My collaborators at SUNY Buffalo recently generated an incredible data set that I've been working on. It is comprised of 80 GB of label free Fusion runs. Its about 2.5 million spectra in total. Even my Destroyer takes about 20 hours to do the peak picking, searching and quantification of an experiment this big.
It gives me plenty of time, however, to figure out what Proteome Discoverer is doing behind the scenes. I really like this shot at the top. This is what PD 2.0 is doing during the "Spectrum Selector" node. It is truly using all 8 of my processing cores for this step. Check out PD 1.x at this step sometime. Its typically maxed out on one core. I'm seriously not trying to rub it in that I have this software and you don't. I'm hoping to get you all excited for when the lawyers finally let them release it! True multicore processing at every step!
Dear Ben,
ReplyDeleteCould you please tell me how you get all your cpu's to work in parallel. Any special setting?
Many thanks in advance.
Peter
Peter,
ReplyDeleteIt depends on the nodes you are using, but most of the settings are in the "Administration" menu. SequestHT, for example, will be set to use "0" cores by default. In this setting it will attempt to determine how many cores are available and use them all. Sometimes PD 1.4 couldn't tell how many cores were present on every PC so you have to manually tell it. Don't know if that would happen in PD 2.0, but it doesn't hurt to try it. In Byonic you have 3 options, I think -- high, medium, and low processor load. On my PC, high load is dramatically faster than medium which is the default.
Hope this helps!
-Ben