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Re: [proteowizard-support] Error running MSConvert
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From: Chambers, M. <mat...@gm...> - 2019-03-15 18:24:07
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Indefinite hangs are certainly extremely undesirable, but if a vendor DLL makes a blocking I/O call and it doesn't time out for some OS reason, there's not much we can do about it. It would need an out-of-process watcher to look when the CPU usage had gone to 0 for a certain amount of time. Kind of like the "timeout" command, but conditioned on activity rather than absolute time. Do you know of something like that? On 3/15/2019 2:08 PM, Manuel Belmadani wrote: > Hi, > > It doesn't do it consistently actually, I reran it after I noticed and it terminated pretty quickly. > > This was run on a Google Cloud Compute VM running Ubuntu 18.04 using data stored on a local disk (local to the VM). I don't think it's > revelant in this case but I was running 7 concurrent calls (suing `xargs -P7`) with the same command this over 24 files and this is the > only one that failed. > > I noticed a similar issue when using gscfuse (a network mounted filesystem using the google cloud buckets) on multiple concurrent > processes (using different files in each process). gscfuse is known to have issues when multiple process try to read from a mount at the > same time, so the performance got quite bad (as expected) but it also seemed to leave the processes in a zombie state (Ssl state > Interruptible sleep, multithreaded). > > Sorry I don't have more information on how to reproduce this consistently. It would be nice if the docker image would exit/terminate (or > have an option to specify that) when that failure occurs. > > Hope this is useful! And thank you for your development/support of this software. > > On Fri, Mar 15, 2019 at 10:58 AM Chambers, Matthew <mat...@gm... <mailto:mat...@gm...>> wrote: > > Hi Manuel, > > Does this error repeat at the same scan every time? If so, does it also happen on native Windows? If not, does it always error, or > only sometimes? > > Thanks for the report, > -Matt > > > On 3/15/2019 1:12 PM, Manuel Belmadani wrote: >> Hi, >> >> Encountered a crash using the msconvert docker image on Linux. >> >> Process was hanging a few days after it stopped working. Noticed the STDERR had this info. It seems like the output mzML file is not >> empty either. It's about 1.5Gb (gzipped) while the other >> .RAW files are 2.5Gb and completed correctly and have nothing in the STDERR logs. >> * >> * >> *COMMAND:* >> docker run --rm -e WINEDEBUG=-all -v /home/z/local/RAW:/data -v /home/z/development/TMT/RawData:/RawData >> chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/tmt_b04_07.raw --gzip -o /RawData >> * >> * >> *STDERR:* >> $ cat RawData/rushtmt_b04_07.raw.err >> [SpectrumWorkerThreads::work] error in thread: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum >> "controllerType=0 controllerNumber=1 scan=43319" >> [C:\pwiz\msconvert.exe] Caught unknown exception. >> Please report this error to su...@pr... <mailto:su...@pr...>. >> Attach the command output and this version information in your report: >> >> ProteoWizard release: 3.0.19056 (6b6b0a2b4) >> Build date: Feb 25 2019 17:17:16 >> >> *STDOUT:* >> RawData/rushtmt_b04_07.raw.log >> format: mzML >> m/z: Compression-None, 64-bit >> intensity: Compression-None, 32-bit >> rt: Compression-None, 64-bit >> ByteOrder_LittleEndian >> indexed="true" >> outputPath: /RawData >> extension: .mzML.gz >> contactFilename: >> runIndexSet: >> >> spectrum list filters: >> >> chromatogram list filters: >> >> filenames: >> /data\rushtmt_b04_07.raw >> >> processing file: /data\rushtmt_b04_07.raw >> calculating source file checksums >> writing output file: /RawData\rushtmt_b04_07.mzML.gz >> >> >> >> _______________________________________________ >> proteowizard-support mailing list >> pro...@li... <mailto:pro...@li...> >> https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
