slow regex [BENCHMARK]
hi. i'm running mod_perl 1.26 + apache 1.3.14 + perl 5.6.1
i have a loop in a mod_perl handler like so:
my $stime = time ();
while ($seq =~ /CG/og)
{
push @cg, pos ($seq);
}
my $etime = time ();
warn "time was: ", scalar localtime ($stime), " ",
scalar localtime ($etime), " ", $etime - $stime;
under mod_perl this takes 23 seconds. running the perl "by hand" (via
extracting this piece into a seperate perl script) on the same data takes
less than 1 second.
has anyone seen this kind of extreme slowdown before?
-- p
info:
apache build options:
CFLAGS="-g -g -O3 -funroll-loops" \
LDFLAGS="-L/home/aerives/lib -L/home/aerives/lib/mysql" \
LIBS="-L/home/aerives/genegrokker-interface/lib
-L/home/aerives/genegrokker-interface/ext/lib -L/home/aerives/lib
-L/home/aerives/lib/mysql" \
./configure \
"--prefix=/home/aerives/genegrokker-interface/ext" \
"--enable-rule=EAPI" \
"--enable-module=most" \
"--enable-shared=max" \
"--with-layout=GNU" \
"--disable-rule=EXPAT" \
"$@"
mod_perl build options:
configure_options="PERL_USELARGEFILES=0 USE_APXS=1
WITH_APXS=$PLAYPEN_ROOT/ext/sbin/apxs EVERYTHING=1
INC=$PLAYPEN_ROOT/ext/include -DEAPI"
perl -V:
Summary of my perl5 (revision 5.0 version 6 subversion 1) configuration:
Platform:
osname=linux, osvers=2.4.13, archname=i386-linux
uname='linux duende 2.4.13 #1 wed oct 31 19:18:07 est 2001 i686 unknown '
config_args='-Dccflags=-DDEBIAN -Dcccdlflags=-fPIC -Darchname=i386-linux
-Dprefix=/usr -Dprivlib=/usr/share/perl/5.6.1 -Darchlib=/usr/lib/perl/5.6.1
-Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/perl5
-Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.6.1
-Dsitearch=/usr/local/lib/perl/5.6.1 -Dman1dir=/usr/share/man/man1
-Dman3dir=/usr/share/man/man3 -Dman1ext=1 -Dman3ext=3perl
-Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Uusesfio -Duseshrplib
-Dlibperl=libperl.so.5.6.1 -Dd_dosuid -des'
hint=recommended, useposix=true, d_sigaction=define
usethreads=undef use5005threads=undef useithreads=undef
usemultiplicity=undef
useperlio=undef d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=undef use64bitall=undef uselongdouble=undef
Compiler:
cc='cc', ccflags ='-DDEBIAN -fno-strict-aliasing -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-DDEBIAN -fno-strict-aliasing -I/usr/local/include'
ccversion='', gccversion='2.95.4 (Debian prerelease)', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
lseeksize=8
alignbytes=4, usemymalloc=n, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -L/usr/local/lib'
libpth=/usr/local/lib /lib /usr/lib
libs=-lgdbm -ldb -ldl -lm -lc -lcrypt
perllibs=-ldl -lm -lc -lcrypt
libc=/lib/libc-2.2.4.so, so=so, useshrplib=true, libperl=libperl.so.5.6.1
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic'
cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib'
Characteristics of this binary (from libperl):
Compile-time options: USE_LARGE_FILES
Built under linux
Compiled at Jan 11 2002 04:09:18
%ENV:
PERL5LIB="/home/aerives/genegrokker-interface/lib/perl5:/home/aerives/genegrokker-interface/ext/lib/perl5:/home/aerives/lib/perl5"
@INC:
/home/aerives/genegrokker-interface/lib/perl5
/home/aerives/genegrokker-interface/ext/lib/perl5
/home/aerives/lib/perl5
/usr/local/lib/perl/5.6.1
/usr/local/share/perl/5.6.1
/usr/lib/perl5
/usr/share/perl5
/usr/lib/perl/5.6.1
/usr/share/perl/5.6.1
/usr/local/lib/site_perl
Re: slow regex [BENCHMARK]
Paul Mineiro wrote:
> hi. i'm running mod_perl 1.26 + apache 1.3.14 + perl 5.6.1
>
> i have a loop in a mod_perl handler like so:
>
> my $stime = time ();
>
> while ($seq =~ /CG/og)
> {
> push @cg, pos ($seq);
> }
>
> my $etime = time ();
>
> warn "time was: ", scalar localtime ($stime), " ",
> scalar localtime ($etime), " ", $etime - $stime;
>
>
> under mod_perl this takes 23 seconds. running the perl "by hand" (via
> extracting this piece into a seperate perl script) on the same data takes
> less than 1 second.
