1. write a short script to split the one file (containing the two columns) into two files( A1, A2) of one column each
2. use your native native sort utility on A1 and A2 to produce two files (B1, B2) containing only unique data
3. use your native diff utility to do the comparison between B1 and B2

The following makes no assumption about which of your input files has duplicates. It demonstrates the use of a hash of arrays to capture multiple values for each key. You may be able to adapt it to produce the results you need.

my %data;

foreach my $line (@ge_data) {
    my ($id, $rest) = split(/\s+/,$line,2);
    push(@{$data{$id}{ge_data}}, $rest);
}
foreach my $line (@file_data) {
    my ($id, $rest) = split(/\s+/,$line,2);
    push(@{$data{$id}{file_data}}, $rest);
}

foreach my $id (sort keys %data) {
    next unless(exists $data{$id}{ge_data});
    next unless(exists $data{$id}{file_data});
    print "$id:\n";
    print "\tge_data:\n";
    print "\t\t" . join("\t\t",@{$data{$id}{ge_data}});
    print "\tfile_data:\n";
    print "\t\t" . join("\t\t",@{$data{$id}{file_data}});
}
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Can you post some representative sample data please?

Although it sounds like you would be better off using a hash for lookups, rather than iterating a whole array for every line - see Tie::File::AsHash.
If you have multiple entries for a given id, you might be better rolling your own

I have posted some sample data.

The data still isn't really representative though is it!? :P

Just store the file with the single entries as a hash:

#!/usr/bin/perl
use strict;
use warnings;
my $first = "single_records.txt"; 
my $second = "multiple_records.txt";
warn "tie-ing $first...\n";
tie my %hsh, 'Tie::File::AsHash', $first, split => qr/\s+/
        or die "Problem tying %hash: $!";
open (my $fh, '<', $second) || die "Failed to open $second : $!" ## al
+ways check for success on fh
while (<$fh>){
  my $line = chomp($_);
  my ($id,) = split /\s+/, $line; ## capture id
  ## compare to tied hsh of single records
  if (exists$hsh{$id}){
    print "$line matched $id : $hsh{$id}\n";
  }
}
## tidy up
close $fh || die "Failed to close $second : $!";
untie %hsh;
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Or you can do the other thing i suggestted and hold an array ref of all the lines with a certain id, then print ot all the lines when you see the id in the single record file.

#!/usr/bin/perl
use strict;
use warnings;
my $first = "single_records.txt"; 
my $second = "multiple_records.txt";

open (my $fh, '<', $second) || die "Failed to open $second : $!" ## al
+ways check for success on fh
my %second_records = ();
while (<$fh>){
  my $line = $_;
  my ($id,) = split /\s+/, $line; ## capture id
  push @{ $second_records{$id} }, $line;
}
## tidy up
close $fh || die "Failed to close $second : $!";
## open single record file and compare
open ($fh, '<', $first) || die "Failed to open $first : $!";
while (<$fh>){
  my $line = chomp( $_ );
  my ($id,) = split /\s+/, $line; ## capture id
  if ( exists$second_records{$id} ){
    print (join '', "$line matches records:\n", @{ $second_records{$id
+} });
  }
}
close $fh || die "Failed to close $first : $!";
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Hope this helps.

Just a something something...

This snipplet just prints common keys in the two files file1.txt and file2.txt:

se strict;
use warnings;

sub get_file {
  open my $FILE, '<', shift or die $!;
  return map {chop; $_ => $_} <$FILE>;
}

my %a = get_file 'file1.txt';
my %b = get_file 'file2.txt';

{
  no warnings 'uninitialized';
  print "$_\n" for grep {$_} @a{keys %b};
}
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The above can easilly be done using sort, uniq and grep.

e.g. file1 contains column1, file2 contains column2 data, type the following on the command line.

sort file1 > file1.sorted
sort file2 > file2.sorted
comm -12 file1.sorted file2.sorted | sort | uniq > result.txt
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system ("sort file2 > file2.sorted");
system ("sort file1 > file1.sorted");
my $result = `comm -12 file1.sorted file2.sorted | sort | uniq`;
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