arvados-cli 0.1.20171103184629 → 0.1.20171211220040

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: accd434dcf518f07bedacd29fbbbb7fc9844501b
-  data.tar.gz: 3820162ed9debcb488b2a26061a7d03d80183f8e
+  metadata.gz: 04d16a74e2d8bb5a6900bbefdce712737cc86254
+  data.tar.gz: cc875fe1b9ebcf42ba402c088f41856b641234ce
 SHA512:
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+  data.tar.gz: 39e36c49d04246ac2381c2c2353cbac34b7d13874367c02f04e7cb7e65ae7f37ecd1246ea13a731be14d694ec376db0268121af14679873226e5488ac59b04fa

data/bin/crunch-job

@@ -1,10 +1,9 @@
 #!/usr/bin/env perl
+# -*- mode: perl; perl-indent-level: 2; indent-tabs-mode: nil; -*-
 # Copyright (C) The Arvados Authors. All rights reserved.
 #
 # SPDX-License-Identifier: AGPL-3.0
 
-# -*- mode: perl; perl-indent-level: 2; indent-tabs-mode: nil; -*-
-
 =head1 NAME
 
 crunch-job: Execute job steps, save snapshots as requested, collate output.
@@ -1188,6 +1187,8 @@ sub reapchildren
                     . $slot[$proc{$pid}->{slot}]->{cpu});
     my $jobstepidx = $proc{$pid}->{jobstepidx};
 
+    readfrompipes_after_exit ($jobstepidx);
+
     $children_reaped++;
     my $elapsed = time - $proc{$pid}->{time};
     my $Jobstep = $jobstep[$jobstepidx];
@@ -1259,7 +1260,6 @@ sub reapchildren
     $Jobstep->{finishtime} = time;
     $Jobstep->{'arvados_task'}->{finished_at} = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($Jobstep->{finishtime});
     retry_op(sub { $Jobstep->{'arvados_task'}->save; }, "job_tasks.update API");
-    process_stderr_final ($jobstepidx);
     Log ($jobstepidx, sprintf("task output (%d bytes): %s",
                               length($Jobstep->{'arvados_task'}->{output}),
                               $Jobstep->{'arvados_task'}->{output}));
@@ -1562,9 +1562,27 @@ sub preprocess_stderr
 }
 
 
-sub process_stderr_final
+# Read whatever is still available on its stderr+stdout pipes after
+# the given child process has exited.
+sub readfrompipes_after_exit
 {
   my $jobstepidx = shift;
+
+  # The fact that the child has exited allows some convenient
+  # simplifications: (1) all data must have already been written, so
+  # there's no need to wait for more once sysread returns 0; (2) the
+  # total amount of data available is bounded by the pipe buffer size,
+  # so it's safe to read everything into one string.
+  my $buf;
+  while (0 < sysread ($reader{$jobstepidx}, $buf, 65536)) {
+    $jobstep[$jobstepidx]->{stderr_at} = time;
+    $jobstep[$jobstepidx]->{stderr} .= $buf;
+  }
+  if ($jobstep[$jobstepidx]->{stdout_r}) {
+    while (0 < sysread ($jobstep[$jobstepidx]->{stdout_r}, $buf, 65536)) {
+      $jobstep[$jobstepidx]->{stdout_captured} .= $buf;
+    }
+  }
   preprocess_stderr ($jobstepidx);
 
   map {
@@ -2036,8 +2054,7 @@ sub srun_sync
   }
   my $exited = $?;
 
-  1 while readfrompipes();
-  process_stderr_final ($jobstepidx);
+  readfrompipes_after_exit ($jobstepidx);
 
   Log (undef, "$label: exit ".exit_status_s($exited));
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20171103184629
+  version: 0.1.20171211220040
 platform: ruby
 authors:
 - Arvados Authors
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-11-03 00:00:00.000000000 Z
+date: 2017-12-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: arvados
@@ -164,7 +164,7 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-description: Arvados command line tools, git commit 7c02cd4b2a226c0e341028379c30fdbad5815d99
+description: Arvados command line tools, git commit 42377686908783fb9d043e616f099e153f7834bc
 email: gem-dev@curoverse.com
 executables:
 - arv