[hdf-forum] Error when exiting program using hdf5 1.6.8

[Mike Jackson]

<off topic>I actually use Virtual Box at the office with 2 flavors of
Ubuntu (32 and 64 Bit) and Windows XP. My home machine is in need of a
hard drive upgrade at this point as it does not have the space left
for those virtual machines.</off topic>

Found the culprit. ITK was allowing me to walk of the end of an array
and set some values so basically I was stomping on some memory. I
would have thought the compiler or something would have asserted when
I tried to set a value off the end of an array or ITK would have
asserted when I tried it. Huh. So much for safety nets.

Valgrind probably would have told me all of this. I should get that
setup in the Virtual Machines.

Thanks everyone for the insight into my errors/bugs. Again, the list
has proved invaluable.

Mike Jackson

On Sat, Jun 6, 2009 at 9:01 AM, Dominik Szczerba<domi at vision.ee.ethz.ch> wrote:
> You may try the free Virtualbox, installing latest Ubuntu takes several
> minutes. Or just boot your Mac off the Live CDROM.
> -- Dominik
>
> Mike Jackson wrote:
>>
>> Seems the problem followed me to another Mac when I came home do
>> definitely something wrong. Almost seems like I am stomping on some
>> memory somewhere. I'll try some other platforms and see what happens.
>> Unfortunately all I have at home this weekend is Windows XP via
>> Bootcamp but at least it would give me a sanity check. Just seems odd
>> that after almost a year of development I start hitting this bug now.
>> I guess more frustrating than anything else.
>>
>> Thanks for the input.
>> Mike
>>
>> On Sat, Jun 6, 2009 at 6:55 AM, Dimitris Servis<servisster at gmail.com>
>> wrote:
>>>
>>> I have seen such messages being due to an overrun unrelated to the
>>> library
>>> itself. You can also get it when killing the process abruptly. Memory
>>> checking is a good starting point.
>>>
>>> HTH
>>>
>>> -- dimitris
>>>
>>> 2009/6/5 Michael Jackson <mike.jackson at bluequartz.net>
>>>>
>>>> I am getting either one of the following errors when my program exits:
>>>>
>>>> Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file
>>>> /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
>>>> Abort trap
>>>>
>>>> HDF5: infinite loop closing library
>>>>
>>>>
>>>>  D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
>>>> Abort trap
>>>>
>>>>
>>>> This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
>>>>
>>>> I googled a bit for the errors but nothing really jumped out at me. Has
>>>> anyone seen this type of error before?
>>>>
>>>> In the same project I have lots of other programs all using the same
>>>> HDF5
>>>> library and I am not getting the error. Just kinda popped up today. I
>>>> rebuilt the hdf5 library and reinstalled but I am still getting the
>>>> errors.
>>>> I have ensured that I am closing all the hdf5 files that are opened. I
>>>> have
>>>> tried several different hdf5 files and all will give the error.
>>>>
>>>> Any help or nudges in the right direction would be appreciated.
>>>>
>>>> Thanks
>>>> _________________________________________________________
>>>> Mike Jackson                  mike.jackson at bluequartz.net
>>

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