X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ad7679cfe57733940f8461097ee01bfd97997ce6..a79deca1f43e0c8854820ec77a1663d8bbf9a034:/sdk/cli/bin/crunch-job

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index b38efdc53e..b2c14d5b71 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 # -*- mode: perl; perl-indent-level: 2; indent-tabs-mode: nil; -*-
 
 =head1 NAME
@@ -126,7 +126,7 @@ my $jobspec;
 my $job_api_token;
 my $no_clear_tmp;
 my $resume_stash;
-my $docker_bin = "/usr/bin/docker.io";
+my $docker_bin = "docker.io";
 GetOptions('force-unlock' => \$force_unlock,
            'git-dir=s' => \$git_dir,
            'job=s' => \$jobspec,
@@ -169,8 +169,7 @@ if ($jobspec =~ /^[-a-z\d]+$/)
 }
 else
 {
-  $Job = JSON::decode_json($jobspec);
-  $local_job = 1;
+  $local_job = JSON::decode_json($jobspec);
 }
 
 
@@ -178,7 +177,7 @@ else
 # at least able to run basic commands: they aren't down or severely
 # misconfigured.
 my $cmd = ['true'];
-if ($Job->{docker_image_locator}) {
+if (($Job || $local_job)->{docker_image_locator}) {
   $cmd = [$docker_bin, 'ps', '-q'];
 }
 Log(undef, "Sanity check is `@$cmd`");
@@ -208,15 +207,15 @@ else
 {
   if (!$resume_stash)
   {
-    map { croak ("No $_ specified") unless $Job->{$_} }
+    map { croak ("No $_ specified") unless $local_job->{$_} }
     qw(script script_version script_parameters);
   }
 
-  $Job->{'is_locked_by_uuid'} = $User->{'uuid'};
-  $Job->{'started_at'} = gmtime;
-  $Job->{'state'} = 'Running';
+  $local_job->{'is_locked_by_uuid'} = $User->{'uuid'};
+  $local_job->{'started_at'} = gmtime;
+  $local_job->{'state'} = 'Running';
 
-  $Job = api_call("jobs/create", job => $Job);
+  $Job = api_call("jobs/create", job => $local_job);
 }
 $job_id = $Job->{'uuid'};
 
@@ -391,12 +390,12 @@ if (!defined $no_clear_tmp) {
   my $cleanpid = fork();
   if ($cleanpid == 0)
   {
-    # Find FUSE mounts that look like Keep mounts (the mount path has the
-    # word "keep") and unmount them.  Then clean up work directories.
-    # TODO: When #5036 is done and widely deployed, we can get rid of the
-    # regular expression and just unmount everything with type fuse.keep.
+    # Find FUSE mounts under $CRUNCH_TMP and unmount them.
+    # Then clean up work directories.
+    # TODO: When #5036 is done and widely deployed, we can limit mount's
+    # -t option to simply fuse.keep.
     srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
-          ['bash', '-ec', 'mount -t fuse,fuse.keep | awk \'($3 ~ /\ykeep\y/){print $3}\' | xargs -r -n 1 fusermount -u -z; sleep 1; rm -rf $JOB_WORK $CRUNCH_INSTALL $CRUNCH_TMP/task $CRUNCH_TMP/src* $CRUNCH_TMP/*.cid']);
+          ['bash', '-ec', '-o', 'pipefail', 'mount -t fuse,fuse.keep | awk "(index(\$3, \"$CRUNCH_TMP\") == 1){print \$3}" | xargs -r -n 1 fusermount -u -z; sleep 1; rm -rf $JOB_WORK $CRUNCH_INSTALL $CRUNCH_TMP/task $CRUNCH_TMP/src* $CRUNCH_TMP/*.cid']);
     exit (1);
   }
   while (1)
@@ -405,11 +404,14 @@ if (!defined $no_clear_tmp) {
     freeze_if_want_freeze ($cleanpid);
     select (undef, undef, undef, 0.1);
   }
-  Log (undef, "Cleanup command exited ".exit_status_s($?));
+  if ($?) {
+    Log(undef, "Clean work dirs: exit ".exit_status_s($?));
+    exit(EX_RETRY_UNLOCKED);
+  }
 }
 
 # If this job requires a Docker image, install that.
-my ($docker_locator, $docker_stream, $docker_hash, $docker_limitmem);
+my ($docker_locator, $docker_stream, $docker_hash, $docker_limitmem, $dockeruserarg);
 if ($docker_locator = $Job->{docker_image_locator}) {
   ($docker_stream, $docker_hash) = find_docker_image($docker_locator);
   if (!$docker_hash)
@@ -447,6 +449,42 @@ fi
       {fork => 1});
   $docker_limitmem = ($? == 0);
 
