Hi Jan,
On Mar 9, 2010, at 12:09 PM, Jan Linxweiler wrote:
> Hi Quincey,
>
> I tried again.. I did not set the the fill value but set the allocation time
> to be incremental. In this case the fill value equals 0... The file size is
> the same...
Hmm, that's odd. Can you send me a C program that shows the issue?
Quincey
>
> Jan
>
> On 09.03.2010, at 18:45, Quincey Koziol wrote:
>
>> Hi Jan,
>>
>> On Mar 9, 2010, at 11:42 AM, Jan Linxweiler wrote:
>>
>>> Hi Quincey,
>>>
>>> thank you for your answer. I tried not setting a fill value, but I think
>>> the dataset is not valid than. I could not figure out how to identify not
>>> valid chunks. Also HDFView was not able to read those files. Therefore I
>>> suppose it is not the common way to use chunked datasets. Isn't it?
>>
>> When you didn't set the fill value, was the file smaller (because the
>> chunks weren't allocated)? If that's true, then I think this is a bug in
>> the HDF5 library and we should fix it so that it doesn't allocate chunks
>> (when the allocation time is increment or late) when a fill value is defined.
>>
>> Quincey
>>
>>> Jan
>>>
>>> On 09.03.2010, at 18:20, Quincey Koziol wrote:
>>>
>>>> Hi Jan,
>>>>
>>>> On Mar 9, 2010, at 5:22 AM, Jan Linxweiler wrote:
>>>>
>>>>> It seems like simply enabling compression does not change anything. The
>>>>> file sizes for sparse and dense matrices still have the same size.
>>>>>
>>>>> Can anyone give me a hint on how to work this out?
>>>>
>>>> Hmm, I would think that you are correct in your expectations. Can you
>>>> try without setting the fill value and see what happens?
>>>>
>>>> Quincey
>>>>
>>>>> On 09.03.2010, at 12:01, Jan Linxweiler wrote:
>>>>>
>>>>>> Hallo all,
>>>>>>
>>>>>> I have a question concerning the allocated file space of chunked
>>>>>> datasets. I use a chunked dataset with a fill value and incremental
>>>>>> allocation time as followed:
>>>>>>
>>>>>> hsize_tchunk_dims[3]={10,10,10};
>>>>>> const int rank = 3;
>>>>>>
>>>>>> H5::DSetCreatPropList cparms;
>>>>>> cparms.setChunk( rank, chunk_dims );
>>>>>>
>>>>>> /* Set fill value for the dataset. */
>>>>>> double fill_val = -999.999;
>>>>>> cparms.setFillValue( datatype, &fill_val );
>>>>>>
>>>>>> /* Set allocation time. */
>>>>>> cparms.setAllocTime(H5D_ALLOC_TIME_INCR);
>>>>>>
>>>>>> /*
>>>>>> * create dataspace with min/max dimensions.
>>>>>> */
>>>>>> hsize_t min_dims[] = {10000,1000,1000};
>>>>>>
>>>>>> hsize_t max_dims[] = {
>>>>>> H5S_UNLIMITED,
>>>>>> H5S_UNLIMITED,
>>>>>> H5S_UNLIMITED
>>>>>> };
>>>>>>
>>>>>> H5::DataSpace dataspace( rank, min_dims, max_dims );
>>>>>>
>>>>>> ....
>>>>>>
>>>>>> As I understand, memory is only allocated for chunks where data is
>>>>>> actually written to. In other words, no data is allocated for chunks
>>>>>> that contain only fill values. My question is, is this also true for the
>>>>>> file space on the disk? My observance is, that memory for the whole
>>>>>> dataset (also "empty" chunks) is allocated on the disk. I compared
>>>>>> sparse matrices with full matrices and the allocated memory is nearly
>>>>>> identical. Is there a way to reduce the size of sparse matrices on the
>>>>>> disc? I am thinking of using compression. Is this a common procedure to
>>>>>> achive this, or do you recommend something different?
>>>>>>
>>>>>> Thank you in advance,
>>>>>>
>>>>>> Jannis
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>>
>>>>>
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>>>>
>>>> _______________________________________________
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>>>
>>> _______________________________________________
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>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
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>
>
> _______________________________________________
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