>
> has anyone seen this kind of extreme slowdown before?
Paul,
Your benchmark is wrong. You cannot benchmark code using wallclocks
unless you run on DOS-like system. On multi-processes systems many
processes compete over CPU, so each process gets a little bit of CPU
time every so often, so if you count wallclocks you don't count the
execution time of your program but of all programs that happen to run at
the same time.
To count CPU clocks use Benchmark.pm, it has a fine documentation and
examples so I won't repeat them here. Please fix your benchmark and run
it again.
Also you may want to check certain sections in
http://perl.apache.org/guide/performance.html
_
Stas Bekman JAm_pH -- Just Another mod_perl Hacker
http://stason.org/ mod_perl Guide http://perl.apache.org/guide
mailto:[EMAIL PROTECTED] http://ticketmaster.com http://apacheweek.com
http://singlesheaven.com http://perl.apache.org http://perlmonth.com/
Re: slow regex [BENCHMARK]
> under mod_perl this takes 23 seconds. running the perl "by hand" (via > extracting this piece into a seperate perl script) on the same data takes > less than 1 second. Are you sure that the string you're regex'ing is the same in both cases? Why are you using the /o operator? CG isn't a variable, is it? - Perrin
Re: slow regex [BENCHMARK]
Paul Mineiro wrote:
i've cleaned up the example to tighten the case:
the mod perl code snippet is:
---
my @cg;
open DIL, '>', "/tmp/seqdata";
print DIL $seq;
close DIL;
warn "length seq = @{[length ($seq)]}";
my $t = timeit (1, sub {
while ($seq =~ /CG/g)
{
push @cg, pos ($seq);
}
});
print STDERR timestr ($t), "\n";
---
which yields
length seq = 21 at
/home/aerives/genegrokker-interface/mod_perl/genomic_img.pm line 634,
line 102
16 wallclock secs (15.56 usr + 0.01 sys = 15.57 CPU) @ 0.06/s (n=1)
and the perl script (command line) version is:
---
#!/usr/bin/perl
use Benchmark;
use strict;
open DIL, '<', "/tmp/seqdata";
my $seq = ;
close DIL;
warn "length seq is @{[length $seq]}";
my @cg;
my $t = timeit (1, sub {
while ($seq =~ /CG/g)
{
push @cg, pos ($seq);
}
});
print STDERR timestr ($t), "\n";
---
which yields:
length seq is 21 at ./t.pl line 10.
0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
the data is pretty big, so i didn't attach it, but feel free to contact
me directly for it.
-- p
>hi. i'm running mod_perl 1.26 + apache 1.3.14 + perl 5.6.1
>
>i have a loop in a mod_perl handler like so:
>
> my $stime = time ();
>
> while ($seq =~ /CG/og)
>{
> push @cg, pos ($seq);
>}
>
> my $etime = time ();
>
> warn "time was: ", scalar localtime ($stime), " ",
>scalar localtime ($etime), " ", $etime - $stime;
>
>
>under mod_perl this takes 23 seconds. running the perl "by hand" (via
>extracting this piece into a seperate perl script) on the same data takes
>less than 1 second.
>
>has anyone seen this kind of extreme slowdown before?
