arvados-cli 0.1.20140320160303 → 0.1.20140321150015

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 651a092a5aa772985641a04cbdda40b255f200b5
-  data.tar.gz: f01664314331a841ba5678962f80c3a95d1a0e7a
+  metadata.gz: 788d5ca44ca9c901b6e8f7c477a69cbc2068d378
+  data.tar.gz: 92c73dae1010cc1ed2f357f769988f18b566ff37
 SHA512:
-  metadata.gz: 8beca4c2358f858685a0b5e6d5d636956b8b345f47befb8be79e99abcca075c1ca910acea8babd87dab8f9c28fb83d45b91c71d47e9be408d61f33df9690ccbc
-  data.tar.gz: 9efe6117d732d33250851f48a7b08601d355562298cc32024f890c851000d67027ece62bb1fde0df6314259c674ecca71ced0743db60f9a396bccd5516491e38
+  metadata.gz: 4f44a6f0f83a3addb71ce85af76b1301824d1a1a7774ce29f6de4784833cc151f751d3cbf0902cc7b9f908a2f5a86388bbc9169f1f8c70c97480e534377d5750
+  data.tar.gz: 242989a230f9a58ac29daa3edd0d259125483e0b5c6d10671efba142a79c1a6bd517160a3f91e73e23d77146831a66c54446cc9ff6b17744ff4b4da514b4dea1

data/bin/crunch-job

@@ -33,6 +33,12 @@ Path to .git directory where the specified commit is found.
 
 Arvados API authorization token to use during the course of the job.
 
+=item --no-clear-tmp
+
+Do not clear per-job/task temporary directories during initial job
+setup. This can speed up development and debugging when running jobs
+locally.
+
 =back
 
 =head1 RUNNING JOBS LOCALLY
@@ -74,6 +80,7 @@ use Getopt::Long;
 use Warehouse;
 use Warehouse::Stream;
 use IPC::System::Simple qw(capturex);
+use Fcntl ':flock';
 
 $ENV{"TMPDIR"} ||= "/tmp";
 unless (defined $ENV{"CRUNCH_TMP"}) {
@@ -92,11 +99,13 @@ my $force_unlock;
 my $git_dir;
 my $jobspec;
 my $job_api_token;
+my $no_clear_tmp;
 my $resume_stash;
 GetOptions('force-unlock' => \$force_unlock,
            'git-dir=s' => \$git_dir,
            'job=s' => \$jobspec,
            'job-api-token=s' => \$job_api_token,
+           'no-clear-tmp' => \$no_clear_tmp,
            'resume-stash=s' => \$resume_stash,
     );
 
@@ -323,6 +332,12 @@ else
 }
 
 
+if (!$have_slurm)
+{
+  must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
+}
+
+
 my $build_script;
 
 
@@ -331,6 +346,11 @@ $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version};
 my $skip_install = ($local_job && $Job->{script_version} =~ m{^/});
 if ($skip_install)
 {
+  if (!defined $no_clear_tmp) {
+    my $clear_tmp_cmd = 'rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*';
+    system($clear_tmp_cmd) == 0
+	or croak ("`$clear_tmp_cmd` failed: ".($?>>8));
+  }
   $ENV{"CRUNCH_SRC"} = $Job->{script_version};
   for my $src_path ("$ENV{CRUNCH_SRC}/arvados/sdk/python") {
     if (-d $src_path) {
@@ -351,22 +371,24 @@ else
   Log (undef, "Install revision ".$Job->{script_version});
   my $nodelist = join(",", @node);
 
-  # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
+  if (!defined $no_clear_tmp) {
+    # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
 
-  my $cleanpid = fork();
-  if ($cleanpid == 0)
-  {
-    srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
-	  ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']);
-    exit (1);
-  }
-  while (1)
-  {
-    last if $cleanpid == waitpid (-1, WNOHANG);
-    freeze_if_want_freeze ($cleanpid);
-    select (undef, undef, undef, 0.1);
+    my $cleanpid = fork();
+    if ($cleanpid == 0)
+    {
+      srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
+	    ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']);
+      exit (1);
+    }
+    while (1)
+    {
+      last if $cleanpid == waitpid (-1, WNOHANG);
+      freeze_if_want_freeze ($cleanpid);
+      select (undef, undef, undef, 0.1);
+    }
+    Log (undef, "Clean-work-dir exited $?");
   }
-  Log (undef, "Clean-work-dir exited $?");
 
   # Install requested code version
 
@@ -463,6 +485,12 @@ else
   Log (undef, "Install exited $?");
 }
 
+if (!$have_slurm)
+{
+  # Grab our lock again (we might have deleted and re-created CRUNCH_TMP above)
+  must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
+}
+
 
 
 foreach (qw (script script_version script_parameters runtime_constraints))
@@ -1346,6 +1374,15 @@ sub ban_node_by_slot {
   Log (undef, "backing off node " . $slot[$slotid]->{node}->{name} . " for 60 seconds");
 }
 
+sub must_lock_now
+{
+  my ($lockfile, $error_message) = @_;
+  open L, ">", $lockfile or croak("$lockfile: $!");
+  if (!flock L, LOCK_EX|LOCK_NB) {
+    croak("Can't lock $lockfile: $error_message\n");
+  }
+}
+
 __DATA__
 #!/usr/bin/perl
 

metadata

@@ -1,138 +1,138 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20140320160303
+  version: 0.1.20140321150015
 platform: ruby
 authors:
 - Arvados Authors
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-20 00:00:00.000000000 Z
+date: 2014-03-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: google-api-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 0.6.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 0.6.3
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.2'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 3.2.13
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.2'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 3.2.13
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.7'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.7.7
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.7'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.7.7
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
 - !ruby/object:Gem::Dependency
   name: andand
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.3
 - !ruby/object:Gem::Dependency
   name: oj
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.3
 - !ruby/object:Gem::Dependency
   name: curb
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-description: This is the Arvados SDK CLI gem, git revision 061dc0bcb7ced7ad196c6cc71dd25aab59948e46
+description: This is the Arvados SDK CLI gem, git revision 2e2ce40b47b9e248805dcccc59baa77591c13d79
 email: gem-dev@curoverse.com
 executables:
 - arv
@@ -157,17 +157,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Arvados SDK CLI