arvados-cli 0.1.20150522214217 → 0.1.20150526143156

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 99b8c07b3475f9b14be3792ee0563dbd9cbd861b
-  data.tar.gz: 1a9c6e8c69eba7197c7f05318c66202f4fd532c1
+  metadata.gz: df49631b2b1c7ae33eb0d5d9e988e50a2fc0a311
+  data.tar.gz: fe0a40bf178a62a8518fec9c8ca699188d2a8d32
 SHA512:
-  metadata.gz: 189053906f0dd364c0423fa8125272c1d769b6bda484686dc75cb0fe0726e11065b34faa1c8d2dff293260b9c346089b37082b99795f1e77c54c80eb79371510
-  data.tar.gz: db61854c2308ac39798ed2a68bc3178b3b9b9ad3080a9f664e28de68a2699b983c1857802a14f60dffe3a21de1ffa4ca07f4fbade7b2e5522c62e5c183d1a5d8
+  metadata.gz: 59df31ffb182cdcc78b960b8ba439bed2f8b2d916d740ace0b92eb76a3de96169c193de30e3cedfb14e0df96cdda9a4eea32562735ff509f4e9a6b273028d1bb
+  data.tar.gz: b2afa69c6273326c575cc6e3c4a8c166c544288cb4d90eb6709ae813b69c953e4fad3aa6444797cba3f7318e3c6304f63afa8b198c635199c94a8422b28d5d65

data/bin/crunch-job

@@ -598,19 +598,42 @@ else {
                   "mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -");
 
   $ENV{"CRUNCH_GIT_ARCHIVE_HASH"} = md5_hex($git_archive);
+  my ($install_stderr_r, $install_stderr_w);
+  pipe $install_stderr_r, $install_stderr_w or croak("pipe() failed: $!");
+  set_nonblocking($install_stderr_r);
   my $installpid = fork();
   if ($installpid == 0)
   {
+    close($install_stderr_r);
+    fcntl($install_stderr_w, F_SETFL, 0) or croak($!); # no close-on-exec
+    open(STDOUT, ">&", $install_stderr_w);
+    open(STDERR, ">&", $install_stderr_w);
     srun (\@srunargs, \@execargs, {}, $build_script . $git_archive);
     exit (1);
   }
-  while (1)
-  {
-    last if $installpid == waitpid (-1, WNOHANG);
+  close($install_stderr_w);
+  my $stderr_buf = '';
+  while ($installpid != waitpid(-1, WNOHANG)) {
     freeze_if_want_freeze ($installpid);
-    select (undef, undef, undef, 0.1);
+    # Wait up to 0.1 seconds for something to appear on stderr, then
+    # do a non-blocking read.
+    my $bits = fhbits($install_stderr_r);
+    select ($bits, undef, $bits, 0.1);
+    if (0 < sysread ($install_stderr_r, $stderr_buf, 8192, length($stderr_buf)))
+    {
+      while ($stderr_buf =~ /^(.*?)\n/) {
+        my $line = $1;
+        substr $stderr_buf, 0, 1+length($line), "";
+        Log(undef, "stderr $line");
+      }
+    }
   }
   my $install_exited = $?;
+  close($install_stderr_r);
+  if (length($stderr_buf) > 0) {
+    Log(undef, "stderr $stderr_buf")
+  }
+
   Log (undef, "Install script exited ".exit_status_s($install_exited));
   foreach my $tar_filename (map { tar_filename_n($_); } (1..$git_tar_count)) {
     unlink($tar_filename);
@@ -700,9 +723,8 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     next;
   }
 
-  pipe $reader{$id}, "writer" or croak ($!);
-  my $flags = fcntl ($reader{$id}, F_GETFL, 0) or croak ($!);
-  fcntl ($reader{$id}, F_SETFL, $flags | O_NONBLOCK) or croak ($!);
+  pipe $reader{$id}, "writer" or croak("pipe() failed: $!");
+  set_nonblocking($reader{$id});
 
   my $childslot = $freeslot[0];
   my $childnode = $slot[$childslot]->{node};
@@ -1862,6 +1884,12 @@ sub combined_git_archive {
   return $tar_contents;
 }
 
+sub set_nonblocking {
+  my $fh = shift;
+  my $flags = fcntl ($fh, F_GETFL, 0) or croak ($!);
+  fcntl ($fh, F_SETFL, $flags | O_NONBLOCK) or croak ($!);
+}
+
 __DATA__
 #!/usr/bin/perl
 #
@@ -1895,6 +1923,9 @@ my $install_dir = $ENV{"CRUNCH_INSTALL"} || (getcwd() . "/opt");
 my $job_work = $ENV{"JOB_WORK"};
 my $task_work = $ENV{"TASK_WORK"};
 
+open(STDOUT_ORIG, ">&", STDOUT);
+open(STDERR_ORIG, ">&", STDERR);
+
 for my $dir ($destdir, $job_work, $task_work) {
   if ($dir) {
     make_path $dir;
@@ -1906,11 +1937,6 @@ if ($task_work) {
   remove_tree($task_work, {keep_root => 1});
 }
 
-open(STDOUT_ORIG, ">&", STDOUT);
-open(STDERR_ORIG, ">&", STDERR);
-open(STDOUT, ">>", "$destdir.log");
-open(STDERR, ">&", STDOUT);
-
 ### Crunch script run mode
 if (@ARGV) {
   # We want to do routine logging during task 0 only.  This gives the user
@@ -1971,10 +1997,6 @@ if (@ARGV) {
     }
   }
 
-  close(STDOUT);
-  close(STDERR);
-  open(STDOUT, ">&", STDOUT_ORIG);
-  open(STDERR, ">&", STDERR_ORIG);
   exec(@ARGV);
   die "Cannot exec `@ARGV`: $!";
 }
@@ -2034,6 +2056,11 @@ if ((-d $python_dir) and can_run("python2.7") and
   close($pysdk_cfg);
 }
 
+# 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);
+
 if (-e "$destdir/crunch_scripts/install") {
     shell_or_die (undef, "$destdir/crunch_scripts/install", $install_dir);
 } elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20150522214217
+  version: 0.1.20150526143156
 platform: ruby
 authors:
 - Arvados Authors
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-22 00:00:00.000000000 Z
+date: 2015-05-26 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 0f125dd51c7dc13047672dee5362866f31885e0a
+description: Arvados command line tools, git commit 9b67268ff45d2a552d21fa39f5086180f537ab4a
 email: gem-dev@curoverse.com
 executables:
 - arv