[ARVADOS] updated: 5c1f03ef1ae45d3ac222542d33b3125ce8678d65
git at public.curoverse.com
git at public.curoverse.com
Fri Oct 3 10:48:03 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 1 +
apps/workbench/Gemfile.lock | 4 +
.../workbench/app/assets/javascripts/log_viewer.js | 2 +-
.../app/controllers/application_controller.rb | 16 +-
.../app/controllers/collections_controller.rb | 28 +-
.../controllers/pipeline_instances_controller.rb | 18 +-
apps/workbench/app/helpers/application_helper.rb | 2 +-
apps/workbench/app/models/arvados_base.rb | 2 +-
apps/workbench/app/models/collection.rb | 2 +-
apps/workbench/app/models/node.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 8 +-
apps/workbench/app/models/user.rb | 2 +-
apps/workbench/app/models/virtual_machine.rb | 2 +-
apps/workbench/app/views/jobs/_show_log.html.erb | 48 ++-
.../app/views/projects/_show_dashboard.html.erb | 49 ++-
apps/workbench/config/application.default.yml | 3 +
.../test/functional/collections_controller_test.rb | 37 +-
.../pipeline_instances_controller_test.rb | 68 ++++
apps/workbench/test/integration/jobs_test.rb | 56 +++
.../test/integration/pipeline_instances_test.rb | 41 +++
apps/workbench/test/integration/projects_test.rb | 11 +
apps/workbench/test/test_helper.rb | 1 +
sdk/cli/bin/crunch-job | 377 ++++++++++++---------
.../app/controllers/arvados/v1/jobs_controller.rb | 9 +-
services/api/app/models/arvados_model.rb | 6 +
services/api/app/models/job.rb | 44 ++-
services/api/config/application.default.yml | 26 +-
services/api/config/routes.rb | 1 +
services/api/script/crunch-dispatch.rb | 204 +++++++----
services/api/test/fixtures/collections.yml | 14 +
services/api/test/fixtures/jobs.yml | 37 ++
services/api/test/fixtures/links.yml | 14 +
services/api/test/fixtures/pipeline_instances.yml | 16 +
services/api/test/fixtures/pipeline_templates.yml | 27 ++
.../functional/arvados/v1/jobs_controller_test.rb | 17 +-
services/api/test/integration/jobs_api_test.rb | 2 +-
services/api/test/unit/job_test.rb | 62 +++-
services/fuse/tests/test_mount.py | 3 +-
38 files changed, 951 insertions(+), 311 deletions(-)
via 5c1f03ef1ae45d3ac222542d33b3125ce8678d65 (commit)
via e5c3609b5ef99cde98e277881fc5b1c53d33df45 (commit)
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via e8376cfb9deac7a50651061e2be99a4bc0c46338 (commit)
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commit 5c1f03ef1ae45d3ac222542d33b3125ce8678d65
Merge: e5c3609 60998a3
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 3 10:47:13 2014 -0400
3775: Merge branch 'master' into 3775-fetch-git-repo
commit e5c3609b5ef99cde98e277881fc5b1c53d33df45
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 3 10:42:23 2014 -0400
3775: Remove redundant log message.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 8a80f9c..eff48a2 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -424,7 +424,6 @@ else {
$repo = "$repo/.git";
}
$repo_location = 'local';
- Log(undef, "Using local repository '$repo'");
} else {
# $repo is none of the above. It must be the name of a hosted
# repository.
commit a8bc91af9fa285665c1e2304bff956bf12a56ec2
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 3 10:41:32 2014 -0400
3775: Clean up reporting of exit codes: say "0 with signal 2", not "512".
