Pecan: They’re not good for pies either.

Pecan has been a thorn in our side for the past month or so. Between the huge memory requirements and the lack of meaningful error messages it’s been slow going for results. At lab meeting last week we kicked around the idea of running Pecan on an AWS instance because of the extreme memory requests of the program (Laura’s data wants ~92gb, Yaaminis’s ~140) and the impending deadlines. So I spent a bit of time today figuring that out.

As it stands, I have it sort of working on a tiny (free) instance. Pecan, Percolator, pyMZML, and numpy installed and working. The final step will be either installing and using Sun Grid Engine (What we use on Emu and Roadrunner), or ensuring that Open Grid Engine (What comes installed on AWS instances) is compatible with SGE and then setting that up.

SGE would be the obvious answer, but in someone’s infinite wisdom, they decided the configuration program amon should be a nice, pretty GUI. All well and good until you have to set it up over SSH.

I’ll try and download a couple of files, and someone’s reference proteome tonight, and will test both solutions tomorrow, and hopefully have someone that we can transfer over to a large server pretty easily.

Advertisements