NAME
NBI::Opts - A class for representing a the SLURM options for NBI::Slurm
VERSION
version 0.9.0
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;header
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 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) License