Hi Chris, I was swamped with other urgent issues to solve. I remember that megatest setup was in my todo list for quite a long time. I will setup as soon as I finished some jobs.
Right now, there is no megatest for BlastDB reading/writing performance checking. I need to add a simple time check when I open BlastDB. If it takes more than a few seconds, there are problems. I posted a bug report in Google Code. It has nothing to do with building/indexing BlastDB. Just opening step. Thanks, Namshin Kim On Wed, Oct 15, 2008 at 12:42 AM, Christopher Lee <[EMAIL PROTECTED]>wrote: > > Namshin, > shouldn't our megatests have caught any such gross performance > decrease?!? I haven't seen a single megatest report in months, let > alone any indication of a performance problem. As I have said before, > I am extremely concerned that we do not seem to be regularly running > the extensive performance tests we have written. Not running the test > suite nightly is like having no test suite at all. > > Regarding this performance problem, please submit a bug report that we > can reproduce, to the issue tracker, not just an email saying "BlastDB > has gotten slow". I've posted several times that people should file > reproducible bug reports, which means > - include an exact series of steps to reproduce the bug. For example, > based on your email I have no idea if the problem occurs when opening > a FASTA sequence file for the first time (which requires building a > shelve index file), or when opening an existing shelve index file... > - include any data files needed to reproduce the bug > - include precise build information (e.g. commit ID) for the version > that has the performance problem. Ideally please indicate the most > recent version that DID NOT have the performance problem. > - include detailed platform information (OS version info, memory size, > etc.) > > This should be trivial to fix, if you can give us a reproducible. As > far as I know, nothing has changed in our seqdb indexing code, so this > highlights how fragile and unreliable shelve / bsddb's performance > is... We do not do anything to load the index into memory. > > -- Chris > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
