mnt\E --exec ";
+    $ENV{TASK_KEEPMOUNT} = "$keep_mnt/by_pdh";
+    $ENV{TASK_KEEPMOUNT_TMP} = "$keep_mnt/tmp";
+
     if ($docker_hash)
     {
       my $containername = "$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}";
       my $cidfile = "$ENV{CRUNCH_TMP}/$containername.cid";
       $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$cidfile -poll=10000 ";
-      $command .= "$docker_bin run --name=$containername --attach=stdout --attach=stderr --attach=stdin -i \Q$dockeruserarg\E --cidfile=$cidfile --sig-proxy ";
+      $command .= "$docker_bin run $docker_run_args --name=$containername --attach=stdout --attach=stderr --attach=stdin -i \Q$dockeruserarg\E --cidfile=$cidfile --sig-proxy ";
       # We only set memory limits if Docker lets us limit both memory and swap.
       # Memory limits alone have been supported longer, but subprocesses tend
       # to get SIGKILL if they exceed that without any swap limit set.
@@ -917,14 +929,18 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       $command .= "--volume=\Q$ENV{CRUNCH_SRC}:$ENV{CRUNCH_SRC}:ro\E ";
       $command .= "--volume=\Q$ENV{CRUNCH_INSTALL}:$ENV{CRUNCH_INSTALL}:ro\E ";
 
-      # Currently, we make arv-mount's mount point appear at /keep
-      # inside the container (instead of using the same path as the
-      # host like we do with CRUNCH_SRC and CRUNCH_INSTALL). However,
-      # crunch scripts and utilities must not rely on this. They must
-      # use $TASK_KEEPMOUNT.
+      # Currently, we make the "by_pdh" directory in arv-mount's mount
+      # point appear at /keep inside the container (instead of using
+      # the same path as the host like we do with CRUNCH_SRC and
+      # CRUNCH_INSTALL). However, crunch scripts and utilities must
+      # not rely on this. They must use $TASK_KEEPMOUNT.
       $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E ";
       $ENV{TASK_KEEPMOUNT} = "/keep";
 
+      # Ditto TASK_KEEPMOUNT_TMP, as /keep_tmp.
+      $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT_TMP}:/keep_tmp\E ";
+      $ENV{TASK_KEEPMOUNT_TMP} = "/keep_tmp";
+
       # TASK_WORK is almost exactly like a docker data volume: it
       # starts out empty, is writable, and persists until no
       # containers use it any more. We don't use --volumes-from to
@@ -965,7 +981,10 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
         $command .= $stdbuf;
         $command .= "perl - \Q$ENV{CRUNCH_SRC}/crunch_scripts/$Job->{script}\E";
       } else {
-        $command .= "/bin/sh -c \'mkdir -p \"$ENV{JOB_WORK}\" \"$ENV{TASK_WORK}\" && " .
+        $command .= "/bin/sh -c \'python -c " .
+            '"from pkg_resources import get_distribution as get; print \"Using Arvados SDK version\", get(\"arvados-python-client\").version"' .
+            ">&2 2>/dev/null; " .
+            "mkdir -p \"$ENV{JOB_WORK}\" \"$ENV{TASK_WORK}\" && " .
             "if which stdbuf >/dev/null ; then " .
             "  exec $stdbuf \Q$ENV{CRUNCH_SRC}/crunch_scripts/$Job->{script}\E ;" .
             " else " .
@@ -1182,6 +1201,9 @@ sub reapchildren
 
   if (!defined $task_success) {
     # task did not indicate one way or the other --> fail
+    Log($jobstepid, sprintf(
+          "ERROR: Task process exited %s, but never updated its task record to indicate success and record its output.",
+          exit_status_s($childstatus)));
     $Jobstep->{'arvados_task'}->{success} = 0;
     $Jobstep->{'arvados_task'}->save;
     $task_success = 0;
@@ -1439,7 +1461,7 @@ sub preprocess_stderr
       # whoa.
       $main::please_freeze = 1;
     }
-    elsif ($line =~ /srun: error: Node failure on/) {
+    elsif ($line =~ /srun: error: (Node failure on|Aborting, io error)/) {
       my $job_slot_index = $jobstep[$job]->{slotindex};
       $slot[$job_slot_index]->{node}->{fail_count}++;
       $jobstep[$job]->{tempfail} = 1;
@@ -2166,10 +2188,11 @@ if (@ARGV) {
     $Log->("Built Python SDK virtualenv");
   }
 
-  my $pip_bin = "pip";
+  my @pysdk_version_cmd = ("python", "-c",
+    "from pkg_resources import get_distribution as get; print get('arvados-python-client').version");
   if ($venv_built) {
     $Log->("Running in Python SDK virtualenv");
-    $pip_bin = "$venv_dir/bin/pip";
+    @pysdk_version_cmd = ();
     my $orig_argv = join(" ", map { quotemeta($_); } @ARGV);
     @ARGV = ("/bin/sh", "-ec",
              ". \Q$venv_dir/bin/activate\E; exec $orig_argv");
@@ -2178,14 +2201,18 @@ if (@ARGV) {
            "\$PATH. Can't install Python SDK.");
   }
 
-  my $pkgs = `(\Q$pip_bin\E freeze 2>/dev/null | grep arvados) || dpkg-query --show '*arvados*'`;
-  if ($pkgs) {
-    $Log->("Using Arvados SDK:");
-    foreach my $line (split /\n/, $pkgs) {
-      $Log->($line);
+  if (@pysdk_version_cmd) {
+    open(my $pysdk_version_pipe, "-|", @pysdk_version_cmd);
+    my $pysdk_version = <$pysdk_version_pipe>;
+    close($pysdk_version_pipe);
+    if ($? == 0) {
+      chomp($pysdk_version);
+      $Log->("Using Arvados SDK version $pysdk_version");
+    } else {
+      # A lot could've gone wrong here, but pretty much all of it means that
+      # Python won't be able to load the Arvados SDK.
+      $Log->("Warning: Arvados SDK not found");
     }
-  } else {
-    $Log->("Arvados SDK packages not found");
   }
 
   while (my ($sdk_dir, $sdk_envkey) = each(%SDK_ENVVARS)) {