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Segmentation fault (core dumped)

by v15 (Sexton)
on Sep 06, 2016 at 21:11 UTC ( [id://1171269]=perlquestion: print w/replies, xml ) Need Help??

v15 has asked for the wisdom of the Perl Monks concerning the following question:

Hi Everyone, I upgraded my UBUNTU 14.04 VERSION TO 16.04 version. It some how screwed my perl. If I run this code, it works fine: 

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

my $a = "string";
print $a,"\n";

[download]
BUT when i try to run the above code with a CPAn module like Data::Dumper , it gives me segmentation error(core dumped) so something like this 

#!/usr/bin/perl-w
use strict;
use warnings;
use Data::Dumper;

my $a = "string";
print $a,"\n";

[download]
Output

Segmentation fault (core dumped)

Same happens with bioperl modules. What is the way to fix it?? Any help would be appreciated. I want to use Data::Dumper for outputting complex data structure but then it is always throwing Segmentation error. My files are not big at all.

UPDATE

So I can run perl scripts with cpan modules like Data::Dumper with sudo in front of perl sudo perl script.pl and this works

Can you guys tell what can be the issue now??

Regards Varun

Replies are listed 'Best First'.
Re: Segmentation fault (core dumped)
by hippo (Bishop) on Sep 06, 2016 at 23:04 UTC

    How did you install Data::Dumper?

    If it was installed via a deb then it's ubuntu's problem because the upgrade should have sorted it. Report it to them as a bug in the upgrade process.

    Alternatively, if it was installed from source then it's your responsibility to re-install (from scratch: configure, compile, test, install) it to match the new version of perl and new system libraries. Why not also take the opportunity to upgrade to the latest version of this and all the other modules you use while you are at it?

[reply]
      This was installed when I was working on Ubuntu 14.04 with install command to CPAN. Can you tell me how to update all the modules? What command should I use?

      cpan on the terminal does not work

      Thanks
[reply]

        As above, so below. If you installed cpan via a deb then it's ubuntu's problem and you should report it to them as a bug. If you installed it from source then it's up to you to reinstall it now.

        cpan on the terminal does not work

        "does not work" is as useful to a developer as "I'm ill" is to a medic. Be specific.

[reply]
Re: Segmentation fault (core dumped)
by choroba (Cardinal) on Sep 06, 2016 at 21:59 UTC
    Note that there's no space between perl and -w : 
    #!/usr/bin/perl-w
               ^
               |
              HERE

    [download]

    What do you get from perl -v on both the systems?

    ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

    [download]
[reply]
[d/l]
[select]
      Hello There are no 2 systems. Only one system. Running 2 codes, one which does not have a line for use Data::Dumper and one that has it. I fixed the -w thing but still same error. Also typing cpan on the command gives segmentation error. Same goes with this code 
      perl -MCPAN -e shell

      [download]
      perl -v gives this

      This is perl 5, version 22, subversion 1 (v5.22.1) built for x86_64-linux-gnu-thread-multi (with 58 registered patches, see perl -V for more detail) Copyright 1987-2015, Larry Wall Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using "man perl" or "perldoc perl". If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page

      Help Please!!
[reply]
[d/l]
        It might be possible that the newer Perl version finds the older version's CPAN modules (but it shouldn't happen under the standard config). Check your configuration and module versions, $PERL5LIB variable, CPAN config, etc.

        ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

        [download]
[reply]
[d/l]
Re: Segmentation fault (core dumped)
by FreeBeerReekingMonk (Deacon) on Sep 07, 2016 at 17:17 UTC
    Well as another monk has hinted, it could be your outdated userspace perl modules that are incompatible with your current (newer) Perl version.

    # update your cpan
cpan cpan
# install these
sudo apt-get install cpanminus cpanoutdated
# upgrade all your modules with:
cpan-outdated -p | cpanm | tee /tmp/upgraded.log

    [download]

    cpanm is verbose enough so that you know what is happening, however, it could take a while if you have many CPAN modules installed...

    OR... it could be there is something fubar in your Perl base package, wipe it and install it: 

    sudo apt-get --reinstall install perl

    [download]

    you can check also other perl related installed software with: dpkg -l |grep -i perl and use  sudo apt-get --reinstall install $package to re-install it.

