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Re: Loading portion of large HDF5 array?

  • To: mathgroup at smc.vnet.net
  • Subject: [mg114113] Re: Loading portion of large HDF5 array?
  • From: Oliver Ruebenkoenig <ruebenko at wolfram.com>
  • Date: Wed, 24 Nov 2010 06:57:55 -0500 (EST)

Paul,

On Tue, 23 Nov 2010, Paul wrote:

> On Nov 22, 4:40 am, Bill Rowe <readn... at sbcglobal.net> wrote:
>> On 11/20/10 at 6:27 PM, pnort... at gmail.com (Paul) wrote:
>>
>>> I have a large matrix (>10gb) in an HDF5 file.
>>> Is there a way to read only a portion of this matrix using Import[]
>>> and the HDF5 import format?
>>
>> Yes. You can read various portions of the file. See
>>
>> ref/format/HDF5
>>
>> in the DocumentCenter for details
>
> A specific example is below (snipped output from h5ls -vlr) with
> matrix '/data' with dimensions ~ {10^9, 51}. How would I read in the
> first 1000 rows, the next 1000? Thanks for the documentation pointer
> but I didn't find any way to do this. I understand you can load in
> datasets separately but maybe not a portion of a single dataset.
>
> Import["file.h5', {"Datasets", "/data"}] attempts to load the full
> matrix.
>
> /data                    Dataset {110945492/Inf, 51/51}
>    Location:  1:800
>    Links:     1
>    Chunks:    {1000, 51} 204000 bytes
>    Storage:   1158043888 logical bytes, 3840201966 allocated bytes,
> 107.67% utilization
>    Filter-0:  deflate-1 OPT {4}
>    Type:      IEEE 32-bit little-endian float
>
>

unfortunately this does not work out of the box right now. There is a 
suggestion for this to happen in a future version. Until then, you'd have 
to read it manually, unfortunately.

Oliver


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