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 04ff82f..8a80f9c 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -376,7 +376,7 @@ if (!defined $no_clear_tmp) {
freeze_if_want_freeze ($cleanpid);
select (undef, undef, undef, 0.1);
}
- Log (undef, "Cleanup command exited $?");
+ Log (undef, "Cleanup command exited ".exit_status_s($?));
}
@@ -465,7 +465,7 @@ else {
# if $local_repo is already initialized:
`$gitcmd init --bare`;
if ($?) {
- croak("Error: $gitcmd init --bare exited $?");
+ croak("Error: $gitcmd init --bare exited ".exit_status_s($?));
}
# If $treeish looks like a hash (or abbrev hash) we look it up in
@@ -473,10 +473,11 @@ else {
# do that with tags/branches though -- those change over time, so
# they should always be resolved by the remote repo.)
if ($treeish =~ /^[0-9a-f]{3,40}$/s) {
- my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E`;
+ # Hide stderr because it's normal for this to fail:
+ my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E 2>/dev/null`;
if ($? == 0 &&
$sha1 =~ /^$treeish/ && # Don't use commit 123 @ branch abc!
- $sha1 =~ /^([0-9a-f]{40})$/) {
+ $sha1 =~ /^([0-9a-f]{40})$/s) {
$commit = $1;
Log(undef, "Commit $commit already present in $local_repo");
}
@@ -495,7 +496,7 @@ else {
Log(undef, "Fetching objects from $repo to $local_repo");
`$gitcmd fetch --no-progress --tags ''\Q$repo\E \Q+refs/heads/*:refs/heads/*\E`;
if ($?) {
- croak("Error: `$gitcmd fetch` exited $?");
+ croak("Error: `$gitcmd fetch` exited ".exit_status_s($?));
}
}
@@ -507,7 +508,9 @@ else {
my $gitcmd = "git --git-dir=\Q$repo\E";
my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E`;
unless ($? == 0 && $sha1 =~ /^([0-9a-f]{40})$/) {
- croak("`$gitcmd rev-list` exited $?, '$treeish' not found. Giving up.");
+ croak("`$gitcmd rev-list` exited "
+ .exit_status_s($?)
+ .", '$treeish' not found. Giving up.");
}
$commit = $1;
Log(undef, "Version $treeish is commit $commit");
@@ -524,7 +527,7 @@ else {
$ENV{"CRUNCH_SRC_COMMIT"} = $commit;
$git_archive = `$gitcmd archive ''\Q$commit\E`;
if ($?) {
- croak("Error: $gitcmd archive exited $?");
+ croak("Error: $gitcmd archive exited ".exit_status_s($?));
}
}
@@ -557,7 +560,7 @@ else {
freeze_if_want_freeze ($installpid);
select (undef, undef, undef, 0.1);
}
- Log (undef, "Install script exited $?");
+ Log (undef, "Install script exited ".exit_status_s($?));
}
if (!$have_slurm)
@@ -596,7 +599,8 @@ fi
}
if ($? != 0)
{
- croak("Installing Docker image from $docker_locator returned exit code $?");
+ croak("Installing Docker image from $docker_locator exited "
+ .exit_status_s($?));
}
}
@@ -974,10 +978,7 @@ sub reapchildren
my $childstatus = $?;
my $exitvalue = $childstatus >> 8;
- my $exitinfo = sprintf("exit %d signal %d%s",
- $exitvalue,
- $childstatus & 127,
- ($childstatus & 128 ? ' core dump' : ''));
+ my $exitinfo = "exit ".exit_status_s($childstatus);
$Jobstep->{'arvados_task'}->reload;
my $task_success = $Jobstep->{'arvados_task'}->{success};
@@ -1411,7 +1412,7 @@ sub save_meta
my $cmd = "arv-put --portable-data-hash --retries $retry_count " .
"--filename ''\Q$keep_logfile\E " . quotemeta($local_logfile->filename);
my $loglocator = `$cmd`;
- die "system $cmd failed: $?" if $?;
+ die "system $cmd exited ".exit_status_s($?) if $?;
chomp($loglocator);
$local_logfile = undef; # the temp file is automatically deleted
@@ -1569,6 +1570,20 @@ sub put_retry_count {
return ($retries > 3) ? $retries : 3;
}
+sub exit_status_s {
+ # Given a $?, return a human-readable exit code string like "0" or
+ # "1" or "0 with signal 1" or "1 with signal 11".
