By does not work I presume you mean that your line counter increments ever upward. You just need to zero it after each file. This will work

#!/usr/bin/perl -w
 
use strict;
 
my $prefixDir = "$ENV{HOME}/sa/current";
my @clusterDirs= ("$prefixDir/cluster1", "$prefixDir/cluster2", "$pref
+ixDir/cluster3", "$prefixDir/cluster4", "$prefixDir/cluster5");
 
use vars qw ($configDir $configFile $lineCount $configFile $fileToComp
+are @configFileList);
 
foreach $configDir (@clusterDirs) {
  opendir DIR, "$configDir" or die "Cannot access $configDir: $!\n";
  @configFileList = grep /[^.]/, readdir DIR;print "$configDir\n";


foreach $fileToCompare (@configFileList) {

  $lineCount = 0; #zero our line count for each file

  open FILE, "$configDir/$fileToCompare" or die "file not available: $
+!\n";
  $lineCount++ while <FILE>;
print "file: $fileToCompare: $lineCount\n";
  }
}
[download]

I would recommend using my over use vars/our as my lexically scopes variables whereas vars and our generate globals. MJD has a great tute at http://perl.plover.com/FAQs/Namespaces.html

Here is a quick recode using my. No globals are required. I've also snipped a bit of redundant code.

my $prefixDir = "$ENV{HOME}/sa/current";
my @clusterDirs= qw(cluster1 cluster2 cluster3 cluster4 cluster5);
 
foreach my $configDir (@clusterDirs) {
    opendir DIR, "$prefixDir/$configDir" or die "Cannot access $prefix
+Dir/$configDir: $!\n";
    my @configFileList = grep /[^.]/, readdir DIR;
    print "$configDir\n";    
    foreach my $fileToCompare (@configFileList) {        
        my $lineCount = 0;        
        open FILE, "$prefixDir/$configDir/$fileToCompare" or die "file
+ not available: $!\n";
        $lineCount++ while <FILE>;
        close FILE;
        print "file: $fileToCompare: $lineCount\n";      
   }
}
[download]

In my opinion once variable names get too long they start to obfuscate the meaning of the code and are also more prone to typos. I try for 7 or less chars in a var name. I got a bit carried away and generated a 2D hash to store the results and then print the results in a formatted HTML table for easy comparison:

#!/usr/bin/perl -w
use strict;

my $base_dir = "$ENV{HOME}/sa/current";
my @sub_dir  = qw(cluster1 cluster2 cluster3 cluster4 cluster5);

my (%all_files, %file);
foreach my $sub_dir (@sub_dir) {
    opendir DIR, "$base_dir/$sub_dir" or die "Cannot access $base_dir/
+$sub_dir: $!\n";
    my @files = grep /[^.]/, readdir DIR;    
    foreach my $file (@files) {        
        my $line_count = 0;        
        open FILE, "$base_dir/$sub_dir/$file" or die "file not availab
+le: $!\n";
        $line_count++ while <FILE>;
        close FILE;
        $file{$sub_dir}{$file} = $line_count;
        $all_files{$file}++;      
   }
}

# print out a nice HTML table
print "<table border='2'>\n";
print "<tr>\n  <td>File name</td>\n";
print "  <td>$_</td>\n" for @sub_dir;
print "</tr>\n";
for my $file (keys %all_files) {
    print "<tr>\n";
    print "  <td>$file</td>\n";
    for my $sub_dir (@sub_dir) {
        # avoid undefined warnings if file does not exist
        # in one or more of our subdirs
        my $file_size = $file{$sub_dir}{$file} || "undef";
        print "  <td>$file_size</td>\n";
    }
    print "</tr>\n";
}
print "</table>\n";
[download]

Hope this helps. cheers

tachyon

s&&rsenoyhcatreve&&&s&n.+t&"$'$`$\"$\&"&ee&&y&srve&&d&&print