Nothing to add! Dave has the right idea for a performance fix, and Natalie is correct about TPP being addicted to Boost already.
Brian On Thu, Feb 4, 2010 at 2:37 PM, Natalie Tasman <[email protected] > wrote: > Hi Dave, Brian, > > Just jumping into comment on Boost. Yes, it is welcomed and in fact > already used in the TPP (as well as the TPP-included ProteoWizard project); > however, because the Boost API and process of building Boost libraries have > not been particularly stable, we've found it necessary to fix the version of > Boost that we work with. Our current version is 1.39.0. As long as you can > test against that, you're contributes would be fine-- and no doubt very > welcomed. > > -Natalie > > > > On 2/4/10 2:26 PM, Dave Trudgian wrote: > >> Brian, >> >> Yup. I just discovered this too, as per other post. On our servers it's >> not disk-bound, as the 1.6GB .pep.xml is fully cached, but the continued >> rpeated slows things down. >> >> R.E. solutions for this, is Boost code welcomed in the main TPP tools? I >> think I can re-write using a single pass parse of the .pep.xml into a >> Boost.MultiIndex hash of structs/classes containing the required peptide >> info. >> >> DT >> >> Brian Pratt wrote: >> >>> Looking at the code I can see where this would easily become diskbound >>> for large data sets - it reads and rereads the same pepXML files repeatedly, >>> but the effect is probably masked by disk cacheing up to a certain point. >>> Somebody would need to write some logic for cacheing the file contents to >>> speed this up properly. >>> >>> Brian >>> >>> On Thu, Feb 4, 2010 at 12:09 PM, Jake W <[email protected] <mailto: >>> [email protected]>> wrote: >>> >>> I've seen the same thing. On datasets where >>> ASAPRatioPeptideRatioParser completes in a few minutes, >>> ASAPRatioProteinRatioParser can take an hour or so. This is on a >>> Windows machine running TPP ver. 4.3.0. >>> >>> Jake >>> >>> -- >>> 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] >>> <mailto:[email protected]>. >>> To unsubscribe from this group, send email to >>> >>> [email protected]<spctools-discuss%[email protected]> >>> <mailto:spctools-discuss%[email protected]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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.