[reply]
[d/l]
[select]
      Hi, I tried that but first of all cpan command is not working. Installed  sudo apt-get install cpanminus cpanoutdated Ran cpan-outdated -p | cpanm | tee /tmp/upgraded.log ran cpan again still the error Help!!
[reply]
[d/l]
[select]
        What errors does "cpan" give? can you give me some output?
[reply]
Re: Segmentation fault (core dumped)
by Anonymous Monk on Sep 06, 2016 at 22:38 UTC
    ? What is the output of perl -V
[reply]
[d/l]
      perl -V gives this 
      Summary of my perl5 (revision 5 version 22 subversion 1) configuration
+:
   
  Platform:
    osname=linux, osvers=3.16.0, archname=x86_64-linux-gnu-thread-mult
+i
    uname='linux localhost 3.16.0 #1 smp debian 3.16.0 x86_64 gnulinux
+ '
    config_args='-Dusethreads -Duselargefiles -Dcc=x86_64-linux-gnu-gc
+c -Dcpp=x86_64-linux-gnu-cpp -Dld=x86_64-linux-gnu-gcc -Dccflags=-DDE
+BIAN -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong 
+-Wformat -Werror=format-security -Dldflags= -Wl,-Bsymbolic-functions 
+-Wl,-z,relro -Dlddlflags=-shared -Wl,-Bsymbolic-functions -Wl,-z,relr
+o -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dpriv
+lib=/usr/share/perl/5.22 -Darchlib=/usr/lib/x86_64-linux-gnu/perl/5.2
+2 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/
+lib/x86_64-linux-gnu/perl5/5.22 -Dsiteprefix=/usr/local -Dsitelib=/us
+r/local/share/perl/5.22.1 -Dsitearch=/usr/local/lib/x86_64-linux-gnu/
+perl/5.22.1 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/ma
+n3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man
+3 -Duse64bitint -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible
+-pager -Uafs -Ud_csh -Ud_ualarm -Uusesfio -Uusenm -Ui_libutil -Uversi
+ononly -DDEBUGGING=-g -Doptimize=-O2 -dEs -Duseshrplib -Dlibperl=libp
+erl.so.5.22.1'
    hint=recommended, useposix=true, d_sigaction=define
    useithreads=define, usemultiplicity=define
    use64bitint=define, use64bitall=define, uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='x86_64-linux-gnu-gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -D
+DEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LAR
+GEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O2 -g',
    cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-
+aliasing -pipe -I/usr/local/include'
    ccversion='', gccversion='5.3.1 20160311', gccosandvers=''
    intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
+, doublekind=3
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=1
+6, longdblkind=3
    ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t',
+ lseeksize=8
    alignbytes=8, prototype=define
  Linker and Libraries:
    ld='x86_64-linux-gnu-gcc', ldflags =' -fstack-protector-strong -L/
+usr/local/lib'
    libpth=/usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/5/include-fixe
+d /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/.
+./lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib
    libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt
    perllibs=-ldl -lm -lpthread -lc -lcrypt
    libc=libc-2.21.so, so=so, useshrplib=true, libperl=libperl.so.5.22
    gnulibc_version='2.21'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
    cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib -fstack-pr
+otector-strong'


