/ 
NBI-Slurm-0.1.1
River stage zero No dependents
/ NBI::Opts

NAME

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

VERSION

version 0.1.1

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 => 8,
 -opts => []
);

SYNOPSIS

SLURM Options for NBI::Slurm .

name

The actual sequence, the only mandatory field (string)

use NBI::Job;
my $opts = new(
   -queue => "short",
   -threads => 4,
   -memory => 8,
   -opts  => ["--output=TestJob.out", "--mail-user user@nmsu.edu"],
);

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, and more.

MAIN METHODS

new()

Create a new instance of NBI::Seq. The sequence is the only required field.

METHODS

new()

Create a new instance of CNBI::Opts.

my $opts = NBI::Opts->new(
  -queue => "short",
  -threads => 4,
  -memory => 8,
  -opts  => ["--option=Value"],
);

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. If not provided, the default queue will be used.

  • -threads (integer, optional)

    The number of threads to allocate for the job. If not provided, the default value is 1.

  • -memory (string or integer (Mb), 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., 1GB). If not provided, the default value is 100 megabytes.

  • -opts (arrayref, optional)

    An array reference containing additional SLURM options to be passed to the job script. Each option should be specified as a string. For example, ["--output=TestJob.out", "--mail-user user@nmsu.edu"]. If not provided, no additional options will be added.

    NOTE that some options are set by other methods (like output_file and email_address): do not specify them manually.

queue

Accessor method for the SLURM queue.

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

This method allows you to get or set the SLURM queue for the job. If called with an argument, it sets the queue to the specified value. If called without an argument, it returns the current queue value.

threads

Accessor method for the number of threads.

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

This method allows you to get or set the number of threads allocated for the job. If called with an argument, it sets the number of threads to the specified value. If called without an argument, it returns the current number of threads.

memory

Accessor method for the allocated memory.

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

This method allows you to get or set the allocated memory for the job. If called with an argument, it sets the memory to the specified value. If called without an argument, it returns the current allocated memory.

email_address

Accessor method for the email address.

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

This method allows you to get or set the email address to which job notifications will be sent. If called with an argument, it sets the email address to the specified value. If called without an argument, it returns the current email address.

email_type

Accessor method for the email type.

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

This method allows you to get or set the type of email notifications to receive. Possible values are "none" (no email notifications), "begin" (send email at the start of the job), "end" (send email at the end of the job), or "all" (send email for all job events). If called with an argument, it sets the email type to the specified value. If called without an argument, it returns the current email type.

hours

Accessor method for the execution time in hours.

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

This method allows you to get or set the execution time for the job in hours. If called with an argument, it sets the execution time to the specified value. If called without an argument, it returns the current execution time.

tmpdir

Accessor method for the temporary directory.

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

This method allows you to get or set the temporary directory path where temporary files for the job will be stored. If called with an argument, it sets the temporary directory to the specified value. If called without an argument, it returns the current temporary directory.

opts

Accessor method for the additional SLURM options.

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

This method allows you to get or set the additional SLURM options for the job. The options should be specified as an array reference, where each element is a string representing a single option. If called with an argument, it sets the additional options to the specified array reference. If called without an argument, it returns the current additional options.

add_option

Add an additional SLURM option.

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

This method allows you to add an additional SLURM option to the options list.

opts_count

Get the number of additional SLURM options.

my $count = $opts->opts_count;

This method returns the number of additional SLURM options specified for the job.

view

Get a string representation of the options.

my $str = $opts->view;

This method returns a string representation of the CNBI::Opts object, including all the options and their values.

Generate the SLURM header for the job script.

my $header = $opts->header;

This method generates the SLURM header for the job script based on the current options and returns it as a string.

timestring

Get the execution time as a formatted string.

my $timestring = $opts->timestring;

This method returns the execution time as a formatted string in the format "DD-HH:MM:SS", where "DD" is the number of days, "HH" is the number of hours (in 2 digits), "MM" is the number of minutes, and "SS" is the number of seconds.

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