NAME

NBI::Job - A class for representing a job for NBI::Slurm

VERSION

version 0.9.0

DESCRIPTION

The NBI::Job module provides a class for representing a job to be submitted to SLURM for High-Performance Computing (HPC). It allows you to define the name of the job, the commands to be executed, and various options related to the job execution.

EXAMPLES

use NBI::Job;
use NBI::Opts;

# Create a simple job
my $job = NBI::Job->new(
  -name => "simple-job",
  -command => "echo 'Hello, World!'"
);

# Create a job with multiple commands
my $multi_job = NBI::Job->new(
  -name => "multi-command-job",
  -commands => ["echo 'Step 1'", "sleep 5", "echo 'Step 2'"]
);

# Create a job with custom options: first define $opts and then $custom_job
my $opts = NBI::Opts->new(
  -queue => "long",
  -memory => "4GB",
  -threads => 2,
  -time => "1h"
);

my $custom_job = NBI::Job->new(
  -name => "custom-job",
  -command => "run_analysis.pl",
  -opts => $opts
);

# Submit the job
my $job_id = $custom_job->run;
print "Job submitted with ID: $job_id\n";

METHODS

new()

Create a new instance of NBI::Job.

my $job = NBI::Job->new(
  -name => "job-name",
  -command => "ls -l",
  -opts => $options
);

# Or with multiple commands
my $job = NBI::Job->new(
  -name => "multi-step-job",
  -commands => ["step1.pl", "step2.pl", "step3.pl"],
  -opts => $options
);

Parameters:

• -name (string, optional): The name of the job. If not provided, a random name will be generated.

• -command (string, optional): A single command to be executed by the job.

• -commands (arrayref, optional): An array reference containing multiple commands to be executed by the job.

• -opts (NBI::Opts object, optional): An instance of the NBI::Opts class representing the options for the job. If not provided, default options will be used.

name

Accessor method for the job name.

$job->name = "new-job-name";
my $name = $job->name;

jobid

Accessor method for the job ID.

$job->jobid = 12345;  # Usually set internally after job submission
my $jobid = $job->jobid;

outputfile

Accessor method for the output file path. Use %j in the filename to include the job ID.

$job->outputfile = "job_output_%j.txt";
my $outputfile = $job->outputfile;
my $interpolated_outputfile = $job->outputfile('-interpolate');

errorfile

Accessor method for the error file path. Use %j in the filename to include the job ID.

$job->errorfile = "job_error_%j.txt";
my $errorfile = $job->errorfile;
my $interpolated_errorfile = $job->errorfile('-interpolate');

script_path

Accessor method for the generated script path.

my $script_path = $job->script_path;

append_command

Append a command to the job.

$job->append_command("echo 'Job finished'");

prepend_command

Prepend a command to the job.

$job->prepend_command("echo 'Job starting'");

commands

Get the list of commands for the job.

my $commands = $job->commands;
foreach my $cmd (@$commands) {
  print "Command: $cmd\n";
}

commands_count

Get the number of commands for the job.

my $count = $job->commands_count;
print "This job has $count commands.\n";

set_opts

Set the options for the job.

my $new_opts = NBI::Opts->new(-queue => "short", -memory => "2GB");
$job->set_opts($new_opts);

get_opts

Get the options for the job.

my $opts = $job->get_opts;
print "Job queue: " . $opts->queue . "\n";

opts

Alias for get_opts.

my $opts = $job->opts;

script

Generate the sbatch script for the job.

my $script_content = $job->script;
print "Generated script:\n$script_content\n";

run

Submit the job to SLURM.

my $submitted_job_id = $job->run;
if ($submitted_job_id) {
  print "Job submitted successfully with ID: $submitted_job_id\n";
} else {
  print "Job submission failed.\n";
}

view

Return a string representation of the job object.

my $job_info = $job->view;
print $job_info;

AUTHOR

Andrea Telatin <proch@cpan.org>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2023 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License

cpanm NBI::Slurm

perl -MCPAN -e shell
install NBI::Slurm