instead of 
while(my ($key2,$value2)=each(%hash2)){
if($key1 eq $key2){

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try 
if(exists $hash2{$key1}){

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you can reduce some time.

UPDATE
is it a typing mistake 

open(FH,"file1.txt")or die "can not open file";
open(FH1,"file1.txt")or die "can not open file";

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opening the same file twice?!

since 

#push(@allhits,$key1);

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so 
foreach(@allhits){

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will iterate over nothing!.

moreover you have to read file1 again to get first column of file1 to be written into file2, so better change(going by your method) 

push(@file1,$list1[1]."#".$list1[2],$list1[4]);

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to 
push(@file1,$list1[1]."#".$list1[2],[$list1[4],$list1[0]]);
and in 
my @val1=split("/",$value1);
use 
my @val1=split("/",$value1->[0]);

and in 
#push(@allhits,$key1);
use 
push(@allhits,[$key1,$value1->[1]]);#(correction from 0 to 1)

and in 
my($id,$location)=split("#",$_);
use
my($id,$location)=split("#",$_[0]);

and in 
print "$_";.
use
print "@{$_}"; # to what you got to write.

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(Untested)

I agree with moritz on 

    while(my $str=<FH1>){

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so use seek to move file pointer to the beginning after while loop ends
Vivek
-- In accordance with the prarabdha of each, the One whose function it is to ordain makes each to act. What will not happen will never happen, whatever effort one may put forth. And what will happen will not fail to happen, however much one may seek to prevent it. This is certain. The part of wisdom therefore is to stay quiet.

In reply to Re: hash to hash comparison on large files by targetsmart
in thread hash to hash comparison on large files by patric

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