Hi Quincey,
I managed to work it out. Seems like I messed up the chunk size. Now it works
like expected. Thank you so much for your support!!
Jan
On 09.03.2010, at 21:41, Quincey Koziol wrote:
> 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.
>>>>>>>>> [email protected]
>>>>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Hdf-forum is for HDF software users discussion.
>>>>>>>> [email protected]
>>>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Hdf-forum is for HDF software users discussion.
>>>>>>> [email protected]
>>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Hdf-forum is for HDF software users discussion.
>>>>>> [email protected]
>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Hdf-forum is for HDF software users discussion.
>>>>> [email protected]
>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>
>>>>
>>>> _______________________________________________
>>>> Hdf-forum is for HDF software users discussion.
>>>> [email protected]
>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>
>>>
>>> _______________________________________________
>>> Hdf-forum is for HDF software users discussion.
>>> [email protected]
>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> [email protected]
>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
