Re: [Pytables-users] File bloat with row.update()

[Francesc A. <fa...@py...>]

A Wednesday 22 September 2010 22:04:53 David E. Sallis escrigué:
> I have a table in an HDF5 file consisting of 9 columns and just over
> 6000 rows, and an application which performs updates on these table
> rows.  The application runs hourly and performs updates to the table
> during each run.  No new table rows are added during a run.  I
> perform updates to the table by using row.update() inside a
> table.where() iterator loop.
> 
> I have noticed that after each application run the size of the file
> increases significantly, and over time the file size balloons from
> just over 21 MB to well over 750 MB, with no new data being added,
> just updated.
> 
> h5repack() run on this file will restore it to its original size with
> no loss of data.
> 
> My questions are:
> 
> 1) What causes the file size increase and
> 2) is there anything I can do to prevent it?
> 
> I am using PyTables 2.1.1, HDF5 1.8.3, Python 2.6 under Linux RedHat
> 5.

Hmm, sounds like a bug somewhere.  Could you try with a recent version 
of HDF5?  If that does not help, could you please send me a small script 
reproducing that?

-- 
Francesc Alted