>
>-- p
>
>info:
>
>apache build options:
>
>CFLAGS="-g -g -O3 -funroll-loops" \
>LDFLAGS="-L/home/aerives/lib -L/home/aerives/lib/mysql" \
>LIBS="-L/home/aerives/genegrokker-interface/lib
>-L/home/aerives/genegrokker-interface/ext/lib -L/home/aerives/lib
>-L/home/aerives/lib/mysql" \
>./configure \
>"--prefix=/home/aerives/genegrokker-interface/ext" \
>"--enable-rule=EAPI" \
>"--enable-module=most" \
>"--enable-shared=max" \
>"--with-layout=GNU" \
>"--disable-rule=EXPAT" \
>"$@"
>
>mod_perl build options:
>
>configure_options="PERL_USELARGEFILES=0 USE_APXS=1
>WITH_APXS=$PLAYPEN_ROOT/ext/sbin/apxs EVERYTHING=1
>INC=$PLAYPEN_ROOT/ext/include -DEAPI"
>
>perl -V:
>Summary of my perl5 (revision 5.0 version 6 subversion 1) configuration:
> Platform:
>osname=linux, osvers=2.4.13, archname=i386-linux
>uname='linux duende 2.4.13 #1 wed oct 31 19:18:07 est 2001 i686 unknown '
>config_args='-Dccflags=-DDEBIAN -Dcccdlflags=-fPIC -Darchname=i386-linux
>-Dprefix=/usr -Dprivlib=/usr/share/perl/5.6.1 -Darchlib=/usr/lib/perl/5.6.1
>-Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/perl5
>-Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.6.1
>-Dsitearch=/usr/local/lib/perl/5.6.1 -Dman1dir=/usr/share/man/man1
>-Dman3dir=/usr/share/man/man3 -Dman1ext=1 -Dman3ext=3perl
>-Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Uusesfio -Duseshrplib
>-Dlibperl=libperl.so.5.6.1 -Dd_dosuid -des'
>hint=recommended, useposix=true, d_sigaction=define
>usethreads=undef use5005threads=undef useithreads=undef
>usemultiplicity=undef
>useperlio=undef d_sfio=undef uselargefiles=define usesocks=undef
>use64bitint=undef use64bitall=undef uselongdouble=undef
> Compiler:
>cc='cc', ccflags ='-DDEBIAN -fno-strict-aliasing -I/usr/local/include
>-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
>optimize='-O2',
>cppflags='-DDEBIAN -fno-strict-aliasing -I/usr/local/include'
>ccversion='', gccversion='2.95.4 (Debian prerelease)', gccosandvers=''
>intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
>d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
>ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
>lseeksize=8
>alignbytes=4, usemymalloc=n, prototype=define
> Linker and Libraries:
>ld='cc', ldflags =' -L/usr/local/lib'
>libpth=/usr/local/lib /lib /usr/lib
>libs=-lgdbm -ldb -ldl -lm -lc -lcrypt
>perllibs=-ldl -lm -lc -lcrypt
>libc=/lib/libc-2.2.4.so, so=so, useshrplib=true, libperl=libperl.so.5.6.1
> Dynamic Linking:
>dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic'
>cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib'
>
>
>Characteristics of this binary (from libperl):
> Compile-time options: USE_LARGE_FILES
> Built under linux
> Compiled at Jan 11 2002 04:09:18
> %ENV:
>
>PERL5LIB="/home/aerives/genegrokker-interface/lib/perl5:/home/aerives/genegrokker-interface/ext/lib/perl5:/home/aerives/lib/perl5"
> @INC:
>/home/aerives/genegrokker-interface/lib/perl5
>/home/aerives/genegrokker
Re: slow regex [BENCHMARK]
On Wed, 23 Jan 2002, Paul Mineiro wrote: > i've cleaned up the example to tighten the case: > > the mod perl code snippet is: Fascinating. The only thing I don't see is where $seq gets assigned to in the CGI case. Where is the data coming from? Is it perhaps a tied variable or otherwise unlike the $seq in the command-line version? If that's not it then I think you might have to build a debugging version of Apache and Perl and break out GDB to get to the bottom of things. -sam
Re: slow regex [BENCHMARK]
At 4:01 PM -0800 1/23/02, Paul Mineiro wrote:
>Paul Mineiro wrote:
>
>i've cleaned up the example to tighten the case:
>
>the mod perl code snippet is:
>
>---
>
> my @cg;
> open DIL, '>', "/tmp/seqdata";
> print DIL $seq;
> close DIL;
> warn "length seq = @{[length ($seq)]}";
> my $t = timeit (1, sub {
> while ($seq =~ /CG/g)
> {
> push @cg, pos ($seq);
> }
>});
> print STDERR timestr ($t), "\n";
I just ran this on my system here... It's completely unloaded (load
average: 0.11, 0.08, 0.02)
Result:
0 wallclock secs ( 0.06 usr + 0.00 sys = 0.06 CPU) @ 16.67/s (n=1)
I ran it on a file that I created with
perl -e "print 'ABCGEFSK' x 25000" > /tmp/seqdata
Which created 25000 entires into @cg.
