File size continuously increase when use h5D.write() to update some data block in original place.

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Hi, I am trying to update a data block into a h5 file using h5D.write.
The updated file opens with no problem, but the file size continuously increased about 6MB everytime I update.
The code is below:
% the data block size is [sizeX,sizeY,1], always at the same position.
fid =,'H5F_ACC_RDWR','H5P_DEFAULT');
dset_id =,['/Data']);
block = [sizeX,sizeY,1];h5_block = fliplr(block); %the same size as original file
dims = [sizeX,sizeY,1];
mem_space_id = H5S.create_simple(length(dims),h5_block,[]);
space_id = H5D.get_space(dset_id);
aStart = [0,0,0];h5_start = fliplr(aStart);
H5D.write(dset_id,'H5ML_DEFAULT',mem_space_id,space_id,'H5P_DEFAULT',aData); %aData is updated data of same size as original file
Since no size expansion is involved, Is there a way to avoid file size increase?

Accepted Answer

Walter Roberson
Walter Roberson on 13 Dec 2021
Sorry, no.
When you update, HDF5 writes a new block in, and then marks the old block as no longer in use.
Unfortunately it also has no defined garbage collection, so although the next time around the now-unused block would in theory be large enough to store the data to be written, in practice it may not be.
There is no inherent HDF5 operation to reclaim space.
Walter Roberson
Walter Roberson on 13 Dec 2021
If the data is being compressed, then remember that a change in value may result in the compressed data being shorter or longer than the previous version.
h5repack appears to support a command line argument to indicate compression type.
For example -f GZIP=9

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