+ my $exitcode = shift;
+ my $s = $exitcode >> 8;
+ if ($exitcode & 0x7f) {
+ $s .= " with signal " . ($exitcode & 0x7f);
+ }
+ if ($exitcode & 0x80) {
+ $s .= " with core dump";
+ }
+ return $s;
+}
+
__DATA__
#!/usr/bin/perl
commit e8376cfb9deac7a50651061e2be99a4bc0c46338
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 3 10:17:07 2014 -0400
3775: Add TODO comments in suspicious-looking collate_output corners.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 24aca33..04ff82f 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -1298,10 +1298,13 @@ sub collate_output
if ($s->can_read(120)) {
sysread($child_out, $joboutput, 64 * 1024 * 1024);
chomp($joboutput);
+ # TODO: Ensure exit status == 0.
} else {
Log (undef, "timed out reading from 'arv-put'");
}
}
+ # TODO: kill $pid instead of waiting, now that we've decided to
+ # ignore further output.
waitpid($pid, 0);
return $joboutput;
commit c1a82be63ffc3b8aa853025672d486758ffc86e6
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 3 10:16:16 2014 -0400
3775: Run local/dev jobs on code from arbitrary remote git repositories.
* repository is a local path X -> use local repository X or X/.git.
* repository is a git url (git://, https://, git at host:repo.git, etc)
fetch branches, tags, and objects from the remote and use the result
to resolve script_version to a commit sha1 and run the job.
* else -> look up the named repository in Arvados and use its
fetch_url as a remote git url as above.
* --git-dir is given on the command line -> use that instead of
$Job->{repository} in the above logic. (This isn't new. It ensures
we don't go off fetching arbitrary remotes when crunch-dispatch.rb
has already pulled the code into its own internal git repo.)
Incidental changes:
* Lose support for looking up subversion revision numbers using
git-svn tags.
* Lose support for CRUNCH_DEFAULT_GIT_DIR environment variable. Pass
--git-dir instead.
* Improve log messages during checkout/install phase.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 3467ec3..24aca33 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -83,7 +83,7 @@ use IPC::Open2;
use IO::Select;
use File::Temp;
use Fcntl ':flock';
-use File::Path qw( make_path );
+use File::Path qw( make_path remove_tree );
use constant EX_TEMPFAIL => 75;
@@ -353,137 +353,195 @@ if (!$have_slurm)
my $build_script;
+do {
+ local $/ = undef;
+ $build_script = <DATA>;
+};
+my $nodelist = join(",", @node);
+if (!defined $no_clear_tmp) {
+ # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
+ Log (undef, "Clean work dirs");
-$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));
+ my $cleanpid = fork();
+ if ($cleanpid == 0)
+ {
+ srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
+ ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then for i in $JOB_WORK/*keep; do /bin/fusermount -z -u $i; done; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']);
+ exit (1);
}
- $ENV{"CRUNCH_SRC"} = $Job->{script_version};
- for my $src_path ("$ENV{CRUNCH_SRC}/arvados/sdk/python") {
- if (-d $src_path) {
- system("virtualenv", "$ENV{CRUNCH_TMP}/opt") == 0
- or croak ("virtualenv $ENV{CRUNCH_TMP}/opt failed: exit ".($?>>8));
- system ("cd $src_path && ./build.sh && \$CRUNCH_TMP/opt/bin/python setup.py install")
- == 0
- or croak ("setup.py in $src_path failed: exit ".($?>>8));
- }
+ while (1)
+ {
+ last if $cleanpid == waitpid (-1, WNOHANG);
+ freeze_if_want_freeze ($cleanpid);
+ select (undef, undef, undef, 0.1);
}
+ Log (undef, "Cleanup command exited $?");
}
-else
-{
- do {
- local $/ = undef;
- $build_script = <DATA>;
- };
- Log (undef, "Install revision ".$Job->{script_version});
- my $nodelist = join(",", @node);
- 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 for i in $JOB_WORK/*keep; do /bin/fusermount -z -u $i; done; 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 $?");
- }
+my $git_archive;
+if (!defined $git_dir && $Job->{'script_version'} =~ m{^/}) {
+ # If we're in user-land (i.e., not called from crunch-dispatch)
+ # script_version can be an absolute directory path, signifying we
+ # should work straight out of that directory instead of using a git
+ # commit.
