Thanks for the response Jimmy. I had compiled comet and the whole tpp pipeline in a 64-bit environment (CENTOS GNU/Linux 7 both with gcc 4.8.3 and gcc 6.0.0) and the problem persisted. Just to verify, I downloaded the recent binaries and source for comet (2015021) and tried them, but the problem persisted.
Basically, what it feels like is that there is something in the mzXML parsing portion that checks the file size (or an index or something) and uses int (instead of int64). GNU/Linux is LP64 and MS Windows is LLP64 both of which use a 32-bit representation for int ( http://www.unix.org/whitepapers/64bit.html https://en.wikipedia.org/wiki/64-bit_computing), so even if you use a 64-bit compiler on a 64-bit system your int will still be 32-bit (unless I misunderstand something) and as far as I know, there's no way to tell gcc to substitute int64 for int. If there aren't any ideas on where to start in the codebase, I'll start digging in with gdb On Fri, Oct 9, 2015 at 1:08 PM, Jimmy Eng <[email protected]> wrote: > Daniel, > > The issue you're seeing might be due to TPP windows programs compiled as > 32-bit binaries. The first thing I'd try is grabbing a 64-bit binary of > one of the tools to see if that fixes things. You can grab a 64-bit Comet > binary from its SourceForge download site if you want to test this. I wish > I could tell you definitively that the 64-bit Comet binary will work for > you but I just don't have access to files >2GB to test with. > > > On Fri, Oct 9, 2015 at 11:09 AM, Daniel Hyduke <[email protected]> > wrote: > >> I've recently noticed some failures when using comet and xtandem! from >> TPP to search some centroided DDA files generated by qtofpeakpicker. These >> failures were all associated with files > 2GB. I was able to reduce the >> file size by increasing the threshold which then lead to readmzXML, tandem, >> and comet actually reading the files and searching them. I'm guessing that >> there's a place in the TPP mzXML code that uses an int (which is 32-bit) >> that's causing this problem. >> >> I've used TPP 4.8.0 on Windows 7 (installed via the exe provided on >> sourceforge) and built the tpp from the svn on GNU/Linux (centos 7) and >> encountered the same problem. >> >> I was wondering if anybody had any thoughts on where I should start >> sifting through the code? >> >> -- >> 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/d/optout. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/-3-ppv8-gVE/unsubscribe > . > To unsubscribe from this group and all its topics, 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/d/optout. > -- 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/d/optout.
