Bug#644994: segfault while using h5dump in /usr/lib/libhdf5.so.6

[Yaroslav Halchenko]

Package: hdf5-tools
Version: 1.8.4-patch1-3
Severity: normal

running a dump on a file we have generated (must be attached to this report or
if cut could be found at http://www.onerussian.com/tmp/plain.hdf5)
results in a segfault:

$> gdb --args h5dump -r /home/yoh/.tmp/tmp76ywfT/plain.hdf5             
GNU gdb (GDB) 7.3-debian
Copyright (C) 2011 Free Software Foundation, Inc.
....

                                                                     ATTRIBUTE "objref" {
                                                                        DATATYPE  H5T_STD_I64LE
                                                                        DATASPACE  SCALAR
                                                                        DATA {
                                                                        (0): 55273664
                                                                        }
                                                                     }
                                                                     GROUP "items" {
                                                                        GROUP "0" {
                                                                           ATTRIBUTE "class" {
                                                                              DATATYPE  H5T_STRING {
error: the indentation exceeds the number of cols.

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff78f8031 in ?? () from /usr/lib/libhdf5.so.6
(gdb) bt
#0  0x00007ffff78f8031 in ?? () from /usr/lib/libhdf5.so.6
#1  0x00007ffff798cbbe in H5I_clear_type () from /usr/lib/libhdf5.so.6
#2  0x00007ffff78f2415 in H5F_term_interface () from /usr/lib/libhdf5.so.6
#3  0x00007ffff785fa35 in H5_term_library () from /usr/lib/libhdf5.so.6
#4  0x00007ffff6e23d82 in __run_exit_handlers (status=1, listp=0x7ffff716b4c8, run_list_atexit=true) at exit.c:78
#5  0x00007ffff6e23dd5 in *__GI_exit (status=6707632) at exit.c:100
#6  0x00000000004251c1 in ?? ()
#7  0x00000000004071a6 in ?? ()
#8  0x0000000000407bb1 in ?? ()
#9  0x000000000040815d in ?? ()
#10 0x00007ffff787e372 in H5A_attr_iterate_table () from /usr/lib/libhdf5.so.6
#11 0x00007ffff79b9e1d in ?? () from /usr/lib/libhdf5.so.6
#12 0x00007ffff79ba094 in H5O_attr_iterate () from /usr/lib/libhdf5.so.6
#13 0x00007ffff7872ff9 in H5Aiterate2 () from /usr/lib/libhdf5.so.6
#14 0x000000000040a4ec in ?? ()
#15 0x000000000040890e in ?? ()

here is the information from valgrind:

     error: the indentation exceeds the number of cols.
==25081== Invalid read of size 4
==25081==    at 0x4EFE031: ??? (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x4F92BBD: H5I_clear_type (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x4EF8414: H5F_term_interface (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x4E65A34: H5_term_library (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x5ACFD81: __run_exit_handlers (exit.c:78)
==25081==    by 0x5ACFDD4: exit (exit.c:100)
==25081==    by 0x4251C0: ??? (in /usr/bin/h5dump)
==25081==    by 0x4071A5: ??? (in /usr/bin/h5dump)
==25081==    by 0x407BB0: ??? (in /usr/bin/h5dump)
==25081==    by 0x40815C: ??? (in /usr/bin/h5dump)
==25081==    by 0x4E84371: H5A_attr_iterate_table (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x4FBFE1C: ??? (in /usr/lib/libhdf5.so.6.0.3)
==25081==  Address 0x52c is not stack'd, malloc'd or (recently) free'd
==25081==
==25081==
==25081== Process terminating with default action of signal 11 (SIGSEGV)
==25081==  Access not within mapped region at address 0x52C
==25081==    at 0x4EFE031: ??? (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x4F92BBD: H5I_clear_type (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x4EF8414: H5F_term_interface (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x4E65A34: H5_term_library (in /usr/lib/libhdf5.so.6.0.3)
==25081==    by 0x5ACFD81: __run_exit_handlers (exit.c:78)
==25081==    by 0x5ACFDD4: exit (exit.c:100)
==25081==    by 0x4251C0: ??? (in /usr/bin/h5dump)
==25081==    by 0x4071A5: ??? (in /usr/bin/h5dump)
==25081==    by 0x407BB0: ??? (in /usr/bin/h5dump)
==25081==    by 0x40815C: ??? (in /usr/bin/h5dump)
==25081==    by 0x4E84371: H5A_attr_iterate_table (in /usr/lib/libhdf5.so.6.0.3)


-- System Information:
Debian Release: wheezy/sid
  APT prefers testing
  APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.0.0-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash

Versions of packages hdf5-tools depends on:
ii  libc6                                 2.13-18       
ii  libhdf5-serial-1.8.4 [libhdf5-1.8.4]  1.8.4-patch1-3
ii  zlib1g                                1:1.2.5.dfsg-1

hdf5-tools recommends no packages.

hdf5-tools suggests no packages.

-- no debconf information
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