Characteristics of this binary (from libperl): 
  Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
                        PERL_DONT_CREATE_GVSV
                        PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
                        PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
                        USE_64_BIT_ALL USE_64_BIT_INT USE_ITHREADS
                        USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
                        USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_LOCALE
+_TIME
                        USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API
  Locally applied patches:
    DEBPKG:debian/cpan_definstalldirs - Provide a sensible INSTALLDIRS
+ default for modules installed from CPAN.
    DEBPKG:debian/db_file_ver - http://bugs.debian.org/340047 Remove o
+verly restrictive DB_File version check.
    DEBPKG:debian/doc_info - Replace generic man(1) instructions with 
+Debian-specific information.
    DEBPKG:debian/enc2xs_inc - http://bugs.debian.org/290336 Tweak enc
+2xs to follow symlinks and ignore missing @INC directories.
    DEBPKG:debian/errno_ver - http://bugs.debian.org/343351 Remove Err
+no version check due to upgrade problems with long-running processes.
    DEBPKG:debian/libperl_embed_doc - http://bugs.debian.org/186778 No
+te that libperl-dev package is required for embedded linking
    DEBPKG:fixes/respect_umask - Respect umask during installation
    DEBPKG:debian/writable_site_dirs - Set umask approproately for sit
+e install directories
    DEBPKG:debian/extutils_set_libperl_path - EU:MM: set location of l
+ibperl.a under /usr/lib
    DEBPKG:debian/no_packlist_perllocal - Don't install .packlist or p
+erllocal.pod for perl or vendor
    DEBPKG:debian/fakeroot - Postpone LD_LIBRARY_PATH evaluation to th
+e binary targets.
    DEBPKG:debian/instmodsh_doc - Debian policy doesn't install .packl
+ist files for core or vendor.
    DEBPKG:debian/ld_run_path - Remove standard libs from LD_RUN_PATH 
+as per Debian policy.
    DEBPKG:debian/libnet_config_path - Set location of libnet.cfg to /
+etc/perl/Net as /usr may not be writable.
    DEBPKG:debian/mod_paths - Tweak @INC ordering for Debian
    DEBPKG:debian/prune_libs - http://bugs.debian.org/128355 Prune the
+ list of libraries wanted to what we actually need.
    DEBPKG:fixes/net_smtp_docs - [rt.cpan.org #36038] http://bugs.debi
+an.org/100195 Document the Net::SMTP 'Port' option
    DEBPKG:debian/perlivp - http://bugs.debian.org/510895 Make perlivp
+ skip include directories in /usr/local
    DEBPKG:debian/deprecate-with-apt - http://bugs.debian.org/747628 P
+oint users to Debian packages of deprecated core modules
    DEBPKG:debian/squelch-locale-warnings - http://bugs.debian.org/508
+764 Squelch locale warnings in Debian package maintainer scripts
    DEBPKG:debian/skip-upstream-git-tests - Skip tests specific to the
+ upstream Git repository
    DEBPKG:debian/patchlevel - http://bugs.debian.org/567489 List pack
+aged patches for 5.22.1-9 in patchlevel.h
    DEBPKG:debian/skip-kfreebsd-crash - http://bugs.debian.org/628493 
+[perl #96272] Skip a crashing test case in t/op/threads.t on GNU/kFre
+eBSD
    DEBPKG:fixes/document_makemaker_ccflags - http://bugs.debian.org/6
+28522 [rt.cpan.org #68613] Document that CCFLAGS should include $Conf
+ig{ccflags}
    DEBPKG:debian/find_html2text - http://bugs.debian.org/640479 Confi
+gure CPAN::Distribution with correct name of html2text
    DEBPKG:debian/perl5db-x-terminal-emulator.patch - http://bugs.debi
+an.org/668490 Invoke x-terminal-emulator rather than xterm in perl5db
+.pl
    DEBPKG:debian/cpan-missing-site-dirs - http://bugs.debian.org/6888
+42 Fix CPAN::FirstTime defaults with nonexisting site dirs if a paren
+t is writable
    DEBPKG:fixes/memoize_storable_nstore - [rt.cpan.org #77790] http:/
+/bugs.debian.org/587650 Memoize::Storable: respect 'nstore' option no
+t respected
    DEBPKG:debian/regen-skip - Skip a regeneration check in unrelated 
+git repositories
    DEBPKG:debian/makemaker-pasthru - http://bugs.debian.org/758471 Pa
+ss LD settings through to subdirectories
    DEBPKG:fixes/pod_man_reproducible_date - http://bugs.debian.org/75
+9405 Support POD_MAN_DATE in Pod::Man for the left-hand footer
    DEBPKG:debian/locale-robustness - http://bugs.debian.org/782068 [p