Your system has to be swapping horribly. I bet that the ulimit for
whoever apache is running as has the memory segment set super low.
Double check everything and if that doesn't work, recompile.
Rob
--
When I used a Mac, they laughed because I had no command prompt. When
I used Linux, they laughed because I had no GUI.
Re: slow regex [BENCHMARK]
> Your system has to be swapping horribly. I bet that the ulimit for > whoever apache is running as has the memory segment set super low. That's a possibility. I was also thinking that maybe mod_perl was built against a different version of Perl, possibly one that has a problem with this particular regex which was fixed in a later version. - Perrin
Re: slow regex [BENCHMARK]
Perrin Harkins wrote: >>Your system has to be swapping horribly. I bet that the ulimit for >>whoever apache is running as has the memory segment set super low. >> apache is running as me on my unloaded desktop (no way this is going to production until i figure this out). my ulimit -v is unlimited. > >That's a possibility. I was also thinking that maybe mod_perl was built >against a different version of Perl, possibly one that has a problem >with this particular regex which was fixed in a later version. > both mod_perl and the script are using the debian packaged perl/libperl, the perl -V dump was given in the initial message. oh, and $seq is a normal scalar, not a tied one. -- p
Re: slow regex [BENCHMARK]
Robert Landrum wrote: > > I just ran this on my system here... It's completely unloaded (load > average: 0.11, 0.08, 0.02) > > Result: > > 0 wallclock secs ( 0.06 usr + 0.00 sys = 0.06 CPU) @ 16.67/s (n=1) > > > I ran it on a file that I created with > > perl -e "print 'ABCGEFSK' x 25000" > /tmp/seqdata right. i probably should've mentioned earlier that "CGAT" x 5 is really fast in both mod_perl and command line. if anybody wants my actual $seq data, please let me know. -- p
Re: slow regex [BENCHMARK]
I recently had a similar problem. A regex that worked fine in sample code
was a dog in the web-server code. It only happened with really long strings.
I tracked down the problem to this from the 'perlre' manpage.
WARNING: Once Perl sees that you need one of "$&", "$`", or "$'"
anywhere in the program, it
has to provide them for every pattern match. This may substantially
slow your program. Perl
uses the same mechanism to produce $1, $2, etc, so you also pay a
price for each pattern that
contains capturing parentheses. (To avoid this cost while retaining
the grouping behaviour,
use the extended regular expression "(?: ... )" instead.) But if you
never use "$&", "$`" or
"$'", then patterns without capturing parentheses will not be
penalized. So avoid "$&",
"$'", and "$`" if you can, but if you can't (and some algorithms
really appreciate them),
once you've used them once, use them at will, because you've already
paid the price. As of
5.005, "$&" is not so costly as the other two.
Basically one of the modules in the web-app I was 'use'ing needed $', but my
test code didn't 'use' that module. The result was pretty dramatic in this
case, something that took approx 1 second in the test code was timing out
after 2 minutes in the web-server.
What I did in the end was something like this:
In the code somewhere add this so it's run when a request hits.
open(F, '>/tmp/modulelist');
print F join("\n", values %INC), "\n";
close(F);
This creates a file which lists all the loaded modules. Then after sticking
a request through the browser, do something like:
grep \$\' `cat /tmp/modulelist`
grep \$\& `cat /tmp/modulelist`
grep \$\` `cat /tmp/modulelist`
to try and track down the offending module. You'll get quite a few false
hits (comments, etc), but you might find an offending module. The main ones
I found were:
Parse::RecDescent
Net::DNS
and a couple of others I can't remember now. I fixed Net::DNS myself and
sent a patch to the maintainer, but haven't heard anything. If you find this
happens to be your problem as well, ask me for the patched version.
