Debug Perl Segmentation Fault - perl

Question

I'm using AcePerl to download data from the wormbase.org database.
When I download certain database objects I get (after a certain number of objects) a segmentation fault. This behaviour is reproducible.
I had a look at the core dump and where prints a huge stack of function calls:
#0 0xb763c0ac in ?? () from /lib/i386-linux-gnu/libc.so.6
#1 0xb763eddc in malloc () from /lib/i386-linux-gnu/libc.so.6
#2 0x080c07ca in Perl_safesysmalloc ()
#3 0x080f3a02 in Perl_sv_grow ()
#4 0x080ebe38 in Perl_sv_setsv_flags ()
#5 0x080ecb76 in Perl_newSVsv ()
#6 0x0811516f in Perl_save_item ()
#7 0x080c7dd8 in Perl_get_db_sub ()
#8 0x080e7a4c in Perl_pp_entersub ()
#9 0x08075570 in Perl_call_sv ()
#10 0x080edd25 in Perl_sv_clear ()
#11 0x080ee3eb in Perl_sv_free2 ()
#12 0x080d79ec in Perl_hv_free_ent ()
#13 0x080d7c8c in ?? ()
#14 0x080db6ff in Perl_hv_undef_flags ()
#15 0x080edf72 in Perl_sv_clear ()
#16 0x080ee3eb in Perl_sv_free2 ()
#17 0x080d79ec in Perl_hv_free_ent ()
#18 0x080d7c8c in ?? ()
#19 0x080db6ff in Perl_hv_undef_flags ()
#20 0x080edf72 in Perl_sv_clear ()
#21 0x080ee3eb in Perl_sv_free2 ()
#22 0x080d79ec in Perl_hv_free_ent ()
#23 0x080d7c8c in ?? ()
#24 0x080db6ff in Perl_hv_undef_flags ()
#25 0x080edf72 in Perl_sv_clear ()
#26 0x080ee3eb in Perl_sv_free2 ()
#27 0x080d79ec in Perl_hv_free_ent ()
#28 0x080d7c8c in ?? ()
#29 0x080db6ff in Perl_hv_undef_flags ()
#30 0x080edf72 in Perl_sv_clear ()
#31 0x080ee3eb in Perl_sv_free2 ()
#32 0x080d79ec in Perl_hv_free_ent ()
#33 0x080d7c8c in ?? ()
#34 0x080db6ff in Perl_hv_undef_flags ()
#35 0x080edf72 in Perl_sv_clear ()
#36 0x080ee3eb in Perl_sv_free2 ()
#37 0x080d79ec in Perl_hv_free_ent ()
#38 0x080d7c8c in ?? ()
#39 0x080db6ff in Perl_hv_undef_flags ()
#40 0x080edf72 in Perl_sv_clear ()
#41 0x080ee3eb in Perl_sv_free2 ()
#42 0x080d79ec in Perl_hv_free_ent ()
#43 0x080d7c8c in ?? ()
#44 0x080db6ff in Perl_hv_undef_flags ()
#45 0x080edf72 in Perl_sv_clear ()
#46 0x080ee3eb in Perl_sv_free2 ()
#47 0x080d79ec in Perl_hv_free_ent ()
#48 0x080d7c8c in ?? ()
#49 0x080db6ff in Perl_hv_undef_flags ()
#50 0x080edf72 in Perl_sv_clear ()
#51 0x080ee3eb in Perl_sv_free2 ()
#52 0x080d79ec in Perl_hv_free_ent ()
#53 0x080d7c8c in ?? ()
...
These function calls are repeated thousands of time.
I also called perl -d:Trace myscript.pl > log but the logfile is about 3 GB large.
Is there a more convenient way to debug this script?
EDIT:
My script: http://paste.ubuntu.com/5564630/ .
My schema file: http://paste.ubuntu.com/5564631/ . It determines which data to download.
The seg fault is raised after ~2300 go_terms.

Answer 1

Install Devel::Trace.
Run your perl script with tracing enabled:
perl -d:Trace myscript.pl >trace 2>&1
Tail the file to see which Perl lines are executed leading up to the segmentation fault.