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NBI-Slurm-0.12.0
River stage zero No dependents
/ NBI::Opts

NAME

NBI::Opts - A class for representing a the SLURM options for NBI::Slurm

VERSION

version 0.12.0

SYNOPSIS

SLURM Options for NBI::Slurm, to be passed to a NBI::Job object.


            

              
              
use NBI::Opts;
my $opts = NBI::Opts->new(
 -queue => "short",
 -threads => 4,
 -memory => "8GB",
 -time => "2h",
 -opts => [],
);

DESCRIPTION

The NBI::Opts module provides a class for representing the SLURM options used by NBI::Slurm for job submission. It allows you to set various options such as the queue, number of threads, allocated memory, execution time, input files, and more.

METHODS

new()

Create a new instance of NBI::Opts. In this case this will imply using a job array over a list of files


            

              
              
my $opts = NBI::Opts->new(
  -queue => "short",
  -threads => 4,
  -memory => "8GB",
  -time => "2h",
  -opts => ["--option=Value"],
  -tmpdir => "/path/to/tmp",
  -email_address => "user@example.com",
  -email_type => "ALL",
  -files => ["file1.txt", "file2.txt"],
  -placeholder => "#FILE#"
);

This method creates a new NBI::Opts object with the specified options. The following parameters are supported:

  • -queue (string, optional)

    The SLURM queue to submit the job to. Default is "nbi-short".

  • -threads (integer, optional)

    The number of threads to allocate for the job. Default is 1.

  • -memory (string or integer, optional)

    The allocated memory for the job. It can be specified as a bare number representing megabytes (e.g., 1024), or with a unit suffix (e.g., "8GB"). Default is 100 megabytes.

  • -time (string or integer, optional)

    The time limit for the job. It can be specified as hours (e.g., 2) or as a string with time units (e.g., "2h", "1d 12h"). Default is 1 hour.

  • -opts (arrayref, optional)

    An array reference containing additional SLURM options to be passed to the job script.

  • -tmpdir (string, optional)

    The temporary directory to use for job execution. Default is the system's temporary directory.

  • -email_address (string, optional)

    The email address for job notifications.

  • -email_type (string, optional)

    The type of email notifications to receive (e.g., "NONE", "BEGIN", "END", "FAIL", "ALL"). Default is "NONE".

  • -files (arrayref, optional)

    An array reference containing input files or file patterns for the job.

  • -placeholder (string, optional)

    A placeholder string to be used in the command for input files. Default is "#FILE#".

queue

Accessor method for the SLURM queue.


            

              
              
$opts->queue = "long";
my $queue = $opts->queue;

threads

Accessor method for the number of threads.


            

              
              
$opts->threads = 8;
my $threads = $opts->threads;

memory

Accessor method for the allocated memory.


            

              
              
$opts->memory = "16GB";
my $memory = $opts->memory;

email_address

Accessor method for the email address.


            

              
              
$opts->email_address = "user@example.com";
my $email_address = $opts->email_address;

email_type

Accessor method for the email notification type.


            

              
              
$opts->email_type = "ALL";
my $email_type = $opts->email_type;

hours

Accessor method for the execution time in hours.


            

              
              
$opts->hours = 24;
my $hours = $opts->hours;

tmpdir

Accessor method for the temporary directory.


            

              
              
$opts->tmpdir = "/path/to/tmpdir";
my $tmpdir = $opts->tmpdir;

opts

Accessor method for the additional SLURM options.


            

              
              
$opts->opts = ["--output=TestJob.out", "--mail-user user@example.com"];
my $opts_array = $opts->opts;

files

Accessor method for the input files or file patterns.


            

              
              
$opts->files = ["file1.txt", "*.fasta"];
my $files = $opts->files;

placeholder

Accessor method for the input file placeholder.


            

              
              
$opts->placeholder = "{INPUT}";
my $placeholder = $opts->placeholder;

add_option

Add an additional SLURM option.


            

              
              
$opts->add_option("--output=TestJob.out");

opts_count

Get the number of additional SLURM options.


            

              
              
my $count = $opts->opts_count;

is_array

Check if the job is an array job (has multiple input files).


            

              
              
my $is_array = $opts->is_array;

view

Get a string representation of the options.


            

              
              
my $str = $opts->view;

Generate the SLURM header for the job script.


            

              
              
my $header = $opts->header;

timestring

Get the execution time as a formatted string.


            

              
              
my $timestring = $opts->timestring;

Returns the execution time in the format "DD-HH:MM:SS".

INTERNAL METHODS

_mem_parse_mb

Parse memory input and convert to megabytes.

_time_to_hour

Convert time input to hours.

AUTHOR

Andrea Telatin <proch@cpan.org>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2023-2025 by Andrea Telatin.

This is free software, licensed under:


            

              
              
The MIT (X11) License