Thank you Brendan for your excellent explanation. Brian
On Wed, Mar 7, 2012 at 12:22 PM, Brendan MacLean <[email protected]>wrote: > Hi Brian, > X! Tandem works as follows: > 1. It loads processed versions of all of your measured spectra into > memory. The memory usage here can be increased or decreased by > keeping or discarding more of the measured peaks. By default X! > Tandem native keeps only 50 (good for the scoring algorithm used), and > k-score keeps all or at least 100 is recommended. > 2. These loaded spectra are divided among the threads you allow X! > Tandem to use. > 3. Each thread loads each FASTA sequence in succession, testing its > assigned spectra against the peptides in the FASTA sequence. > > So, your memory consumption is really bounded by the number of spectra > you are attempting to ID at any given time, and then number of peaks > you are allowing X! Tandem to use to do that. > > If your are working with larger numbers of files, then I suppose you > could force higher memory use by processing multiple files at once and > allowing each to use only a single thread. The more spectra you > attempt to ID at once the higher the memory use, but that is about it > for X! Tandem. > > Also, remember that regardless of your system, you will need a 64-bit > build of X! Tandem for it to be able to address more the 2G of RAM. > > Hope that helps clarify. Unfortunately, in this case, I don't think > the extra memory pays a big dividend. > > --Brendan > > On Mar 6, 4:59 pm, Brian Hampton <[email protected]> wrote: > > On a 64-bit install of Ubuntu 10.10 with 18Gb of RAM I only see about > > 10% of RAM being used during a tandem search. I added 16Gb to the > > existing 2Gb of RAM and the search takes less time to run but I was > > expecting much more RAM to be used than 10%. > > > > I have threads set to 8 on a dual quad core XEON. > > > > I thought tandem was memory intensive so would use much more RAM for > > the search. Is there a setting (such as threads for the processors) > > that allows the search to use more RAM and execute the search faster? > > > > Thanks in advance, > > > > Brian Hamtpton > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" 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/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" 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/spctools-discuss?hl=en.
