Set umask on PBS-job

Question

In the process of writing a Perl-script to submit PBS-jobs, I noticed that the output-files are only usable by the owner (rw-------). After some research, I found that you can put #PBS -W umask=002 in the job-script to make it accessible for others.

Perl:

my $client = PBS::Client->new();

my $wd    = $dir_temp;
my $name  = "demultiplex";
my $queue = "default";
my $wallt = "72:00:00";
my $job_demultiplex = PBS::Client::Job -> new(
    wd    => $wd,
    queue => $queue,
    name  => $name,
    wallt => $wallt,
    cmd   => "perl ".$script_directory."demultiplex.pl ".$dir_in." 2>"."demultiplex_error.log 1>"."demultiplex_output.log"
);

This Perlscript creates the following job:

#!/bin/sh

#PBS -N demultiplex
#PBS -d /store/www/labresults_QC/small_rna_sequence_analyser/data/data_temp/BGI_pilot
#PBS -q default
#PBS -l nodes=1
#PBS -l walltime=72:00:00
#PBS -W umask=002                 <---

perl /store/www/labresults_QC/small_rna_sequence_analyser/scripts/demultiplex.pl /store/www/labresults_QC/small_rna_sequence_analyser/data/data_input/BGI_pilot 2>demultiplex_error.log 1>demultiplex_output.log

Is there a possibility to pass the indicated line (<---) to the job from the Perlscript?

Answer 1

Given the current codebase, no. You'd have to open a bug report to the PBS::Client module and request the feature. Accompany it with a patch - that might help.