+  # Find a non-root Docker user to use.
+  # Tries the default user for the container, then 'crunch', then 'nobody',
+  # testing for whether the actual user id is non-zero.  This defends against
+  # mistakes but not malice, but we intend to harden the security in the future
+  # so we don't want anyone getting used to their jobs running as root in their
+  # Docker containers.
+  my @tryusers = ("", "crunch", "nobody");
+  foreach my $try_user (@tryusers) {
+    my $try_user_arg;
+    if ($try_user eq "") {
+      Log(undef, "Checking if container default user is not UID 0");
+      $try_user_arg = "";
+    } else {
+      Log(undef, "Checking if user '$try_user' is not UID 0");
+      $try_user_arg = "--user=$try_user";
+    }
+    srun(["srun", "--nodelist=" . $node[0]],
+         ["/bin/sh", "-ec",
+          "a=`$docker_bin run $try_user_arg $docker_hash id --user` && " .
+          " test \$a -ne 0"],
+         {fork => 1});
+    if ($? == 0) {
+      $dockeruserarg = $try_user_arg;
+      if ($try_user eq "") {
+        Log(undef, "Container will run with default user");
+      } else {
+        Log(undef, "Container will run with $dockeruserarg");
+      }
+      last;
+    }
+  }
+
+  if (!defined $dockeruserarg) {
+    croak("Could not find a user in container that is not UID 0 (tried default user, @tryusers) or there was a problem running 'id' in the container.");
+  }
+
   if ($Job->{arvados_sdk_version}) {
     # The job also specifies an Arvados SDK version.  Add the SDKs to the
     # tar file for the build script to install.
@@ -596,7 +634,7 @@ else {
   unless ($? == 0 && $sha1 =~ /^([0-9a-f]{40})$/) {
     croak("`$gitcmd rev-list` exited "
           .exit_status_s($?)
-          .", '$treeish' not found. Giving up.");
+          .", '$treeish' not found, giving up");
   }
   $commit = $1;
   Log(undef, "Version $treeish is commit $commit");
@@ -782,6 +820,9 @@ update_progress_stats();
 THISROUND:
 for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
 {
+  # Don't create new tasks if we already know the job's final result.
+  last if defined($main::success);
+
   my $id = $jobstep_todo[$todo_ptr];
   my $Jobstep = $jobstep[$id];
   if ($Jobstep->{level} != $level)
@@ -842,6 +883,14 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       qw(-n1 -c1 -N1 -D), $ENV{'TMPDIR'},
       "--job-name=$job_id.$id.$$",
 	);
+
+    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} "
@@ -852,12 +901,13 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
         .q{&& SWAP=$(awk '($1 == "SwapTotal:"){print $2}' </proc/meminfo) }
         ."&& MEMLIMIT=\$(( (\$MEM * 95) / ($ENV{CRUNCH_NODE_SLOTS} * 100) )) "
         ."&& let SWAPLIMIT=\$MEMLIMIT+\$SWAP ";
-    $command .= "&& exec arv-mount --by-id --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
+    $command .= "&& exec arv-mount --by-pdh --crunchstat-interval=10 --allow-other $arv_file_cache $ENV{TASK_KEEPMOUNT} --exec ";
     if ($docker_hash)
     {
-      my $cidfile = "$ENV{CRUNCH_TMP}/$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}.cid";
+      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 --rm=true --attach=stdout --attach=stderr --attach=stdin -i --user=crunch --cidfile=$cidfile --sig-proxy ";
+      $command .= "$docker_bin run --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.
@@ -866,13 +916,6 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
         $command .= "--memory=\${MEMLIMIT}k --memory-swap=\${SWAPLIMIT}k ";
       }
 
-      # 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]}') };
-
       # The source tree and $destdir directory (which we have
       # installed on the worker host) are available in the container,
       # under the same path.
@@ -922,12 +965,25 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       }
       $command .= "--env=\QHOME=$ENV{HOME}\E ";
       $command .= "\Q$docker_hash\E ";
-      $command .= "stdbuf --output=0 --error=0 ";
-      $command .= "perl - $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+
+      if ($Job->{arvados_sdk_version}) {
+        $command .= $stdbuf;
+        $command .= "perl - \Q$ENV{CRUNCH_SRC}/crunch_scripts/$Job->{script}\E";
+      } else {
+        $command .= "/bin/sh -c \'python -c " .
+            '"from pkg_resources import get_distribution as get; print \"Using Arvados SDK version\", get(\"arvados-python-client\").version"' .
+            ">&2 2>/dev/null; " .
+            "mkdir -p \"$ENV{JOB_WORK}\" \"$ENV{TASK_WORK}\" && " .
+            "if which stdbuf >/dev/null ; then " .
+            "  exec $stdbuf \Q$ENV{CRUNCH_SRC}/crunch_scripts/$Job->{script}\E ;" .
+            " else " .
+            "  exec \Q$ENV{CRUNCH_SRC}/crunch_scripts/$Job->{script}\E ;" .
+            " fi\'";
+      }
     } else {
       # Non-docker run
       $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 ";
-      $command .= "stdbuf --output=0 --error=0 ";
+      $command .= $stdbuf;
       $command .= "perl - $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
     }
 
