Hi Jimmy, Many thanks - the "spectrum_batch_size" trick worked! Are the results (e.g. the expectation values) dependent on the batch size?
Cheers, Magnus On Monday, 3 March 2014 19:05:21 UTC+1, Jimmy Eng wrote: > > Mangus, > > There's something broken with our latest Comet 2013.02 rev. 2 release > under Windows. We attempted to address large memory search performance, > which appeared to work fine in our limited testing, but we definitely broke > something else in the process and are actively working on addressing this > issue now. > > The current suggested work-around would be: > a). make use of the "spectrum_batch_size" parameter; set it to some > value, say 3000 or 5000 to allow you to process your data by searching > smaller batches of spectra at a time > b). revert the Comet binary to the previous 2013.02 rev. 1 release. > > - Jimmy > > > On Mon, Mar 3, 2014 at 9:46 AM, [email protected] <javascript:> < > [email protected] <javascript:>> wrote: > >> Dear TPP developers and users, >> >> I took the the new Comet in TPP 4.7 (POLAR VORTEX) out for spin, but keep >> getting errors like "Error - >> CometMemMgr::CometMemAlloc(pdTmpFastXcorrData[1374])" and "Operation not >> permitted" when searching an mzXML made from some 5 GB Orbitrap E. coli >> data. This mzXML file works fine with both X!Tandem and SpectraST. To get a >> parameter file, I created one with "comet -p". >> >> When I search a tiny mzXML file with one MS1 and three MS2 spectra I >> created myself, it works, and I get reasonable results. But I have tried it >> with reasonably small ion trap datasets of <100 MB, I get the errors as for >> the 5 GB Orbi data. >> >> Any suggestions? Should I allocate more memory to comet somewhere? >> >> >> Cheers, >> >> Magnus >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
