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

[Neil Fortner]

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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