arvados-cli 0.1.20150323181012 → 0.1.20150408134718

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d2252134e27620eaa1147541b7454f7aca71f0eb
-  data.tar.gz: 2d196c22729eb463cddc1016d51d7a27e7c5559e
+  metadata.gz: e449c9c026214121443a9ad97d7cc09ae6f2c3e6
+  data.tar.gz: 90798faa1b238688f89c8a7b663ef01ee2e88eca
 SHA512:
-  metadata.gz: b15ca8ad6b008a4eadbca525f5c6f58b170fc158f5dd63e62a7f2f4b2b316cc39f2eb47845da2220d7ab17bcaccca116fd69a74839d7ca7865c445147707c035
-  data.tar.gz: 12046acc2de9a57f0f02375604c9cb185710cf0331d6f9ed76bc0a4722119667abc038ec9ae7a0f1f3dd8f1e567430fa06aa0a5e276fe2d31777aefdadf675fd
+  metadata.gz: 5647d10464a059f48e80497b8c8ccdc43aa4285f832407712cb6edf1d5133425750433764765aad1537018bff850b2ee01287726cf495f175ab6282d089caef6
+  data.tar.gz: 1c166d1f37f97014e3183f63e3a818c8400b37fd6b8ef2f1f4758e9e69eefa6825edb5159910797bc0ed73e84d0c52bd6b217a3e962a703d996231c3fe75c81b

data/bin/crunch-job

@@ -376,7 +376,7 @@ if (!defined $no_clear_tmp) {
 
 # If this job requires a Docker image, install that.
 my $docker_bin = "/usr/bin/docker.io";
-my ($docker_locator, $docker_stream, $docker_hash);
+my ($docker_locator, $docker_stream, $docker_hash, $docker_limitmem);
 if ($docker_locator = $Job->{docker_image_locator}) {
   ($docker_stream, $docker_hash) = find_docker_image($docker_locator);
   if (!$docker_hash)
@@ -408,6 +408,12 @@ fi
           .exit_status_s($?));
   }
 
+  # Determine whether this version of Docker supports memory+swap limits.
+  srun(["srun", "--nodelist=" . $node[0]],
+       ["/bin/sh", "-ec", "$docker_bin run --help | grep -qe --memory-swap="],
+      {fork => 1});
+  $docker_limitmem = ($? == 0);
+
   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.
@@ -653,6 +659,10 @@ update_progress_stats();
 
 
 THISROUND:
+my $tasks_this_level = 0;
+foreach my $id (@jobstep_todo) {
+  $tasks_this_level++ if ($jobstep[$id]->{level} == $level);
+}
 for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
 {
   my $id = $jobstep_todo[$todo_ptr];
@@ -710,6 +720,11 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
 
     $ENV{"GZIP"} = "-n";
 
+    my $max_node_concurrent_tasks = $ENV{CRUNCH_NODE_SLOTS};
+    if ($tasks_this_level < $max_node_concurrent_tasks) {
+      $max_node_concurrent_tasks = $tasks_this_level;
+    }
+
     my @srunargs = (
       "srun",
       "--nodelist=".$childnode->{name},
@@ -720,14 +735,25 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
 	"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 $ENV{CRUNCH_TMP} "
-        ."&& MEM=\$(cat /proc/meminfo | grep MemTotal | sed 's/\\s\\s*/ /g' |cut -d' ' -f2) "
-        ."&& MEMLIMIT=\$(( (\$MEM * 95) / ($ENV{CRUNCH_NODE_SLOTS} * 100) )) ";
+        # 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 $2}' </proc/meminfo) }
+        ."&& MEMLIMIT=\$(( (\$MEM * 95) / ($max_node_concurrent_tasks * 100) )) "
+        ."&& let SWAPLIMIT=\$MEMLIMIT+\$SWAP ";
     $command .= "&& exec arv-mount --by-id --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
     if ($docker_hash)
     {
       my $cidfile = "$ENV{CRUNCH_TMP}/$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}.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 --memory=\${MEMLIMIT}k ";
+      $command .= "$docker_bin run --rm=true --attach=stdout --attach=stderr --attach=stdin -i --user=crunch --cidfile=$cidfile --sig-proxy ";
+      # We only set memory limits if Docker lets us limit both memory and swap.
+      # Memory limits alone have been supported longer, but subprocesses tend
+      # to get SIGKILL if they exceed that without any swap limit set.
+      # See #5642 for additional background.
+      if ($docker_limitmem) {
+        $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,

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20150323181012
+  version: 0.1.20150408134718
 platform: ruby
 authors:
 - Arvados Authors
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-23 00:00:00.000000000 Z
+date: 2015-04-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: arvados
@@ -178,7 +178,7 @@ dependencies:
     - - "<"
       - !ruby/object:Gem::Version
         version: 1.0.0
-description: Arvados command line tools, git commit c1b4ee5b62630d6df3037955b68aa77ec3ee1f5a
+description: Arvados command line tools, git commit e009f03d9f3a620f375cf187291bd12c2bf1d74c
 email: gem-dev@curoverse.com
 executables:
 - arv