+ $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{'script_version'};
+ $ENV{"CRUNCH_SRC"} = $Job->{'script_version'};
+}
+else {
+ $ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src";
# Install requested code version
-
- my @execargs;
- my @srunargs = ("srun",
- "--nodelist=$nodelist",
- "-D", $ENV{'TMPDIR'}, "--job-name=$job_id");
+ Log (undef, "Looking for version ".$Job->{script_version}." from repository ".$Job->{repository});
$ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version};
- $ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src";
- my $commit;
- my $git_archive;
- my $treeish = $Job->{'script_version'};
-
- # If we're running under crunch-dispatch, it will have pulled the
- # appropriate source tree into its own repository, and given us that
- # repo's path as $git_dir. If we're running a "local" job, and a
- # script_version was specified, it's up to the user to provide the
- # full path to a local repository in Job->{repository}.
+ # If we're running under crunch-dispatch, it will have already
+ # pulled the appropriate source tree into its own repository, and
+ # given us that repo's path as $git_dir.
#
- # TODO: Accept URLs too, not just local paths. Use git-ls-remote and
- # git-archive --remote where appropriate.
+ # If we're running a "local" job, we might have to fetch content
+ # from a remote repository.
#
- # TODO: Accept a locally-hosted Arvados repository by name or
- # UUID. Use arvados.v1.repositories.list or .get to figure out the
- # appropriate fetch-url.
- my $repo = $git_dir || $ENV{'CRUNCH_DEFAULT_GIT_DIR'} || $Job->{'repository'};
-
+ # (Currently crunch-dispatch gives a local path with --git-dir, but
+ # we might as well accept URLs there too in case it changes its
+ # mind.)
+ my $repo = $git_dir || $Job->{'repository'};
+
+ # Repository can be remote or local. If remote, we'll need to fetch it
+ # to a local dir before doing `git log` et al.
+ my $repo_location;
+
+ if ($repo =~ m{://|\@.*:}) {
+ # $repo is a git url we can clone, like git:// or https:// or
+ # file:/// or git at host:repo.git
+ $repo_location = 'remote';
+ } elsif ($repo =~ m{^\.*/}) {
+ # $repo is a local path to a git index. We'll also resolve ../foo
+ # to ../foo/.git if the latter is a directory.
+ if (-d "$repo/.git") {
+ $repo = "$repo/.git";
+ }
+ $repo_location = 'local';
+ Log(undef, "Using local repository '$repo'");
+ } else {
+ # $repo is none of the above. It must be the name of a hosted
+ # repository.
+ my $arv_repo_list = $arv->{'repositories'}->{'list'}->execute(
+ 'filters' => [['name','=',$repo]]
+ )->{'items'};
+ my $n_found = scalar @{$arv_repo_list};
+ if ($n_found > 0) {
+ Log(undef, "Repository '$repo' -> "
+ . join(", ", map { $_->{'uuid'} } @{$arv_repo_list}));
+ }
+ if ($n_found != 1) {
+ croak("Error: Found $n_found repositories with name '$repo'.");
+ }
+ $repo = $arv_repo_list->[0]->{'fetch_url'};
+ $repo_location = 'remote';
+ }
+ Log(undef, "Using $repo_location repository '$repo'");
$ENV{"CRUNCH_SRC_URL"} = $repo;
- if (-d "$repo/.git") {
- # We were given a working directory, but we are only interested in
- # the index.
- $repo = "$repo/.git";
- }
+ # Resolve given script_version (we'll call that $treeish here) to a
+ # commit sha1 ($commit).
+ my $treeish = $Job->{'script_version'};
+ my $commit;
+ if ($repo_location eq 'remote') {
+ # We minimize excess object-fetching by re-using the same bare
+ # repository in CRUNCH_TMP/.git for multiple crunch-jobs -- we
+ # just keep adding remotes to it as needed.
+ my $local_repo = $ENV{'CRUNCH_TMP'}."/.git";
+ my $gitcmd = "git --git-dir=\Q$local_repo\E";
+
+ # Set up our local repo for caching remote objects, making
+ # archives, etc.
