I have got familiar with Devel::NYTProf and it gave a response, that function initDefinesList() is bottleneck. I have isolated it into script below and started further checks. I copied whole function body to the script body and it took only 1s to run. Copied it back to the function - 30s. NYTprof showed, that push @$rresult_list, ... line is consuming 29 out of total 30s, so I commented it out. One more run, and surprisingly my $balloon = genDivBalloon(...) line indicated as guilty. So I removed everything inside while($str =~ /.../) loop and according to next report now this regexp consumes all the time. I have written simple one liner with $str filled and while loop and it takes less than second... Another one liner producing huge hash of hashes - run in miliseconds. So every piece of code separately is running in a blink of eye, together it forms a tortoise.

In __DATA__ section I added few example defines just to show you how it looks like.

Has someone an idea what can be wrong and where?

#!perl

use 5.10.0;
use re 'eval';

use strict;
use warnings;

use HTML::Entities qw/encode_entities decode_entities/;
use DefineAnalyser;

our $parens;
$parens = qr{
        (?:
            (?: [^()](?!<_MY_STRING_TO_REPLACE>) )+
            |
            \( (??{$parens}) \)
        )*
    }x;

sub initDefinesList
{
    my %args = @_;
    my $filename = $args{-filename};
    my $rresult_list;

#     if(!open FH, $filename)
#     {
#         print STDERR "Couldn't open define base($filename): ", $!;
#         return ();
#     }
#     
#     my $str = join"", <FH>;
#     close FH;
    my $str = "#define abc(def) /*sourcepath: abc.h*/\\\n def*2+5\n"x 
+10000;
    my $begintime=time;
    print STDERR "begin:", $begintime, "\n";
    
    while($str =~ /\#define  \s+  (?<n>\w+)   (?<p>\([^)]*\))?    (?<c
+>(.*\\\n)*.*\n)/gx)
    {
        my ($name, $params, $content) = ($+{n}, $+{p}, $+{c});
        if(!defined($params))
            { $params='' }
        $content =~ s/\\\n/\n/g;
        $content =~ s/^\s+//;
        $content =~ s/\s+$//;
        $content =~ s!(/\*sourcepath: .*?\*/)!!;
        my $source = $1;
        my @params = $params=~/\w+/g;
        my $macro_def = $name;
        my $pattern = "\\b$name\\b";
        if(@params>0)
        {
            $macro_def .= '('.join(', ', @params).')';
            $pattern .= qr{\((?<p>$parens)\)};
        }
        else
        {
            $pattern .= qr{(\(\s*\))?};
        }
        my $balloon = genDivBalloon(
                -divid => $name,
                -sourcefilename => $source,
                -macrodefinition => $macro_def,
                -balloontext => $content
            );
        
        push @$rresult_list,
            {
                source=>$source,
                name=>$name,
                params=>[@params],
                content=>$content,
                macro_def => $macro_def,
                pattern => $pattern,
                balloon => $balloon
            };
    }
    my $endtime=time;
    print STDERR "end:", $endtime, "\n";
    print STDERR "total time: ", $endtime-$begintime, "\n";
    return $rresult_list
}

sub genDivBalloon
{
    my %args = @_;
    my ($divid, $sourcefilename, $macro_def, $balloontext) = @args{-di
+vid, -sourcefilename, -macrodefinition, -balloontext};
    
    if(!defined $divid)
        { say STDERR "divid not defined" }
    if(!defined $sourcefilename)
        { say STDERR "$divid: sourcefilename not defined" }
    if(!defined $macro_def)
        { say STDERR "$divid: macro_def not defined" }
    if(!defined $balloontext)
        { say STDERR "$divid: balloontext not defined" }
    
    return "<div id=\"$divid\" class=\"balloonstyle\">"
                . encode_entities($sourcefilename)
                . "<BR />#define <b>" . $macro_def . "</b> <pre>"
                . encode_entities($balloontext)
                . "</pre></div>";
}    

initDefinesList(-filename => 'all_defines_tidy.txt');

__DATA__
#define _APS_NEXT_COMMAND_VALUE         32768  /*sourcepath: ./src/Res
+ource.h*/
#define _APS_NEXT_CONTROL_VALUE         201  /*sourcepath: ./src/Resou
+rce.h*/
#define COUNT_STR_LEN_FROM_BSRELAYDATA(start, count)   /*sourcepath: .
+/src/ImplXX.cpp*/\
    count = 0; \
    for (i = start; i < bsRelayData.data.length && \
                    i < bsRelayData.data.MAX_LENGTH_C && \
                    bsRelayData.data.user_data[i] != 0; i++) \
    { \
        count++; \
    } \
    dwCountStart += count+1;
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