Parse::RecDescent makes heavy use of the above vars, no chance of fixing
that in a hurry.
Rob
- Original Message -
From: "Paul Mineiro" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
Sent: Thursday, January 24, 2002 11:01 AM
Subject: Re: slow regex [BENCHMARK]
> Paul Mineiro wrote:
>
> i've cleaned up the example to tighten the case:
>
> the mod perl code snippet is:
>
> ---
>
> my @cg;
>
> open DIL, '>', "/tmp/seqdata";
> print DIL $seq;
> close DIL;
>
> warn "length seq = @{[length ($seq)]}";
>
> my $t = timeit (1, sub {
> while ($seq =~ /CG/g)
> {
> push @cg, pos ($seq);
> }
> });
>
> print STDERR timestr ($t), "\n";
>
> ---
>
> which yields
> length seq = 21 at
> /home/aerives/genegrokker-interface/mod_perl/genomic_img.pm line 634,
> line 102
> 16 wallclock secs (15.56 usr + 0.01 sys = 15.57 CPU) @ 0.06/s (n=1)
>
> and the perl script (command line) version is:
>
> ---
>
> #!/usr/bin/perl
>
> use Benchmark;
> use strict;
>
> open DIL, '<', "/tmp/seqdata";
> my $seq = ;
> close DIL;
>
> warn "length seq is @{[length $seq]}";
>
> my @cg;
>
> my $t = timeit (1, sub {
> while ($seq =~ /CG/g)
> {
> push @cg, pos ($seq);
> }
>});
>
> print STDERR timestr ($t), "\n";
>
> ---
> which yields:
>
> length seq is 21 at ./t.pl line 10.
> 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
>
> the data is pretty big, so i didn't attach it, but feel free to contact
> me directly for it.
>
> -- p
>
> >hi. i'm running mod_perl 1.26 + apache 1.3.14 + perl 5.6.1
> >
> >i have a loop in a mod_perl handler like so:
> >
> > my $stime = time ();
> >
> > while ($seq =~ /CG/og)
> >{
> > push @cg, pos ($seq);
> >}
> >
> > my $etime = time ();
> >
> > warn "time was: ", scalar localtime ($stime), " ",
> >scalar localtime ($etime), " ", $etime - $stime;
> >
> >
> >under mod_perl t
Re: slow regex [BENCHMARK]
Rob Mueller (fastmail) wrote:
> I recently had a similar problem. A regex that worked fine in sample code
> was a dog in the web-server code. It only happened with really long strings.
> I tracked down the problem to this from the 'perlre' manpage.
>
>WARNING: Once Perl sees that you need one of "$&", "$`", or "$'"
> anywhere in the program, it
>has to provide them for every pattern match. This may substantially
> slow your program. Perl
>uses the same mechanism to produce $1, $2, etc, so you also pay a
> price for each pattern that
>contains capturing parentheses. (To avoid this cost while retaining
> the grouping behaviour,
>use the extended regular expression "(?: ... )" instead.) But if you
> never use "$&", "$`" or
>"$'", then patterns without capturing parentheses will not be
> penalized. So avoid "$&",
>"$'", and "$`" if you can, but if you can't (and some algorithms
> really appreciate them),
>once you've used them once, use them at will, because you've already
> paid the price. As of
>5.005, "$&" is not so costly as the other two.
>
> Basically one of the modules in the web-app I was 'use'ing needed $', but my
> test code didn't 'use' that module. The result was pretty dramatic in this
> case, something that took approx 1 second in the test code was timing out
> after 2 minutes in the web-server.
>
> What I did in the end was something like this:
>
> In the code somewhere add this so it's run when a request hits.
