#!/usr/bin/perl
-# -*- mode: perl; perl-indent-level: 2; -*-
+# -*- mode: perl; perl-indent-level: 2; indent-tabs-mode: nil; -*-
=head1 NAME
$ENV{"CRUNCH_WORK"} = $ENV{"JOB_WORK"}; # deprecated
mkdir ($ENV{"JOB_WORK"});
+my $arv_cli;
+
+if (defined $ENV{"ARV_CLI"}) {
+ $arv_cli = $ENV{"ARV_CLI"};
+}
+else {
+ $arv_cli = 'arv';
+}
+
my $force_unlock;
my $git_dir;
my $jobspec;
}
if (exists $ENV{SLURM_NODELIST})
{
- push @sinfo, `sinfo -h --format='%c %N' --nodes='$ENV{SLURM_NODELIST}'`;
+ push @sinfo, `sinfo -h --format='%c %N' --nodes=\Q$ENV{SLURM_NODELIST}\E`;
}
foreach (@sinfo)
{
my $commit;
my $git_archive;
my $treeish = $Job->{'script_version'};
- my $repo = $git_dir || $ENV{'CRUNCH_DEFAULT_GIT_DIR'};
- # Todo: let script_version specify repository instead of expecting
- # parent process to figure it out.
- $ENV{"CRUNCH_SRC_URL"} = $repo;
- # Create/update our clone of the remote git repo
+ # 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}.
+ #
+ # TODO: Accept URLs too, not just local paths. Use git-ls-remote and
+ # git-archive --remote where appropriate.
+ #
+ # 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'};
+
+ $ENV{"CRUNCH_SRC_URL"} = $repo;
- if (!-d $ENV{"CRUNCH_SRC"}) {
- system(qw(git clone), $repo, $ENV{"CRUNCH_SRC"}) == 0
- or croak ("git clone $repo failed: exit ".($?>>8));
- system("cd $ENV{CRUNCH_SRC} && git config clean.requireForce false");
+ if (-d "$repo/.git") {
+ # We were given a working directory, but we are only interested in
+ # the index.
+ $repo = "$repo/.git";
}
- `cd $ENV{CRUNCH_SRC} && git remote set-url origin \"\$CRUNCH_SRC_URL\" && git fetch -q origin`;
# If this looks like a subversion r#, look for it in git-svn commit messages
if ($treeish =~ m{^\d{1,4}$}) {
- my $gitlog = `cd $ENV{CRUNCH_SRC} && git log --pretty="format:%H" --grep="git-svn-id:.*\@$treeish " origin/master`;
+ my $gitlog = `git --git-dir=\Q$repo\E log --pretty="format:%H" --grep="git-svn-id:.*\@"\Q$treeish\E" " master`;
chomp $gitlog;
if ($gitlog =~ /^[a-f0-9]{40}$/) {
$commit = $gitlog;
# If that didn't work, try asking git to look it up as a tree-ish.
if (!defined $commit) {
-
- my $cooked_treeish = $treeish;
- if ($treeish !~ m{^[0-9a-f]{5,}$}) {
- # Looks like a git branch name -- make sure git knows it's
- # relative to the remote repo
- $cooked_treeish = "origin/$treeish";
- }
-
- my $found = `cd $ENV{CRUNCH_SRC} && git rev-list -1 $cooked_treeish`;
+ my $found = `git --git-dir=\Q$repo\E rev-list -1 ''\Q$treeish\E`;
chomp $found;
if ($found =~ /^[0-9a-f]{40}$/s) {
$commit = $found;
$ENV{"CRUNCH_SRC_COMMIT"} = $commit;
@execargs = ("sh", "-c",
"mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -");
- $git_archive = `cd $ENV{CRUNCH_SRC} && git archive $commit`;
+ $git_archive = `git --git-dir=\Q$repo\E archive ''\Q$commit\E`;
}
else {
croak ("could not figure out commit id for $treeish");
$ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name};
$ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
$ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/$id.$$";
- $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}."/keep";
+ $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep";
$ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
$ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
$ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};
if ($Job->{'output'})
{
eval {
- my $manifest_text = `arv keep get \Q$Job->{'output'}\E`;
+ my $manifest_text = `arv keep get ''\Q$Job->{'output'}\E`;
$arv->{'collections'}->{'create'}->execute('collection' => {
'uuid' => $Job->{'output'},
'manifest_text' => $manifest_text,
});
+ if ($Job->{'output_is_persistent'}) {
+ $arv->{'links'}->{'create'}->execute('link' => {
+ 'tail_kind' => 'arvados#user',
+ 'tail_uuid' => $User->{'uuid'},
+ 'head_kind' => 'arvados#collection',
+ 'head_uuid' => $Job->{'output'},
+ 'link_class' => 'resources',
+ 'name' => 'wants',
+ });
+ }
};
if ($@) {
Log (undef, "Failed to register output manifest: $@");
sub fetch_block
{
my $hash = shift;
- my ($child_out, $child_in, $output_block);
+ my ($keep, $child_out, $output_block);
- my $pid = open2($child_out, $child_in, 'arv', 'keep', 'get', $hash);
- sysread($child_out, $output_block, 64 * 1024 * 1024);
- waitpid($pid, 0);
+ my $cmd = "$arv_cli keep get \Q$hash\E";
+ open($keep, '-|', $cmd) or die "fetch_block: $cmd: $!";
+ sysread($keep, $output_block, 64 * 1024 * 1024);
+ close $keep;
return $output_block;
}
Log (undef, "collate");
my ($child_out, $child_in);
- my $pid = open2($child_out, $child_in, 'arv', 'keep', 'put', '--raw');
+ my $pid = open2($child_out, $child_in, $arv_cli, 'keep', 'put', '--raw');
my $joboutput;
for (@jobstep)
{
my $s = IO::Select->new($child_out);
if ($s->can_read(120)) {
sysread($child_out, $joboutput, 64 * 1024 * 1024);
+ chomp($joboutput);
} else {
Log (undef, "timed out reading from 'arv keep put'");
}
return if $justcheckpoint; # checkpointing is not relevant post-Warehouse.pm
$local_logfile->flush;
- my $cmd = "arv keep put --filename \Q$keep_logfile\E "
+ my $cmd = "$arv_cli keep put --filename ''\Q$keep_logfile\E "
. quotemeta($local_logfile->filename);
my $loglocator = `$cmd`;
die "system $cmd failed: $?" if $?;
projects / arvados.git / blobdiff