Re: Segmentation fault during regex match

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Re^2: Segmentation fault during regex match by Berislav (Acolyte) on Jun 29, 2006 at 09:37 UTC
This is the output of perl -V Summary of my perl5 (revision 5 version 8 subversion 6) configuration: Platform: osname=linux, osvers=2.4.21-27.0.2.elsmp, archname=i386-linux-thre +ad-multi uname='linux decompose.build.redhat.com 2.4.21-27.0.2.elsmp #1 smp + wed jan 12 23:35:44 est 2005 i686 i686 i386 gnulinux ' config_arg +s='-des -Doptimize=-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions +-m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -Dversi +on=5.8.6 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc - +Dcf_by=Red Hat, Inc. -Dinstallprefix=/usr -Dprefix=/usr -Darchname=i3 +86-linux -Dvendorprefix=/usr -Dsiteprefix=/usr -Duseshrplib -Dusethre +ads -Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db +-Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Di +nstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/les +s -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_endprotoent_ +r_proto -Ud_endservent_r_proto -Ud_sethostent_r_proto -Ud_setprotoent +_r_proto -Ud_setservent_r_proto -Dinc_version_list=5.8.5 5.8.4 5.8.3' hint=recommended, useposix=true, d_sigaction=define usethreads=define use5005threads=undef useithreads=define usemulti +plicity=define useperlio=define d_sfio=undef uselargefiles=define usesocks=undef use64bitint=undef use64bitall=undef uselongdouble=undef usemymalloc=n, bincompat5005=undef Compiler: cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-st +rict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_ +OFFSET_BITS=64 -I/usr/include/gdbm', optimize='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 - +march=i386 -mtune=pentium4 -fasynchronous-unwind-tables', cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-alias +ing -pipe -I/usr/local/include -I/usr/include/gdbm' ccversion='', gccversion='4.0.0 20050516 (Red Hat 4.0.0-6)', gccos +andvers='' intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=1 +2 ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', + lseeksize=8 alignbytes=4, prototype=define Linker and Libraries: ld='gcc', ldflags =' -L/usr/local/lib' libpth=/usr/local/lib /lib /usr/lib libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread +-lc perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc libc=/lib/libc-2.3.5.so, so=so, useshrplib=true, libperl=libperl.s +o gnulibc_version='2.3.5' Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E - +Wl,-rpath,/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE' cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib' Characteristics of this binary (from libperl): Compile-time options: DEBUGGING MULTIPLICITY USE_ITHREADS USE_LARGE_ +FILES PERL_IMPLICIT_CONTEXT Built under linux Compiled at May 18 2005 18:21:23 @INC: /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.6/i386-linux-thread-multi /usr/lib/perl5/5.8.6 . [download] And this is the sample file AT (327658) Locus: 1 3 8 17 26 31 + 48 54 58 87 96 103 110 116 130 145 + 156 168 176 194 200 241 246 260 266 297 + 312 339 341 351 354 365 371 401 416 443 + 448 555 560 567 607 635 690 703 705 737 + 757 777 788 792 794 819 882 897 902 940 + 948 964 969 973 983 986 1005 1015 1029 1060 + 1063 1086 1088 1100 1106 1128 1140 1152 1159 1166 + 1188 1215 1229 1253 1257 1263 1276 1287 1291 1298 + 1313 1326 1328 1348 1350 1358 1376 1397 1401 1424 + 1429 1452 1466 1472 1491 1505 1545 1550 1557 1563 + 1566 1585 1597 1614 1616 1635 1641 1649 1654 1666 + 1686 1727 1729 1737 1744 1748 1751 1753 1757 1762 + 1782 1787 1798 1845 1867 1879 1906 1915 1917 1927 + 1935 1945 1962 1970 1975 2006 2021 2025 2068 2070 + 2078 2100 2104 2112 2122 2133 2149 2188 2195 2270 + 2280 2293 2305 2318 2328 2332 2338 2362 2368 2396 + 2399 2409 2427 2453 2472 2479 2482 2499 2513 2518 + 2526 2532 2539 2545 2557 2562 2585 2589 2593 2608 + 2611 2622 2638 2652 2659 2694 2704 2711 2723 2731 + 2737 2743 2764 2779 2787 2794 2796 2802 2807 2809 + 2815 2819 2829 2839 2848 2857 2875 2881 2884 2892 + 2898 2911 2932 2941 2947 2956 2964 2970 2981 2985 + 2994 2997 3003 3018 3034 3059 3073 3075 3082 3111 + 3127 3160 3162 3172 3177 3187 3196 3201 3204 3231 + 3237 3251 3263 3267 3277 3283 3305 3331 3352 3354 + 3357 3361 3364 3394 3402 3427 3440 3442 3445 3469 + 3471 3528 3539 3549 3592 3607 3620 3628 3636 3647 + 3664 3677 3680 3697 3700 3706 3712 3727 3773 3781 + 3787 3790 3794 3815 3822 3825 3830 3846 3852 3859 + 3868 3884 3887 3892 3895 3908 3913 3936 3944 3953 + 3972 3985 3988 4006 4012 4023 4030 4034 4037 4042 + 4048 4051 4063 4079 [download]	[reply] [d/l] [select]
Re^3: Segmentation fault during regex match by Corion (Patriarch) on Jun 29, 2006 at 09:45 UTC
I can't reproduce that error with the below program, but on 5.8.2 and 5.8.3 on Win32. Does the below program crash for you? Does it crash every time or only from time to time? If the below program works for you, please try to find some other complete example which crashes predictably. If the below program crashes for you, that's "good", as the bug is then reproducible. use strict; use warnings; undef $/; my $dna = <DATA>; print $dna; while ($dna=~ m/(^\w{2}\s\(\d+\)\sLocus:(\s\d+)+)/mg) { print "Found: $1\n"; }; __DATA__ AT (327658) Locus: 1 3 8 17 26 31 + 48 54 58 87 96 103 110 116 130 145 + 156 168 176 194 200 241 246 260 266 297 + 312 339 341 351 354 365 371 401 416 443 + 448 555 560 567 607 635 690 703 705 737 + 757 777 788 792 794 819 882 897 902 940 + 948 964 969 973 983 986 1005 1015 1029 1060 + 1063 1086 1088 1100 1106 1128 1140 1152 1159 1166 + 1188 1215 1229 1253 1257 1263 1276 1287 1291 1298 + 1313 1326 1328 1348 1350 1358 1376 1397 1401 1424 + 1429 1452 1466 1472 1491 1505 1545 1550 1557 1563 + 1566 1585 1597 1614 1616 1635 1641 1649 1654 1666 + 1686 1727 1729 1737 1744 1748 1751 1753 1757 1762 + 1782 1787 1798 1845 1867 1879 1906 1915 1917 1927 + 1935 1945 1962 1970 1975 2006 2021 2025 2068 2070 + 2078 2100 2104 2112 2122 2133 2149 2188 2195 2270 + 2280 2293 2305 2318 2328 2332 2338 2362 2368 2396 + 2399 2409 2427 2453 2472 2479 2482 2499 2513 2518 + 2526 2532 2539 2545 2557 2562 2585 2589 2593 2608 + 2611 2622 2638 2652 2659 2694 2704 2711 2723 2731 + 2737 2743 2764 2779 2787 2794 2796 2802 2807 2809 + 2815 2819 2829 2839 2848 2857 2875 2881 2884 2892 + 2898 2911 2932 2941 2947 2956 2964 2970 2981 2985 + 2994 2997 3003 3018 3034 3059 3073 3075 3082 3111 + 3127 3160 3162 3172 3177 3187 3196 3201 3204 3231 + 3237 3251 3263 3267 3277 3283 3305 3331 3352 3354 + 3357 3361 3364 3394 3402 3427 3440 3442 3445 3469 + 3471 3528 3539 3549 3592 3607 3620 3628 3636 3647 + 3664 3677 3680 3697 3700 3706 3712 3727 3773 3781 + 3787 3790 3794 3815 3822 3825 3830 3846 3852 3859 + 3868 3884 3887 3892 3895 3908 3913 3936 3944 3953 + 3972 3985 3988 4006 4012 4023 4030 4034 4037 4042 + 4048 4051 4063 4079 [download] Update: I realized that your regular expression is too strict to properly match the data given, at least on Win32 (but I guess on other OSes as well). When modifying the code to the below code, it matches but still doesn't crash for me: `use strict; use warnings; undef $/; my $dna = <DATA>; while ($dna=~ m/(^\w{2}\s+\(\d+\)\s+Locus:(\s+\d+)+)/smg) { print "Found: $1\n"; }; __DATA__ ... dataset elided ...` [download]	[reply] [d/l] [select]
Re^4: Segmentation fault during regex match by Berislav (Acolyte) on Jun 29, 2006 at 10:35 UTC
Segmentation fault again, I'm afraid. I can send you the entire file if you think that will solve the problem, the exemple data i posted is less than 0.01% of the entire data set.	[reply]
Re^5: Segmentation fault during regex match by Corion (Patriarch) on Jun 29, 2006 at 11:50 UTC