+ if (!-d $local_repo) {
+ make_path($local_repo) or croak("Error: could not create $local_repo");
+ }
+ # This works (exits 0 and doesn't delete fetched objects) even
+ # if $local_repo is already initialized:
+ `$gitcmd init --bare`;
+ if ($?) {
+ croak("Error: $gitcmd init --bare exited $?");
+ }
+
+ # If $treeish looks like a hash (or abbrev hash) we look it up in
+ # our local cache first, since that's cheaper. (We don't want to
+ # do that with tags/branches though -- those change over time, so
+ # they should always be resolved by the remote repo.)
+ if ($treeish =~ /^[0-9a-f]{3,40}$/s) {
+ my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E`;
+ if ($? == 0 &&
+ $sha1 =~ /^$treeish/ && # Don't use commit 123 @ branch abc!
+ $sha1 =~ /^([0-9a-f]{40})$/) {
+ $commit = $1;
+ Log(undef, "Commit $commit already present in $local_repo");
+ }
+ }
- # If this looks like a subversion r#, look for it in git-svn commit messages
+ if (!defined $commit) {
+ # If $treeish isn't just a hash or abbrev hash, or isn't here
+ # yet, we need to fetch the remote to resolve it correctly.
- if ($treeish =~ m{^\d{1,4}$}) {
- my $gitlog = `git --git-dir=\Q$repo\E log --pretty="format:%H" --grep="git-svn-id:.*\@"\Q$treeish\E" " master`;
- chomp $gitlog;
- Log(undef, "git Subversion search exited $?");
- if (($? == 0) && ($gitlog =~ /^[a-f0-9]{40}$/)) {
- $commit = $gitlog;
- Log(undef, "Using commit $commit for Subversion revision $treeish");
+ # First, remove all local heads. This prevents a name that does
+ # not exist on the remote from resolving to (or colliding with)
+ # a previously fetched branch or tag (possibly from a different
+ # remote).
+ remove_tree("$local_repo/refs/heads", {keep_root => 1});
+
+ Log(undef, "Fetching objects from $repo to $local_repo");
+ `$gitcmd fetch --no-progress --tags ''\Q$repo\E \Q+refs/heads/*:refs/heads/*\E`;
+ if ($?) {
+ croak("Error: `$gitcmd fetch` exited $?");
+ }
}
+
+ # Now that the data is all here, we will use our local repo for
+ # the rest of our git activities.
+ $repo = $local_repo;
}
- # If that didn't work, try asking git to look it up as a tree-ish.
-
- if (!defined $commit) {
- my $found = `git --git-dir=\Q$repo\E rev-list -1 ''\Q$treeish\E`;
- chomp $found;
- Log(undef, "git rev-list exited $? with result '$found'");
- if (($? == 0) && ($found =~ /^[0-9a-f]{40}$/s)) {
- $commit = $found;
- Log(undef, "Using commit $commit for tree-ish $treeish");
- if ($commit ne $treeish) {
- # Make sure we record the real commit id in the database,
- # frozentokey, logs, etc. -- instead of an abbreviation or a
- # branch name which can become ambiguous or point to a
- # different commit in the future.
- $Job->{'script_version'} = $commit;
- !$job_has_uuid or
- $Job->update_attributes('script_version' => $commit) or
- croak("Error while updating job");
- }
+ my $gitcmd = "git --git-dir=\Q$repo\E";
+ my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E`;
+ unless ($? == 0 && $sha1 =~ /^([0-9a-f]{40})$/) {
+ croak("`$gitcmd rev-list` exited $?, '$treeish' not found. Giving up.");
+ }
+ $commit = $1;
+ Log(undef, "Version $treeish is commit $commit");
+
+ if ($commit ne $Job->{'script_version'}) {
+ # Record the real commit id in the database, frozentokey, logs,
+ # etc. -- instead of an abbreviation or a branch name which can
+ # become ambiguous or point to a different commit in the future.