>
> open(F, '>/tmp/modulelist');
> print F join("\n", values %INC), "\n";
> close(F);
>
> This creates a file which lists all the loaded modules. Then after sticking
> a request through the browser, do something like:
>
> grep \$\' `cat /tmp/modulelist`
> grep \$\& `cat /tmp/modulelist`
> grep \$\` `cat /tmp/modulelist`
>
> to try and track down the offending module. You'll get quite a few false
> hits (comments, etc), but you might find an offending module. The main ones
Also check Devel::FindAmpersand and Devel::SawAmpersand.
cpan> i /ampersand/
DistributionA/AN/ANDK/Devel-SawAmpersand-0.20.tar.gz
Module Apache::SawAmpersand (Contact Author The Perl/Apache
Mailing List <[EMAIL PROTECTED]>)
Module B::FindAmpersand (A/AN/ANDK/Devel-SawAmpersand-0.20.tar.gz)
Module Devel::FindAmpersand
(A/AN/ANDK/Devel-SawAmpersand-0.20.tar.gz)
Module Devel::SawAmpersand
(A/AN/ANDK/Devel-SawAmpersand-0.20.tar.gz)
5 items found
The Devel::SawAmpersand also explains a workaround for using &.
_
Stas Bekman JAm_pH -- Just Another mod_perl Hacker
http://stason.org/ mod_perl Guide http://perl.apache.org/guide
mailto:[EMAIL PROTECTED] http://ticketmaster.com http://apacheweek.com
http://singlesheaven.com http://perl.apache.org http://perlmonth.com/
Re: slow regex [BENCHMARK]
Paul Mineiro wrote: > > right. i probably should've mentioned earlier that "CGAT" x 5 is > really fast in both mod_perl and command line. > > if anybody wants my actual $seq data, please let me know. i neglected to mention something big: the production version is identical but using perl 5.005 and it doesn't have this problem. perl -V of the production perl follows. thanks, -- p Summary of my perl5 (5.0 patchlevel 5 subversion 3) configuration: Platform: osname=linux, osvers=2.4.4-xfs, archname=i686-linux uname='linux rock.codegrok.lab 2.4.4-xfs #8 smp wed may 30 17:37:44 pdt 2001 i686 unknown ' hint=recommended, useposix=true, d_sigaction=define usethreads=undef useperlio=undef d_sfio=undef Compiler: cc='cc', optimize='-O2', gccversion=2.95.4 20010319 (Debian prerelease) cppflags='-Dbool=char -DHAS_BOOL -I/usr/local/include' ccflags ='-Dbool=char -DHAS_BOOL -I/usr/local/include' stdchar='char', d_stdstdio=undef, usevfork=false intsize=4, longsize=4, ptrsize=4, doublesize=8 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12 alignbytes=4, usemymalloc=n, prototype=define Linker and Libraries: ld='cc', ldflags =' -L/usr/local/lib' libpth=/usr/local/lib /lib /usr/lib libs=-lnsl -lgdbm -ldbm -ldb -ldl -lm -lc -lcrypt libc=, so=so, useshrplib=false, libperl=libperl.a Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic' cccdlflags='-fpic', lddlflags='-shared -L/usr/local/lib' Characteristics of this binary (from libperl): Built under linux Compiled at Oct 30 2001 10:33:04 %ENV: PERL5LIB="/home/codegrok/genegrokker-interface/lib/perl5:/home/codegrok/genegrokker-interface/ext/lib/perl5" @INC: /home/codegrok/genegrokker-interface/lib/perl5 /home/codegrok/genegrokker-interface/ext/lib/perl5 /home/codegrok/genegrokker-interface/ext/lib/perl5/5.00503/i686-linux /home/codegrok/genegrokker-interface/ext/lib/perl5/5.00503 /home/codegrok/genegrokker-interface/ext/lib/perl5/site_perl/5.005/i686-linux /home/codegrok/genegrokker-interface/ext/lib/perl5/site_perl/5.005 .
Re: slow regex [BENCHMARK]
Rob Mueller (fastmail) wrote:
>I recently had a similar problem. A regex that worked fine in sample code
>was a dog in the web-server code. It only happened with really long strings.
>I tracked down the problem to this from the 'perlre' manpage.
>
> WARNING: Once Perl sees that you need one of "$&", "$`", or "$'"
>anywhere in the program, it
>
>
>What I did in the end was something like this:
>
>In the code somewhere add this so it's run when a request hits.
