Indeed, 

Variable length data does not get compressed with HDF5 at this point. Some
earlier posts in this forum already mention this. 

Actually variable data is stored elsewhere and only the references are
compressed. You have two solutions as explained in this previous post:

http://mail.hdfgroup.org/pipermail/hdf-forum_hdfgroup.org/2011-October/005136.html

Good luck!



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