On Fri, Nov 16, 2012 at 9:02 AM, Jon Wilson <jsw@fnal.gov> wrote:
Hi all,
I am trying to find the best way to make histograms from large data
sets.  Up to now, I've been just loading entire columns into in-memory
numpy arrays and making histograms from those.  However, I'm currently
working on a handful of datasets where this is prohibitively memory
intensive (causing an out-of-memory kernel panic on a shared machine
that you have to open a ticket to have rebooted makes you a little
gun-shy), so I am now exploring other options.

I know that the Column object is rather nicely set up to act, in some
circumstances, like a numpy ndarray.  So my first thought is to try just
creating the histogram out of the Column object directly. This is,
however, 1000x slower than loading it into memory and creating the
histogram from the in-memory array.  Please see my test notebook at:
http://www-cdf.fnal.gov/~jsw/pytables%20test%20stuff.html

For such a small table, loading into memory is not an issue.  For larger
tables, though, it is a problem, and I had hoped that pytables was
optimized so that histogramming directly from disk would proceed no
slower than loading into memory and histogramming. Is there some other
way of accessing the column (or Array or CArray) data that will make
faster histograms?

Hi Jon, 

This is not surprising since the column object itself is going to be iterated
over per row.  As you found, reading in each row individually will be 
prohibitively expensive as compared to reading in all the data at one.  

To do this in the right way for data that is larger than system memory, you
need to read it in in chunks.  Luckily there are tools to help you automate 
this process already in PyTables.  I would recommend that you use 
expressions [1] or queries [2] to do your historgramming more efficiently.

Be Well
Anthony 

1. http://pytables.github.com/usersguide/libref/expr_class.html
2. http://pytables.github.com/usersguide/libref/structured_storage.html?#table-methods-querying

 
Regards,
Jon

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