>
>open(F, '>/tmp/modulelist');
>print F join("\n", values %INC), "\n";
>close(F);
>
>This creates a file which lists all the loaded modules. Then after sticking
>a request through the browser, do something like:
>
>grep \$\' `cat /tmp/modulelist`
>grep \$\& `cat /tmp/modulelist`
>grep \$\` `cat /tmp/modulelist`
>
>to try and track down the offending module.
>
well, the good (bad?) news is, none of the modules in the module list
have the expensive regex variables in them.
i've attached the module list, in case it is of interest.
thanks,
-- p
/home/aerives/genegrokker-interface/lib/perl/Keys.pm
/usr/share/perl/5.6.1/Carp.pm
/usr/share/perl/5.6.1/unicode/To/Upper.pl
/home/aerives/genegrokker-interface/lib/perl/PrimerFunctions.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/auto/Storable/autosplit.ix
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/Common.pm
/usr/share/perl/5.6.1/IO/Socket/UNIX.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/Annotation.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Constants.pm
/usr/share/perl/5.6.1/IO/Socket/INET.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/XML/Parser.pm
/usr/share/perl/5.6.1/strict.pm
/usr/share/perl/5.6.1/base.pm
/usr/share/perl/5.6.1/vars.pm
/usr/share/perl/5.6.1/utf8.pm
/usr/lib/perl/5.6.1/Config.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/Feature.pm
/home/aerives/genegrokker-interface/mod_perl/tools.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Crypt/CBC.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Digest/SHA1.pm
/usr/lib/perl/5.6.1/Data/Dumper.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Session.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Server.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/URI/Escape.pm
/home/aerives/genegrokker-interface/lib/perl/Validate.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/GskXmlProtocol.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Connection.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/User.pm
/usr/share/perl/5.6.1/Symbol.pm
/usr/share/perl/5.6.1/Exporter/Heavy.pm
/home/aerives/genegrokker-interface/mod_perl/genomic_img.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Storable.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Session/Lock/File.pm
/home/aerives/genegrokker-interface/mod_perl/genomicbrowser.pm
/home/aerives/genegrokker-interface/lib/perl/Authenticate.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/mod_perl.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/AnnotationSequence.pm
/home/aerives/genegrokker-interface/ext/var/tmp/genegrokker-interface-aerives/ssl_mod_perl_apache-startup.pl
/usr/share/perl/5.6.1/Benchmark.pm
/usr/lib/perl/5.6.1/IO/Handle.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/MD5.pm
/usr/lib/perl/5.6.1/Fcntl.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/XML/Parser/Expat.pm
/usr/lib/perl/5.6.1/IO/Seekable.pm
/usr/share/perl/5.6.1/Exporter.pm
/usr/lib/perl/5.6.1/IO/Socket.pm
/usr/share/perl/5.6.1/utf8_heavy.pl
/usr/lib/perl/5.6.1/Errno.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/SequenceRegion.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/Object.pm
/usr/lib/perl/5.6.1/DynaLoader.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Request.pm
/usr/share/perl/5.6.1/FileHandle.pm
/usr/share/perl/5.6.1/File/Spec/Unix.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Session/Serialize/Storable.pm
/usr/share/perl/5.6.1/SelectSaver.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/HTML/Template.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/DNAregex.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Apache/Session/Generate/MD5.pm
/usr/lib/perl/5.6.1/IO.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/auto/Storable/nfreeze.al
/usr/lib/perl/5.6.1/Socket.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/GD.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Genegrokker/Sequence.pm
/home/aerives/genegrokker-interface/lib/perl/GenegrokkerUtil.pm
/usr/lib/perl/5.6.1/IO/File.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/auto/Storable/_freeze.al
/usr/share/perl/5.6.1/integer.pm
/home/aerives/genegrokker-interface/lib/perl/SequenceNavigator.pm
/usr/lib/perl/5.6.1/XSLoader.pm
/home/aerives/genegrokker-interface/ext/lib/perl5/Digest/MD5.pm
/usr/share/perl/5.6.1/File/Spec
