> it is very reasonable to code that part in some fast language while delegating the bigger (and often more complex) part in a higher level language such as Rub

> it is very reasonable to code that part in some fast language while delegating the bigger (and often more complex) part in a higher level language such as Ruby. Agreed. Contrary to what lbrandy said, I've tried it, and it works very well. Writing Ruby extensions in C, or wrapping C libraries for Ruby, is really easy. Wrapping a PNG library for Ruby allowed us to draw about a trillion pixels' worth of images based on the human genome across a modest cluster of ~100 cores in a few days [1,2,3]. For reference, a terapixel image is about ~4TB of uncompressed data and ~800GB compressed, with Microsoft putting up comparable numbers for a project they ran on a fancier HPC cluster in 2010 [4]. We were heavily compressing it into PNG tiles on the fly so ours came down to ~60GB. Regarding pointers to pointers to ints--if you keep all the data within the heap of the Ruby extension, as we did with the wrapped PNG library, then it can be stored in whatever simple data structure you want. [1] http://chromozoom.org/?db=hg19 http://chromozoom.org/?db=hg19 [2] https://github.com/rothlab/chromozoom https://github.com/rothlab/chromozoom [3] http://bioinformatics.oxfordjournals.org/content/29/3/384.full#sec-3 http://bioinformatics.oxfordjournals.org/content/29/3/384.fu... [4] http://research.microsoft.com/en-us/projects/terapixel/ http://research.microsoft.com/en-us/projects/terapixel/