HPC-Runner-Command

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lib/HPC/Runner/Command/execute_job/Logger/JSON.pm  view on Meta::CPAN

            $self->lock_file->remove;
        };
    }

    return $task_obj;
}

##TODO Once we add to the complete
## Get all the for the tasks
## Compute mean, min, max of all tasks
sub update_json_task {
    my $self = shift;

    # my @stats    = ( 'vmpeak', 'vmrss', 'vmsize', 'vmhwm' );
    # my $job_meta = $self->parse_meta_str;
    # my $basename = $self->data_tar->basename('.tar.gz');
    # my $data_dir = File::Spec->catdir( $basename, $job_meta->{jobname} );

    my $data_dir = File::Spec->catdir( $self->data_dir, $self->task_jobname );
    make_path($data_dir);

lib/HPC/Runner/Command/submit_jobs/Logger/JSON.pm  view on Meta::CPAN

}

=head3 update_json_submission

Take the initial submission and update it to contain the hpcmeta

We only rerun this here to get the submission status

=cut

sub update_json_submission {
    my $self = shift;

    make_path($self->data_dir);
    my $hpc_meta = $self->gen_hpc_meta;
    my $json_text = encode_json $hpc_meta;

    # my $file_name = File::Spec->catdir( $self->logdir, 'submission.json' );
    $self->_make_the_dirs( $self->logdir );

    # write_file($file_name, $json_text);

lib/HPC/Runner/Command/submit_jobs/Plugin/Dummy.pm  view on Meta::CPAN

    return $jobid;
}

=head3 update_job_deps

Update the job dependencies if using job_array (not batches)

=cut

sub update_job_deps {
    my $self = shift;

    return unless $self->has_array_deps;

    my $array_deps_file = File::Spec->catdir( $self->logdir, 'array_deps.tsv' );

    foreach my $current_task ( sort keys %{ $self->array_deps } ) {
        my $v = $self->array_deps->{$current_task};

        my $dep_tasks = join( ':', @$v );

lib/HPC/Runner/Command/submit_jobs/Plugin/PBS.pm  view on Meta::CPAN

Update the job dependencies if using job_array (not batches)

TODO - not entirely sure this will work...

# This is for Torque
# http://docs.adaptivecomputing.com/torque/4-1-4/Content/topics/commands/qalter.htm
# $tv = $tmp[0] . ' -t '.$tmp[1];

=cut

sub update_job_deps {
    my $self = shift;

    return unless $self->has_array_deps;

    $self->log->warn('Task dependencies in PBS is still very experimental!');
    $self->log->warn( 'Please raise any problems as an issue at github.' . "\n"
          . "\thttp://github.com/biosails/HPC-Runner-Command" );

    while ( my ( $current_task, $v ) = each %{ $self->array_deps } ) {

lib/HPC/Runner/Command/submit_jobs/Plugin/SGE.pm  view on Meta::CPAN

=head3 update_job_deps

Update the job dependencies if using job_array (not batches)

NOTE - Task dependencies may not be supported.


=cut

sub update_job_deps {
    my $self = shift;

    return unless $self->has_array_deps;

    $self->log->warn('Task dependencies in SGE is still very experimental!');
    $self->log->warn( 'Please raise any problems as an issue at github.' . "\n"
          . "\thttp://github.com/biosails/HPC-Runner-Command" );

    while ( my ( $current_task, $v ) = each %{ $self->array_deps } ) {

lib/HPC/Runner/Command/submit_jobs/Plugin/Slurm.pm  view on Meta::CPAN

    return $jobid;
}

=head3 update_job_deps

Update the job dependencies if using job_array (not batches)

=cut

sub update_job_deps {
    my $self = shift;

    return unless $self->has_array_deps;

    my $array_deps_file = File::Spec->catdir( $self->logdir, 'array_deps.tsv' );
    my $array_log_file  = File::Spec->catdir( $self->logdir, 'array_deps.log' );

    ##TODO Add TaskID, TaskTags, Task Tags
    while ( my ( $current_task, $v ) = each %{ $self->array_deps } ) {
        my $dep_tasks = join( ':', @{$v} );

lib/HPC/Runner/Command/submit_jobs/Utils/Scheduler/ResolveDeps/AssignTaskDeps.pm  view on Meta::CPAN

#TODO do this after the all batches for a single job have been passed

#DEPRACATED job_scheduler_ids_by_array

for job at jobs
  for batch at batches
    for task at tasks

=cut

sub update_job_scheduler_deps_by_task {
    my $self = shift;

    $self->app_log->info(
        'Updating task dependencies. This may take some time...');

    foreach my $job ( $self->all_schedules ) {
        next if $self->jobs->{$job}->submission_failure;
        $self->current_job($job);
        $self->batch_scheduler_ids_by_task;
    }

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