[R] how to sort huge (> 2^31 row) dataframes quickly
mckellercran at gmail.com
Mon Jul 30 18:25:55 CEST 2012
I have some genetic datasets (gzipped) that contain 6 columns and
upwards of 10s of billions of rows. The largest dataset is about 16 GB
on file, gzipped (!). I need to sort them according to columns 1, 2,
and 3. The setkey() function in the data.table package does this
quickly, but of course we're limited by R not being able to index
vectors with > 2^31 elements, and bringing in only the parts of the
dataset we need is not applicable here.
I'm asking for practical advice from people who've done this or who
have ideas. We'd like to be able to sort the biggest datasets in hours
rather than days (or weeks!). We cannot have any process take over 50
GB RAM max (we'd prefer smaller so we can parallelize). .
Relational databases seem too slow, but maybe I am wrong. A quick look
at the bigmemory package doesn't turn up an ability to sort like this,
but again, maybe I'm wrong. My computer programmer writes in C++, so
if you have ideas in C++, that works too.
Any help would be much appreciated... Thanks!
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
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