#!usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use File::Find::Rule;

# use Benchmark qw(:all) ; # WindowsOS
# use Benchmark::Forking qw( timethese cmpthese ); # LinuxOS

sub get_files {
    my @dirs = ('.');
    my $level = shift // 2;

    my @files = File::Find::Rule->file()
	->name('*.out')
	->maxdepth($level)
	->in(@dirs);

    return @files;
}

my @files = get_files();

# print Dumper \@files if @files;

# open files and load them into an array

my %HoA;
foreach my $path_to_file (@files) {
    open my $fh, '<', $path_to_file;
    chomp(my @lines = <$fh>);
    splice @lines, 1, 1;
    $HoA{$path_to_file} = \@lines;
    close $fh;
}

print Dumper \%HoA;

__END__

$ perl test.pl
$VAR1 = {
          'mySubDir/molec1-cluster2.out' => [
                                              'This is a sample line 1 file 2',
                                              'This is a sample line 3 file 2'
                                            ],
          'mySubDir/molec1-cluster1.out' => [
                                              'This is a sample line 1 file 1',
                                              'This is a sample line 3 file 1'
                                            ]
        };

# file 1
$ cat mySubDir/molec1-cluster1.out
This is a sample line 1 file 1
This is a sample line 2 (to be skipped) file 1
This is a sample line 3 file 1

# file 2
$ cat mySubDir/molec1-cluster2.out
This is a sample line 1 file 2
This is a sample line 2 (to be skipped) file 2
This is a sample line 3 file 2