Summary of my perl5 (revision 5 version 8 subversion 6) configuration:
  Platform:
    osname=linux, osvers=2.4.21-27.0.2.elsmp, archname=i386-linux-thre
+ad-multi
    uname='linux decompose.build.redhat.com 2.4.21-27.0.2.elsmp #1 smp
+ wed jan 12 23:35:44 est 2005 i686 i686 i386 gnulinux '    config_arg
+s='-des -Doptimize=-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions 
+-m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -Dversi
+on=5.8.6 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -
+Dcf_by=Red Hat, Inc. -Dinstallprefix=/usr -Dprefix=/usr -Darchname=i3
+86-linux -Dvendorprefix=/usr -Dsiteprefix=/usr -Duseshrplib -Dusethre
+ads -Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db 
+-Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Di
+nstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/les
+s -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_endprotoent_
+r_proto -Ud_endservent_r_proto -Ud_sethostent_r_proto -Ud_setprotoent
+_r_proto -Ud_setservent_r_proto -Dinc_version_list=5.8.5 5.8.4 5.8.3'
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=define use5005threads=undef useithreads=define usemulti
+plicity=define
    useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=undef use64bitall=undef uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-st
+rict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_
+OFFSET_BITS=64 -I/usr/include/gdbm',
    optimize='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -
+march=i386 -mtune=pentium4 -fasynchronous-unwind-tables',
    cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-alias
+ing -pipe -I/usr/local/include -I/usr/include/gdbm'
    ccversion='', gccversion='4.0.0 20050516 (Red Hat 4.0.0-6)', gccos
+andvers=''
    intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=1
+2
    ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
+ lseeksize=8
    alignbytes=4, prototype=define
  Linker and Libraries:
    ld='gcc', ldflags =' -L/usr/local/lib'
    libpth=/usr/local/lib /lib /usr/lib
    libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread 
+-lc
    perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
    libc=/lib/libc-2.3.5.so, so=so, useshrplib=true, libperl=libperl.s
+o
    gnulibc_version='2.3.5'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E -
+Wl,-rpath,/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE'
    cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib'


