Hi Jan,
On Mar 9, 2010, at 2:31 PM, Jan Linxweiler wrote:
> Hi Quincey,
>
> I prepared a little program to show you the issue and now it works like
> charm. In this example every second chunk is empty and the file size seems
> to be half of the completely filled dataset. Is this reasonable?
Yes, that's what I would expect.
> Or did I possibly make a mistake again? Maybe I messed up with the chunk size
> is my real world example. I'm going to find out what the difference in the
> two is and than report to you.
Yes, please let us know what the difference is.
Quincey
> Thank you very, very much so far.
>
> Jan
>
> On 09.03.2010, at 19:19, Quincey Koziol wrote:
>
>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Hdf-forum is for HDF software users discussion.
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>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> [email protected]
>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Hdf-forum is for HDF software users discussion.
>>>>> [email protected]
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>>>>
>>>>
>>>> _______________________________________________
>>>> Hdf-forum is for HDF software users discussion.
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>>>
>>>
>>> _______________________________________________
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>>
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
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>
>
> _______________________________________________
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