Use a hash, with your numbers as keys. That way, grepping through the entire array would become a simple hash lookup.

#!/usr/bin/perl

my @array = map {int rand 1e6} 1..400000;

# create file with numbers to look up
open my $fh, ">", "in.txt" or die "$!";
for (1..1000000) {
    print $fh int rand 1e6, "\n";
}
close $fh;

my %lookup_table;
$lookup_table{$_}++ for @array;

open (in , "<", "in.txt") || die "$!";
while (<in>){
    my ($num) = m/^(\d+)/;
    print "$num, " if $lookup_table{$num};
} 
close in;

__END__
$ time ./757954.pl >out

real    0m4.141s
user    0m4.004s
sys     0m0.132s
[download]

(Memory requirement approx. 100 M — or 80 M, if you get rid of the map for the @array initialisation)

Update: with 300_000_000 rows, it takes about 15 min., which includes creating the 2 Gig random data file "in.txt" plus writing a 760 M output file. (Memory requirement is the same.)

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