On Mon, Sep 08, 2008 at 09:50:18AM -0700, Russell wrote: -> This is kind of a dumb question, but do you ever find 32-bit mode to -> be a problem for bioinformatics programming? My friend Andrew has been -> helping me look into some MemoryOverflow bugs that were cropping up -> with tests of very large arrays in h5py, and we finally traced them to -> the fact that I'm running h5py in 32-bit mode, and he runs his -> development box in 64-bit mode. -> -> HDF5 will happily create arrays longer than 2**31 on a 32 bit machine, -> but array indexes are evidently limited to Py_ssize_t, which is a C -> signed long. So you can create the database, but you can't index -> anything beyond dset[2**31-1]. If we were talking about an normal -> numpy array, this question would be moot, but HDF5 makes it easy to -> create datasets that are much bigger than memory. Since HDF5 -> gracefully handles sparse arrays, it's *really* easy. -> -> Well, iorich has a 32-bit kernel. D'oh.
:) I don't imagine we'll be taking slices of sequences larger than 1 gb; I don't know of any chromosomes that big. Chris is really much more of an expert than I am on super-large data sets... --titus -- C. Titus Brown, [EMAIL PROTECTED] --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
