Hi David, I tested it with the new version. Now it works well, but CPU usage problem still exists. I change threads from 24, 20 to 16 and 8, but the TPP searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe running.
Thanks again! Anyway, it can still run, though may take a bit longer time. Best, Zeyu On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote: > Hello Zeyu, > > Sorry I don't know the answer to your question but if it helps I corrected > the issue you identified in the previously distributed version compiled > with gcc for the TPP distribution installer. > I placed the gcc compiled version of Kojak.exe here: > https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download > > Perhaps this one exhibits a different behavior when running > multi-threaded. In my tests the two version ran nearly at the same speed > on my computer. > > Cheers, > -David > > On Tue, May 28, 2024 at 7:27 PM Zeyu Wang <wangze...@gmail.com> wrote: > >> Hi all, >> >> I notice another small issue (maybe this is my win11 problem?): when >> running Kojak within TPP, I set the threads to 24 or 28. However, in the >> task manager, I notice the main search was always running on exact >> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice >> similar problem? >> >> [image: Snipaste_2024-05-28_22-14-14.png] >> [image: Snipaste_2024-05-28_22-15-57.png] >> >> Best, >> Zeyu >> >> >> >> >> >> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote: >> >>> Hi David, >>> >>> Thanks! After replacing the current kojak.exe, It seems that now the >>> kojak searching can continue without error message. >>> >>> Best, >>> Zeyu >>> >>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote: >>> >>>> Hello again, >>>> >>>> After a bit of digging I found that this is likely caused by a bug in >>>> the current TPP compiled and distributed version of Kojak that will have >>>> to >>>> be corrected for the next release. Meanwhile you should be able to >>>> download and use the official Kojak build available here: >>>> https://kojak-ms.systemsbiology.net/download.html >>>> >>>> >>>> This version will require additional .net dependecies! >>>> >>>> Please replace the current kojak executable in c:/TPP/bin with the >>>> executable from the zip file and try running kojak again. >>>> >>>> >>>> Best of luck and keep us posted to your progress. >>>> >>>> -David >>>> >>>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang <wangze...@gmail.com> wrote: >>>> >>>>> Hi David, >>>>> >>>>> Thank you! Here are the two kojak parameter files I tested (the >>>>> original and the customized). Link: Kojak_Troubleshooting >>>>> <https://gtvault-my.sharepoint.com/:f:/g/personal/zwang3136_gatech_edu/EnxqUYYUZGNDvCEG8kB-vtsB3Q2GfNvcqaAygJ_0ttBEFA?e=Ub1nub> >>>>> . >>>>> >>>>> Best, >>>>> Zeyu >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote: >>>>> >>>>> Hello Zeyu, >>>>> >>>>> Thanks for your interest in TPP and Kojak. Yes we maintain and use >>>>> Kojak in the latest release. To help us troubleshoot this problem, would >>>>> you mind sharing the parameter file used in your test? >>>>> >>>>> Thank you! >>>>> -David >>>>> >>>>> On Fri, May 24, 2024, 12:28 AM Zeyu Wang <wangze...@gmail.com> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Are there anyone using Kojak in the TPP v7.0.0 ? Today I follow the >>>>> instruction and try to run a quick test. But at the very beginning, it >>>>> reports an error. >>>>> >>>>> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, >>>>> Institute for Systems Biology Visit http://kojak-ms.org for full >>>>> documentation. ****** Begin Kojak Analysis ****** Time at start: Fri May >>>>> 24 >>>>> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12 >>>>> preconfigured crosslinkers. Reading FASTA database: >>>>> c:/TPP/data/dbase/UP000005640_9606_20230222.fasta >>>>> ... >>>>> Total Proteins: 20594 >>>>> Adding Kojak-generated decoys. New Total Proteins: 41188 >>>>> 5658462 peptides to search (2785870 linkable). >>>>> >>>>> Fri May 24 02:52:45 2024 ERROR: >>>>> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt >>>>> for output. Please ensure path and write permissions are correct." >>>>> >>>>> Is the error due to the output file path format? Or shall I adjust the >>>>> read/write permission of the TPP? >>>>> >>>>> Best, >>>>> Zeyu >>>>> >>>>> -- >>>>> 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 spctools-discu...@googlegroups.com. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com >>>>> >>>>> <https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>>> -- >>>>> 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 spctools-discu...@googlegroups.com. >>>>> >>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com >>>>> >>>>> <https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> -- >> 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 spctools-discu...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/db56c834-5f2b-486f-a160-9b3bf9228ed2n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/db56c834-5f2b-486f-a160-9b3bf9228ed2n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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