Characteristics of this binary (from libperl):
  Compile-time options: DEBUGGING MULTIPLICITY USE_ITHREADS USE_LARGE_
+FILES PERL_IMPLICIT_CONTEXT
  Built under linux
  Compiled at May 18 2005 18:21:23
  @INC:
    /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi
    /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
    /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
    /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
    /usr/lib/perl5/site_perl/5.8.6
    /usr/lib/perl5/site_perl/5.8.5
    /usr/lib/perl5/site_perl/5.8.4
    /usr/lib/perl5/site_perl/5.8.3
    /usr/lib/perl5/site_perl
    /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.8.6
    /usr/lib/perl5/vendor_perl/5.8.5
    /usr/lib/perl5/vendor_perl/5.8.4
    /usr/lib/perl5/vendor_perl/5.8.3
    /usr/lib/perl5/vendor_perl
    /usr/lib/perl5/5.8.6/i386-linux-thread-multi
    /usr/lib/perl5/5.8.6
    .
[download]

AT    (327658)
Locus:
          1          3          8         17         26         31    
+     48         54         58         87
         96        103        110        116        130        145    
+    156        168        176        194
        200        241        246        260        266        297    
+    312        339        341        351
        354        365        371        401        416        443    
+    448        555        560        567
        607        635        690        703        705        737    
+    757        777        788        792
        794        819        882        897        902        940    
+    948        964        969        973
        983        986       1005       1015       1029       1060    
+   1063       1086       1088       1100
       1106       1128       1140       1152       1159       1166    
+   1188       1215       1229       1253
       1257       1263       1276       1287       1291       1298    
+   1313       1326       1328       1348
       1350       1358       1376       1397       1401       1424    
+   1429       1452       1466       1472
       1491       1505       1545       1550       1557       1563    
+   1566       1585       1597       1614
       1616       1635       1641       1649       1654       1666    
+   1686       1727       1729       1737
       1744       1748       1751       1753       1757       1762    
+   1782       1787       1798       1845
       1867       1879       1906       1915       1917       1927    
+   1935       1945       1962       1970
       1975       2006       2021       2025       2068       2070    
+   2078       2100       2104       2112
       2122       2133       2149       2188       2195       2270    
+   2280       2293       2305       2318
       2328       2332       2338       2362       2368       2396    
+   2399       2409       2427       2453
       2472       2479       2482       2499       2513       2518    
+   2526       2532       2539       2545
       2557       2562       2585       2589       2593       2608    
+   2611       2622       2638       2652
       2659       2694       2704       2711       2723       2731    
+   2737       2743       2764       2779
       2787       2794       2796       2802       2807       2809    
+   2815       2819       2829       2839
       2848       2857       2875       2881       2884       2892    
+   2898       2911       2932       2941
       2947       2956       2964       2970       2981       2985    
+   2994       2997       3003       3018
       3034       3059       3073       3075       3082       3111    
+   3127       3160       3162       3172
       3177       3187       3196       3201       3204       3231    
+   3237       3251       3263       3267
       3277       3283       3305       3331       3352       3354    
+   3357       3361       3364       3394
       3402       3427       3440       3442       3445       3469    
+   3471       3528       3539       3549
       3592       3607       3620       3628       3636       3647    
+   3664       3677       3680       3697
       3700       3706       3712       3727       3773       3781    
+   3787       3790       3794       3815
       3822       3825       3830       3846       3852       3859    
+   3868       3884       3887       3892
       3895       3908       3913       3936       3944       3953    
+   3972       3985       3988       4006
       4012       4023       4030       4034       4037       4042    
+   4048       4051       4063       4079
[download]