+ if (!$Job->update_attributes('script_version' => $commit)) {
+ croak("Error: failed to update job's script_version attribute");
}
}
- if (defined $commit) {
- $ENV{"CRUNCH_SRC_COMMIT"} = $commit;
- @execargs = ("sh", "-c",
- "mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -");
- $git_archive = `git --git-dir=\Q$repo\E archive ''\Q$commit\E`;
- croak("git archive failed: exit " . ($? >> 8)) if ($? != 0);
+ $ENV{"CRUNCH_SRC_COMMIT"} = $commit;
+ $git_archive = `$gitcmd archive ''\Q$commit\E`;
+ if ($?) {
+ croak("Error: $gitcmd archive exited $?");
}
- else {
- croak ("could not figure out commit id for $treeish");
+}
+
+if (!defined $git_archive) {
+ Log(undef, "Skip install phase (no git archive)");
+ if ($have_slurm) {
+ Log(undef, "Warning: This probably means workers have no source tree!");
}
+}
+else {
+ Log(undef, "Run install script on all workers");
+
+ my @srunargs = ("srun",
+ "--nodelist=$nodelist",
+ "-D", $ENV{'TMPDIR'}, "--job-name=$job_id");
+ my @execargs = ("sh", "-c",
+ "mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -");
# Note: this section is almost certainly unnecessary if we're
# running tasks in docker containers.
@@ -499,7 +557,7 @@ else
freeze_if_want_freeze ($installpid);
select (undef, undef, undef, 0.1);
}
- Log (undef, "Install exited $?");
+ Log (undef, "Install script exited $?");
}
if (!$have_slurm)
commit 256ceb11e3b67dbe68b955ed09ac0df9f6cda2ba
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 3 09:42:33 2014 -0400
3775: Remove stagnant $job_has_uuid flag. Every job has a uuid. The
only time to skip updating the job record on the server side is when
croak() happens before $Job is created/fetched.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 1f7c191..3467ec3 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -125,8 +125,7 @@ if (defined $job_api_token) {
}
my $have_slurm = exists $ENV{SLURM_JOBID} && exists $ENV{SLURM_NODELIST};
-my $job_has_uuid = $jobspec =~ /^[-a-z\d]+$/;
-my $local_job = !$job_has_uuid;
+my $local_job = 0;
$SIG{'USR1'} = sub
@@ -145,12 +144,13 @@ my $local_logfile;
my $User = $arv->{'users'}->{'current'}->execute;
-my $Job = {};
+my $Job;
my $job_id;
my $dbh;
my $sth;
-if ($job_has_uuid)
+if ($jobspec =~ /^[-a-z\d]+$/)
{
+ # $jobspec is an Arvados UUID, not a JSON job specification
$Job = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec);
if (!$force_unlock) {
# If some other crunch-job process has grabbed this job (or we see
@@ -193,8 +193,6 @@ else
$Job->{'started_at'} = gmtime;
$Job = $arv->{'jobs'}->{'create'}->execute('job' => $Job);
-
- $job_has_uuid = 1;
}
$job_id = $Job->{'uuid'};
@@ -283,20 +281,17 @@ foreach (@sinfo)
my $jobmanager_id;
-if ($job_has_uuid)
-{
- # Claim this job, and make sure nobody else does
- unless ($Job->update_attributes('is_locked_by_uuid' => $User->{'uuid'}) &&
- $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) {
- Log(undef, "Error while updating / locking job, exiting ".EX_TEMPFAIL);
- exit EX_TEMPFAIL;
- }
- $Job->update_attributes('state' => 'Running',
- 'tasks_summary' => { 'failed' => 0,
- 'todo' => 1,
- 'running' => 0,
- 'done' => 0 });
+# Claim this job, and make sure nobody else does
+unless ($Job->update_attributes('is_locked_by_uuid' => $User->{'uuid'}) &&
+ $Job->{'is_locked_by_uuid'} == $User->{'uuid'}) {
+ Log(undef, "Error while updating / locking job, exiting ".EX_TEMPFAIL);
+ exit EX_TEMPFAIL;
}
+$Job->update_attributes('state' => 'Running',
+ 'tasks_summary' => { 'failed' => 0,
+ 'todo' => 1,
+ 'running' => 0,
+ 'done' => 0 });