@@ -973,7 +1029,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
 	 ||
 	 ($round_num_freeslots > @freeslot && $todo_ptr+1 > $#jobstep_todo))
   {
-    last THISROUND if $main::please_freeze || defined($main::success);
+    last THISROUND if $main::please_freeze;
     if ($main::please_info)
     {
       $main::please_info = 0;
@@ -985,14 +1041,14 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     my $gotsome
 	= readfrompipes ()
 	+ reapchildren ();
-    if (!$gotsome)
+    if (!$gotsome || ($latest_refresh + 2 < scalar time))
     {
       check_refresh_wanted();
       check_squeue();
       update_progress_stats();
       select (undef, undef, undef, 0.1);
     }
-    elsif (time - $progress_stats_updated >= 30)
+    elsif (time - $progress_stats_updated >= 30 || $progress_is_dirty)
     {
       update_progress_stats();
     }
@@ -1099,8 +1155,8 @@ sub update_progress_stats
   $progress_stats_updated = time;
   return if !$progress_is_dirty;
   my ($todo, $done, $running) = (scalar @jobstep_todo,
-				 scalar @jobstep_done,
-				 scalar @slot - scalar @freeslot - scalar @holdslot);
+                                 scalar @jobstep_done,
+                                 scalar keys(%proc));
   $Job->{'tasks_summary'} ||= {};
   $Job->{'tasks_summary'}->{'todo'} = $todo;
   $Job->{'tasks_summary'}->{'done'} = $done;
@@ -1134,6 +1190,9 @@ sub reapchildren
 
   if (!defined $task_success) {
     # task did not indicate one way or the other --> fail
+    Log($jobstepid, sprintf(
+          "ERROR: Task process exited %d, 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;
@@ -1650,20 +1709,24 @@ sub log_writer_finish()
 
   close($log_pipe_in);
 
+  my $logger_failed = 0;
   my $read_result = log_writer_read_output(120);
   if ($read_result == -1) {
+    $logger_failed = -1;
     Log (undef, "timed out reading from 'arv-put'");
   } elsif ($read_result != 0) {
+    $logger_failed = -2;
     Log(undef, "failed to read arv-put log manifest to EOF");
   }
 
   waitpid($log_pipe_pid, 0);
   if ($?) {
+    $logger_failed ||= $?;
     Log(undef, "log_writer_finish: arv-put exited " . exit_status_s($?))
   }
 
   close($log_pipe_out);
-  my $arv_put_output = $log_pipe_out_buf;
+  my $arv_put_output = $logger_failed ? undef : $log_pipe_out_buf;
   $log_pipe_pid = $log_pipe_in = $log_pipe_out = $log_pipe_out_buf =
       $log_pipe_out_select = undef;
 
@@ -1729,13 +1792,13 @@ sub save_meta
   my $justcheckpoint = shift; # false if this will be the last meta saved
   return if $justcheckpoint;  # checkpointing is not relevant post-Warehouse.pm
   return unless log_writer_is_active();
+  my $log_manifest = log_writer_finish();
+  return unless defined($log_manifest);
 
-  my $log_manifest = "";
   if ($Job->{log}) {
     my $prev_log_coll = api_call("collections/get", uuid => $Job->{log});
-    $log_manifest .= $prev_log_coll->{manifest_text};
+    $log_manifest = $prev_log_coll->{manifest_text} . $log_manifest;
   }
-  $log_manifest .= log_writer_finish();
 
   my $log_coll = api_call(
     "collections/create", ensure_unique_name => 1, collection => {
@@ -2042,7 +2105,7 @@ sub set_nonblocking {
 }
 
 __DATA__
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #
 # This is crunch-job's internal dispatch script.  crunch-job running on the API
 # server invokes this script on individual compute nodes, or localhost if we're
@@ -2114,10 +2177,11 @@ 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");
@@ -2126,14 +2190,18 @@ 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)) {
@@ -2210,11 +2278,12 @@ if (-d $sdk_root) {
 my $python_dir = "$install_dir/python";
 if ((-d $python_dir) and can_run("python2.7")) {
   open(my $egg_info_pipe, "-|",
-       "python2.7 \Q$python_dir/setup.py\E --quiet egg_info 2>&1 >/dev/null");
+       "python2.7 \Q$python_dir/setup.py\E egg_info 2>&1 >/dev/null");
   my @egg_info_errors = <$egg_info_pipe>;
   close($egg_info_pipe);
+
   if ($?) {
-    if (@egg_info_errors and ($egg_info_errors[-1] =~ /\bgit\b/)) {
+    if (@egg_info_errors and (($egg_info_errors[-1] =~ /\bgit\b/) or ($egg_info_errors[-1] =~ /\[Errno 2\]/))) {
       # egg_info apparently failed because it couldn't ask git for a build tag.
       # Specify no build tag.
       open(my $pysdk_cfg, ">>", "$python_dir/setup.cfg");
@@ -2223,7 +2292,7 @@ if ((-d $python_dir) and can_run("python2.7")) {
     } else {
       my $egg_info_exit = $? >> 8;
       foreach my $errline (@egg_info_errors) {
-        print STDERR_ORIG $errline;
+        warn $errline;
       }
       warn "python setup.py egg_info failed: exit $egg_info_exit";
       exit ($egg_info_exit || 1);