+erl #124310] Make t/run/locale.t survive missing locales masked by LC
+_ALL
    DEBPKG:fixes/podman-utc - http://bugs.debian.org/780259 Make the e
+mbedded date from Pod::Man reproducible
    DEBPKG:fixes/podman-utc-docs - http://bugs.debian.org/780259 Docum
+entation and test suite updates for UTC fix
    DEBPKG:fixes/podman-empty-date - http://bugs.debian.org/780259 Sup
+port an empty POD_MAN_DATE environment variable
    DEBPKG:fixes/podman-pipe - http://bugs.debian.org/777405 Better er
+rors for man pages from standard input
    DEBPKG:debian/pod2man-customized - Update porting/customized.dat f
+or pod2man modifications
    DEBPKG:debian/makemaker-manext - http://bugs.debian.org/247370 Mak
+e EU::MakeMaker honour MANnEXT settings in generated manpage headers
    DEBPKG:debian/makemaker_customized - Update t/porting/customized.d
+at for files patched in Debian
    DEBPKG:debian/do-not-record-build-date - [6baa8db] http://bugs.deb
+ian.org/774422 [perl #125830] Allow overriding the compile time in "p
+erl -V" output
    DEBPKG:fixes/podman-source-date-epoch - http://bugs.debian.org/801
+621 Make Pod::Man honor the SOURCE_DATE_EPOCH environment variable
    DEBPKG:fixes/podman-source-date-epoch-cleanups - http://bugs.debia
+n.org/801621 Coding style and documentation for SOURCE_EPOCH_DATE
    DEBPKG:fixes/podman-source-date-epoch-testfix - http://bugs.debian
+.org/807086 Guard for building with SOURCE_DATE_EPOCH or POD_MAN_DATE
+ set
    DEBPKG:debian/devel-ppport-reproducibility - http://bugs.debian.or
+g/801523 Sort the list of XS code files when generating RealPPPort.xs
    DEBPKG:fixes/encode-unicode-bom - http://bugs.debian.org/798727 [r
+t.cpan.org #107043] Address https://rt.cpan.org/Public/Bug/Display.ht
+ml?id=107043
    DEBPKG:debian/encode-unicode-bom-doc - http://bugs.debian.org/7987
+27 Document Debian backport of Encode::Unicode fix
    DEBPKG:debian/kfreebsd-softupdates - http://bugs.debian.org/796798
+ Work around Debian Bug#796798
    DEBPKG:fixes/autodie-scope - http://bugs.debian.org/798096 Fix a s
+coping issue with "no autodie" and the "system" sub
    DEBPKG:debian/debugperl-compat-fix - [perl #127212] http://bugs.de
+bian.org/810326 Disable PERL_TRACK_MEMPOOL for debugging builds
    DEBPKG:fixes/CVE-2015-8607_file_spec_taint_fix - http://bugs.debia
+n.org/810719 [perl #126862] ensure File::Spec::canonpath() preserves 
+taint
    DEBPKG:fixes/mkstemp-umask - http://bugs.debian.org/810924 [perl #
+127322] [e57270b] Fix umask for mkstemp(3) calls
    DEBPKG:fixes/crosscompile-no-targethost - [perl #127234] Fix the C
+onfigure escape with usecrosscompile but no targethost
    DEBPKG:fixes/podlators-no-encode - [rt.cpan.org #111156] Degrade g
+racefully if utf8 is requested but Encode is not available
    DEBPKG:debian/cross-time-hires - [rt.cpan.org #111391] Add an envi
+ronment variable to skip running configuration probes
    DEBPKG:fixes/encode-unicode-pod - Unicode.pm: Fix POD error
    DEBPKG:fixes/memoize-pod - [rt.cpan.org #89441] Fix POD errors in 
+Memoize
    DEBPKG:fixes/ok-pod - Added encoding for pod.
    DEBPKG:fixes/CVE-2016-2381_duplicate_env - remove duplicate enviro
+nment variables from environ
  Built under linux
  Compiled at Mar 13 2016 11:54:18
  %ENV:
    PERL5LIB="/home/varun/perl5/lib/perl5"
    PERL_LOCAL_LIB_ROOT="/home/varun/perl5"
    PERL_MB_OPT="--install_base "/home/varun/perl5""
    PERL_MM_OPT="INSTALL_BASE=/home/varun/perl5"
  @INC:
    /home/varun/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
    /home/varun/perl5/lib/perl5
    /etc/perl
    /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
    /usr/local/share/perl/5.22.1
    /usr/lib/x86_64-linux-gnu/perl5/5.22
    /usr/share/perl5
    /usr/lib/x86_64-linux-gnu/perl/5.22
    /usr/share/perl/5.22
    /usr/local/lib/site_perl
    /usr/lib/x86_64-linux-gnu/perl-base
    .

      [download]
[reply]
[d/l]
Re: Segmentation fault (core dumped)
by RonW (Parson) on Sep 08, 2016 at 21:51 UTC

    Try using PerlBrew to install a separate Perl from the one Ubuntu includes. That way, you can set up Perl exactly the way you need (Possibly even the previous version of Perl you were using) without messing with Ubuntu's Perl - or Ubuntu's Perl messing with your Perl.

[reply]

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