Saturday, May 10, 2014

Proteome Discoverer 1.4 on a server

I get this question a lot, get the answers mixed up, and wonder "why haven't I just posted this on the blog where I can find it?"


Can I install PD 1.4 on a Windows Server?
Answer: Yes!  People all over have PD 1.4 running on their servers.  We know that it works for sure on Windows Server 2008 and Windows Server 2012.

We also know that PD 1.4 works well with multiple cores.  It appears to work best, however (according to anecdotal evidence) when up to 24 cores are being used.  I have heard of two situations (which, honestly, may have been the same situation, I just heard it from different people) where devoting more cores from a cluster to run PD 1.4 didn't improve speed the way we might expect.  For example, 48 threads from the cluster weren't twice as fast as 24 threads from the cluster (maybe it was 80% faster, I don't know, but I've heard that it wasn't 2x, thats all).  But I only run 4 threads on my laptop and on my team's server.  And I can knock out a 1.5GB RAW file with 3 dynamic mods in 6 minutes (SSD buffers..woooo!) so 24 threads sounds hella fast to me!

Keep in mind that PD 1.4 is a couple of years old now.  Maybe there will be a new version soon!


  1. 1.5GB RAW file in 6 minutes, that's really fast!

  2. Not all nodes are multithreaded in PD. So besides the actual search it does not benefit too much from many more cores. And with e.g. hundred cores or more, the search itself isn't the limiting factor anymore.
    You can start several searches in parallel which speeds up things a lot, but thats not really recommended or tested and also requires some modifications to work.