Update: Do not run the in-memory demo below. Unfortunately, each worker makes a copy. Another possibility, on Linux platforms, is taking the prior demonstration and opening the Kyoto DB file in /dev/shm. Follow-up: From testing, storing in /dev/shm is not necessary. The Linux OS typically caches the entire file into memory, if available. Subsequent scans pull from the file system cache. For extra performance, see the parallel chunking demonstration on the same page.

# open the database
if (! $db->open('/dev/shm/db.kch#msiz=128m', $db->OREADER)) {
    die "open error (db): ", $db->error;
}

[download]

Yes, of course ++ when data fits in-memory. The following constructs an in-memory DB. Combine the script in Part Three with Part Four or Part Five.

# https://www.perlmonks.org/?node_id=11110379
# usage: perl search_in_memory.pl > Outfile.txt

use strict;
use warnings;
use KyotoCabinet;
use MCE;

###########################################################
# Part Three
###########################################################

# construct the database object
my $db = KyotoCabinet::DB->new();

# open the database - in memory (i.e. *)
if (! $db->open('*#msiz=128m', $db->OREADER | $db->OWRITER | $db->OCRE
+ATE)) {
    die "open error (db): ", $db->error;
}

open my $fh, '<', 'NR.fasta' or die "open error: $!\n";

my $nrid = '';
my $seq  = '';

while ( <$fh> ) {
    chomp; $_ =~ s/\r$//g;
    if ( /^>/ ) {
        $db->set($nrid, $seq) if $seq;
        $nrid = ( split /\s/, $_, 2 )[0];
        $seq  = '';
    }
    else {
        $seq .= $_;
    }
}

$db->set($nrid, $seq) if $seq;

close $fh;

###########################################################
# Part Five
###########################################################

my $cur;

my $mce = MCE->new(
    max_workers => MCE::Util::get_ncpu(),
    chunk_size  => 1,
    init_relay  => 1,

    user_begin => sub {
        $cur = $db->cursor;
    },

    user_end => sub {
        $cur->disable;
    },

    user_func => sub {
        my $pep = $_; chomp $pep;
        my $ids = '';

        $cur->jump; # first record
        while ( my ($key, $val) = $cur->get(1) ) {
            $ids .= ",$key" if index($val, $pep) >= 0;
        }
    
        # output serially, one worker at a time
        MCE::relay {
            print "$pep\t", substr($ids, 1), "\n" if $ids;
        };
    }
);

$mce->process('peptides.txt');
$mce->shutdown;

$db->close;

[download]

Regards, Mario

In reply to Re^3: Problem in RAM usage while threading the program by marioroy
in thread Problem in RAM usage while threading the program by beherasan

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