[reply]
[d/l]
[select]

I can't reproduce that error with the below program, but on 5.8.2 and 5.8.3 on Win32. Does the below program crash for you? Does it crash every time or only from time to time? If the below program works for you, please try to find some other complete example which crashes predictably. If the below program crashes for you, that's "good", as the bug is then reproducible.

use strict;
use warnings;
undef $/;

my $dna = <DATA>;
print $dna;
while ($dna=~ m/(^\w{2}\s\(\d+\)\sLocus:(\s\d+)+)/mg) {
        print "Found: $1\n";
};

__DATA__
AT    (327658)
Locus:
          1          3          8         17         26         31    
+     48         54         58         87
         96        103        110        116        130        145    
+    156        168        176        194
        200        241        246        260        266        297    
+    312        339        341        351
        354        365        371        401        416        443    
+    448        555        560        567
        607        635        690        703        705        737    
+    757        777        788        792
        794        819        882        897        902        940    
+    948        964        969        973
        983        986       1005       1015       1029       1060    
+   1063       1086       1088       1100
       1106       1128       1140       1152       1159       1166    
+   1188       1215       1229       1253
       1257       1263       1276       1287       1291       1298    
+   1313       1326       1328       1348
       1350       1358       1376       1397       1401       1424    
+   1429       1452       1466       1472
       1491       1505       1545       1550       1557       1563    
+   1566       1585       1597       1614
       1616       1635       1641       1649       1654       1666    
+   1686       1727       1729       1737
       1744       1748       1751       1753       1757       1762    
+   1782       1787       1798       1845
       1867       1879       1906       1915       1917       1927    
+   1935       1945       1962       1970
       1975       2006       2021       2025       2068       2070    
+   2078       2100       2104       2112
       2122       2133       2149       2188       2195       2270    
+   2280       2293       2305       2318
       2328       2332       2338       2362       2368       2396    
+   2399       2409       2427       2453
       2472       2479       2482       2499       2513       2518    
+   2526       2532       2539       2545
       2557       2562       2585       2589       2593       2608    
+   2611       2622       2638       2652
       2659       2694       2704       2711       2723       2731    
+   2737       2743       2764       2779
       2787       2794       2796       2802       2807       2809    
+   2815       2819       2829       2839
       2848       2857       2875       2881       2884       2892    
+   2898       2911       2932       2941
       2947       2956       2964       2970       2981       2985    
+   2994       2997       3003       3018
       3034       3059       3073       3075       3082       3111    
+   3127       3160       3162       3172
       3177       3187       3196       3201       3204       3231    
+   3237       3251       3263       3267
       3277       3283       3305       3331       3352       3354    
+   3357       3361       3364       3394
       3402       3427       3440       3442       3445       3469    
+   3471       3528       3539       3549
       3592       3607       3620       3628       3636       3647    
+   3664       3677       3680       3697
       3700       3706       3712       3727       3773       3781    
+   3787       3790       3794       3815
       3822       3825       3830       3846       3852       3859    
+   3868       3884       3887       3892
       3895       3908       3913       3936       3944       3953    
+   3972       3985       3988       4006
       4012       4023       4030       4034       4037       4042    
+   4048       4051       4063       4079
[download]

Update: I realized that your regular expression is too strict to properly match the data given, at least on Win32 (but I guess on other OSes as well). When modifying the code to the below code, it matches but still doesn't crash for me:

use strict;
use warnings;
undef $/;

my $dna = <DATA>;
while ($dna=~ m/(^\w{2}\s+\(\d+\)\s+Locus:(\s+\d+)+)/smg) {
        print "Found: $1\n";
};

__DATA__
... dataset elided ...
[download]

[reply]
[d/l]
[select]

Segmentation fault again, I'm afraid. I can send you the entire file if you think that will solve the problem, the exemple data i posted is less than 0.01% of the entire data set.

[reply]