I have uploaded the files bsa-20fmol-2.wiff/.scan. Although the converter doesn't crash on this file, it did reach > 300 MB memory usage in my attempt.
Let me know if you need anything else for your debugging. Thanks, Moyez On Mar 16, 5:46 pm, Natalie Tasman <[email protected]> wrote: > http://groups.google.com/group/spctools-discuss/web/how-to-upload-fil... > > > > On Mon, Mar 16, 2009 at 2:43 PM, Moe <[email protected]> wrote: > > > Thanks for the VC tips. Where can I upload the BSA file? > > > Moyez > > > On Mar 16, 5:25 pm, Natalie Tasman <[email protected]> wrote: > >> Hi Moyez, > > >> Of course we have our own files to test, but yes, please upload your > >> file, as we've never observed the behavior you're reporting. > > >> And also please rerun your conversions with the "-v" (verbose) option > >> and copy and paste the output up to the "sha-1" calculation. > > >> You're welcome to rebuild and debug the converter on your own. Just > >> open the TPP.sln file and build the mzWiff project from there. Note > >> you'll also need the "win_lib" project to be checked out at the same > >> level as the TPP code for boost, zlib, etc. > > >> -Natalie > > >> On Mon, Mar 16, 2009 at 2:07 PM, Moe <[email protected]> wrote: > > >> > Hi Natalie, > > >> > The leak is apparent in QStar WIFF files of any size. For a 30 minute > >> > BSA QC run (25 MB file size), peak memory usage reached 314 MB (to > >> > produce ~195 MB mzXML output), which doesn't seem reasonable. Do you > >> > have your own data files that you can debug with? If not, I can upload > >> > the BSA run to your FTP site (need the details). > > >> > The data I'm trying to analyze consists of 2 hour runs at about 500 MB > >> > each. mzWiff crashes about halfway through a data file, leaving a 1.3 > >> > GB (incomplete) mzXML file which ends at an elution time of about 60 > >> > minutes (when memory reaches slightly > 2 GB). > > >> > I have tried older releases of the executable up to 4.0.0 and all > >> > behave the same. I am considering recompiling a 64-bit executable, or > >> > trying to locate the leak. I'll check out the code from SourceForge, > >> > but if you have additional instructions for setting up the VC project, > >> > please let me know. > > >> > Thanks, > >> > Moyez > > >> > On Mar 16, 1:41 pm, Natalie Tasman <[email protected]> wrote: > >> >> Hello Moyez, > > >> >> Thank you for the detailed bug report. I haven't heard of issues with > >> >> mzWiff. Thanks for the MSVC hint-- I'm pretty sure this is not turned > >> >> on yet, but actually probably shouldn't be necessary. I agree with > >> >> you that that much memory usage sounds like a memory leak. The > >> >> converters are designed to process data scan-by-scan with a relatively > >> >> low memory overhead. > > >> >> If you can upload a sample file we can take a look and see if we can > >> >> replicate behavior and then fix it. > > >> >> Thanks, > > >> >> Natalie > > >> >> On Mon, Mar 16, 2009 at 9:11 AM, Moe <[email protected]> wrote: > > >> >> > I'm trying to convert Analyst QStar Elite data acquired with Analyst > >> >> > QS 2.0, with mzWiff version 4.2.0(build Feb 19 2009 09:48:08), on > >> >> > Windows XP Pro SP3 and Windows Server 2003 R2 x64 Standard SP2. > > >> >> > There appears to be a memory leak causing process memory to accumulate > >> >> > to > 2GB, shortly after which the program crashes with error: > > >> >> > ERROR: COM error 80004005 while processing sample#2 > >> >> > INFO: error message: Unspecified error > > >> >> > This happens both on 32-bit XP and 64-bit Server 2003, both systems > >> >> > have > 4GB physical memory. The per-process addressable limit for a > >> >> > 32- > >> >> > bit process is 2GB unless compiled with the /LARGEADDRESSAWARE Visual > >> >> > C > >> >> > ++ linker flag. > > >> >> > Is anyone aware of this problem? Is this in fact a leak that can be > >> >> > avoided? > > >> >> > Thanks, > >> >> > Moyez- Hide quoted text - > > >> >> - Show quoted text -- Hide quoted text - > > >> - Show quoted text -- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
