12550: Fix race: read buffered data from stderr after child exits.

[arvados.git] / sdk / cli / bin / crunch-job

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index fd598c9dd37bbfdd88aa12e2e84d5d73c6929bf9..9343fcfbfd2f97bc182daa788f5c45f74b8ae078 100755 (executable)
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/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.
@@ -837,8 +836,8 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       close($_);
     }
     fcntl ("writer", F_SETFL, 0) or croak ($!); # no close-on-exec
-    open(STDOUT,">&writer");
-    open(STDERR,">&writer");
+    open(STDOUT,">&writer") or croak ($!);
+    open(STDERR,">&writer") or croak ($!);
 
     undef $dbh;
     undef $sth;
@@ -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 {
@@ -1996,8 +2014,8 @@ sub srun_sync
     close($stdout_r);
     fcntl($stderr_w, F_SETFL, 0) or croak($!); # no close-on-exec
     fcntl($stdout_w, F_SETFL, 0) or croak($!);
-    open(STDERR, ">&", $stderr_w);
-    open(STDOUT, ">&", $stdout_w);
+    open(STDERR, ">&", $stderr_w) or croak ($!);
+    open(STDOUT, ">&", $stdout_w) or croak ($!);
     srun ($srunargs, $execargs, $opts, $stdin);
     exit (1);
   }
@@ -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));
 
@@ -2493,8 +2510,8 @@ if ((-d $python_dir) and can_run("python2.7")) {
 
 # Hide messages from the install script (unless it fails: shell_or_die
 # will show $destdir.log in that case).
-open(STDOUT, ">>", "$destdir.log");
-open(STDERR, ">&", STDOUT);
+open(STDOUT, ">>", "$destdir.log") or die ($!);
+open(STDERR, ">&", STDOUT) or die ($!);
 
 if (-e "$destdir/crunch_scripts/install") {
     shell_or_die (undef, "$destdir/crunch_scripts/install", $install_dir);
@@ -2515,7 +2532,7 @@ close L;
 
 sub can_run {
   my $command_name = shift;
-  open(my $which, "-|", "which", $command_name);
+  open(my $which, "-|", "which", $command_name) or die ($!);
   while (<$which>) { }
   close($which);
   return ($? == 0);