Log (undef, "start");
@@ -866,7 +861,7 @@ else {
});
Log(undef, "output uuid " . $output->{uuid});
Log(undef, "output hash " . $output->{portable_data_hash});
- $Job->update_attributes('output' => $output->{portable_data_hash}) if $job_has_uuid;
+ $Job->update_attributes('output' => $output->{portable_data_hash});
};
if ($@) {
Log (undef, "Failed to register output manifest: $@");
@@ -900,9 +895,7 @@ sub update_progress_stats
$Job->{'tasks_summary'}->{'todo'} = $todo;
$Job->{'tasks_summary'}->{'done'} = $done;
$Job->{'tasks_summary'}->{'running'} = $running;
- if ($job_has_uuid) {
- $Job->update_attributes('tasks_summary' => $Job->{'tasks_summary'});
- }
+ $Job->update_attributes('tasks_summary' => $Job->{'tasks_summary'});
Log (undef, "status: $done done, $running running, $todo todo");
$progress_is_dirty = 0;
}
@@ -1031,23 +1024,21 @@ sub check_refresh_wanted
my @stat = stat $ENV{"CRUNCH_REFRESH_TRIGGER"};
if (@stat && $stat[9] > $latest_refresh) {
$latest_refresh = scalar time;
- if ($job_has_uuid) {
- my $Job2 = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec);
- for my $attr ('cancelled_at',
- 'cancelled_by_user_uuid',
- 'cancelled_by_client_uuid',
- 'state') {
- $Job->{$attr} = $Job2->{$attr};
- }
- if ($Job->{'state'} ne "Running") {
- if ($Job->{'state'} eq "Cancelled") {
- Log (undef, "Job cancelled at " . $Job->{'cancelled_at'} . " by user " . $Job->{'cancelled_by_user_uuid'});
- } else {
- Log (undef, "Job state unexpectedly changed to " . $Job->{'state'});
- }
- $main::success = 0;
- $main::please_freeze = 1;
+ my $Job2 = $arv->{'jobs'}->{'get'}->execute('uuid' => $jobspec);
+ for my $attr ('cancelled_at',
+ 'cancelled_by_user_uuid',
+ 'cancelled_by_client_uuid',
+ 'state') {
+ $Job->{$attr} = $Job2->{$attr};
+ }
+ if ($Job->{'state'} ne "Running") {
+ if ($Job->{'state'} eq "Cancelled") {
+ Log (undef, "Job cancelled at " . $Job->{'cancelled_at'} . " by user " . $Job->{'cancelled_by_user_uuid'});
+ } else {
+ Log (undef, "Job state unexpectedly changed to " . $Job->{'state'});
}
+ $main::success = 0;
+ $main::please_freeze = 1;
}
}
}
@@ -1333,7 +1324,7 @@ sub croak
Log (undef, $message);
freeze() if @jobstep_todo;
collate_output() if @jobstep_todo;
- cleanup();
+ cleanup() if $Job;
save_meta() if $local_logfile;
die;
}
@@ -1341,7 +1332,6 @@ sub croak
sub cleanup
{
- return if !$job_has_uuid;
if ($Job->{'state'} eq 'Cancelled') {
$Job->update_attributes('finished_at' => scalar gmtime);
} else {
@@ -1366,7 +1356,7 @@ sub save_meta
$local_logfile = undef; # the temp file is automatically deleted
Log (undef, "log manifest is $loglocator");
$Job->{'log'} = $loglocator;
- $Job->update_attributes('log', $loglocator) if $job_has_uuid;
+ $Job->update_attributes('log', $loglocator);
}
commit 2198f66d230634ab4e7e511e176bfbc4af632f0a
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 3 09:33:46 2014 -0400
3775: Fix syntax error 2 commits ago.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 9c32d8e..1f7c191 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -883,7 +883,7 @@ if ($collated_output && $main::success) {
} else {
$final_state = 'Failed';
}
-$Job->update_attributes('state' => $final_state)
+$Job->update_attributes('state' => $final_state);
exit (($final_state eq 'Complete') ? 0 : 1);
commit 7d9cfb6e0716239f996bae054bc9345a663e0b7e
Merge: 75be748 62790d7
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Oct 2 11:13:19 2014 -0400
3775: Merge branch 'master' into 3775-fetch-git-repo
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