Here's how I'd do it (for clarity, this was basically suggested in the first reply) - code untested :

use strict;
use warnings;
use Tie::Hash::Indexed;
tie my %lines1, 'Tie::Hash::Indexed';    # gives you the ordered hash

open my $IN1, '<', "tmp12"           or die "Cannot open this file: $!
+";
open my $IN2, '<', "donor_82_01.csv" or die "Cannot open this file: $?
+";

# step 1, cache contents of $IN1 (read the first file once)

# populate %lines1 "cache"
for my $item1 (<$IN1>) {
    @tmp1 = split( /\t+/, $item1 );
    $lines1{ $tmp[1] } = \@tmp1;    # save full $item1 line, keyed on 
+$tmp[1]
}   

# step 2, iterate over contents of $IN2 / look up in %lines1 to compar
+e

open my $OUT, '>', "tmp12_01" or die "Cannot open this file: $?";
LOOKUP_AND_COMPARE:
for $item2 (@lines2) {
    
    #chomp $item2;       # not needed, see last line
    my @tmp2 = split( /\,+/, $item2 );
    
    # -- look up 
    if ( 'ARRAY' eq $lines1{ $tmp2[0] } ) {
        my @tmp1 = @{ $lines1{ $tmp2[0] } };    # for clarity, not act
+ually needed; can get value via "$lines1{ $tmp2[0] }->[0]"
        print $OUT $tmp1[0], ",", $item2;            #<-updated to fix
+ bareword from old code
        last LOOKUP_AND_COMPARE;
    }
}

#print $OUT "\n";        # probably don't need if you don't "chomp $it
+em2"
[download]

Additional optimizations, depending on your constraint (timeversus space):

• if time, cache the larger of the 2 files
• if space, cache the smaller of the 2 files

The lesson here, as stated below is to not nest your loops. It's called "computational complexity". Basically only want to have at most 1 level of looping. The line, if ( 'ARRAY' eq $lines1{ $tmp2[0] } ) { is the "constant time" look up capability that is being provided for by the ordered caching of the first file above and how you avoid the inner loop.

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