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

[Michael Jackson]

Thanks everyone for the suggestions. I did not know about the 1.6.9  
release. I'll have to take some time this weekend to move that into my  
CMake build system for HDF5. Hopefully the changes from 1.6.8 to 1.6.9  
are not too extreme.

  Version 1.8 is not going to happen for a while (even with the 1.6  
API enabled.)


I'll take a look into the H5set_free_list_limits function and  
documentation to see if that is causing any problems.

  Is the reason for the error known? Maybe something I am doing in my  
code perhaps. Currently the hdf5 code was used in tandem with some ITK  
code, but only one specific program out of 10 that I wrote. Really  
odd. I guess I am just massaging something wrong.

Thanks to all.
---
Mike Jackson                 www.bluequartz.net



On Jun 5, 2009, at 2:47 PM, Neil Fortner wrote:

> Mike,
>
> Neil Fortner wrote:
>> Mike,
>>
>> I have seen a similar problem before, but only when using 1.8  
>> features.  However, it could still be the same underlying problem  
>> with the shutdown routines in the free list code.  I had originally  
>> assumed that it would be extremely rare, but now I will see if I  
>> can add that bug to the list of bugs to fix for 1.8.4, and  
>> hopefully 1.6.10.  If you have an example program that would be  
>> helpful.
>
> As a work around, you can try using H5set_free_list_limits to set  
> lower (or 0) limits for different types of free lists (probably  
> array and/or block).  Alternatively, you can try compiling the  
> library with free lists disabled.
>
> -Neil
>
>> Thanks,
>> Neil Fortner
>> The HDF Group
>>
>>
>> Michael Jackson wrote:
>>> And if I don't have valgrind? ;-)
>>>
>>> ---
>>> Mike Jackson                 www.bluequartz.net
>>>
>>>
>>>
>>> On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:
>>>
>>>> I would run the code through valgrind.
>>>> -- Dominik
>>>>
>>>> Michael Jackson wrote:
>>>>> 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
>>>>> BlueQuartz Software                    www.bluequartz.net
>>>>> Principal Software Engineer                  Dayton, Ohio
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>>>>
>>>
>>>
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>>
>
>
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