}
}
$ENV{"JOB_WORK"} = $ENV{"CRUNCH_TMP"} . "/work";
+$ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";
$ENV{"CRUNCH_WORK"} = $ENV{"JOB_WORK"}; # deprecated
mkdir ($ENV{"JOB_WORK"});
-my $arv = Arvados->new;
-my $metastream = Warehouse::Stream->new(whc => new Warehouse);
-$metastream->clear;
-$metastream->write_start('log.txt');
+my $arv = Arvados->new('apiVersion' => 'v1');
+my $metastream;
my $User = $arv->{'users'}->{'current'}->execute;
}
$job_id = $Job->{'uuid'};
+$metastream = Warehouse::Stream->new(whc => new Warehouse);
+$metastream->clear;
+$metastream->name('.');
+$metastream->write_start($job_id . '.log.txt');
$Job->{'runtime_constraints'} ||= {};
if ($skip_install)
{
$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));
+ }
+ }
}
else
{
Log (undef, "Install revision ".$Job->{script_version});
my $nodelist = join(",", @node);
- # Clean out crunch_tmp/work and crunch_tmp/opt
+ # 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 sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt']);
+ ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']);
exit (1);
}
while (1)
$ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version};
$ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src";
- $ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";
my $commit;
my $git_archive;
$ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name};
$ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
$ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/".$slot[$childslot]->{cpu};
+ $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"};
$ENV{"GZIP"} = "-n";
my $build_script_to_send = "";
my $command =
"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
- ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} "
+ ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
."&& cd $ENV{CRUNCH_TMP} ";
if ($build_script)
{
$command .=
"&& perl -";
}
- $ENV{"PYTHONPATH"} =~ s{^}{:} if $ENV{"PYTHONPATH"};
- $ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/sdk/python}; # xxx hack
- $ENV{"PYTHONPATH"} =~ s{$}{:/usr/local/arvados/src/sdk/python}; # xxx hack
$command .=
- "&& exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+ "&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
my @execargs = ('bash', '-c', $command);
srun (\@srunargs, \@execargs, undef, $build_script_to_send);
exit (111);
my $m = $metastream;
$m = $m->copy if $justcheckpoint;
$m->write_finish;
- my $loglocator = $m->as_key;
+ my $whc = Warehouse->new;
+ my $loglocator = $whc->store_block ($m->as_string);
+ $arv->{'collections'}->{'create'}->execute('collection' => {
+ 'uuid' => $loglocator,
+ 'manifest_text' => $m->as_string,
+ });
undef $metastream if !$justcheckpoint; # otherwise Log() will try to use it
- Log (undef, "meta key is $loglocator");
+ Log (undef, "log manifest is $loglocator");
$Job->{'log'} = $loglocator;
$Job->update_attributes('log', $loglocator) if $job_has_uuid;
}
open L, ">", "$destdir.lock" or die "$destdir.lock: $!";
flock L, LOCK_EX;
-if (readlink ("$destdir.commit") eq $commit) {
+if (readlink ("$destdir.commit") eq $commit && -d $destdir) {
exit 0;
}
open STDERR, ">&STDOUT";
mkdir $destdir;
-open TARX, "|-", "tar", "-C", $destdir, "-xf", "-";
-print TARX <DATA>;
-if(!close(TARX)) {
- die "'tar -C $destdir -xf -' exited $?: $!";
+my @git_archive_data = <DATA>;
+if (@git_archive_data) {
+ open TARX, "|-", "tar", "-C", $destdir, "-xf", "-";
+ print TARX @git_archive_data;
+ if(!close(TARX)) {
+ die "'tar -C $destdir -xf -' exited $?: $!";
+ }
}
my $pwd;
chomp ($pwd = `pwd`);
my $install_dir = $ENV{"CRUNCH_INSTALL"} || "$pwd/opt";
mkdir $install_dir;
+
+for my $src_path ("$destdir/arvados/sdk/python") {
+ if (-d $src_path) {
+ shell_or_die ("virtualenv", $install_dir);
+ shell_or_die ("cd $src_path && ./build.sh && $install_dir/bin/python setup.py install");
+ }
+}
+
if (-e "$destdir/crunch_scripts/install") {
shell_or_die ("$destdir/crunch_scripts/install", $install_dir);
} elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {