Hello Zeyu, Would you mind installing the latest update and report back if you still have an issue here?
Thanks, -David On Thu, Jul 18, 2024 at 1:35 PM Zeyu Wang <wangzeyuu...@gmail.com> wrote: > Hi David, > > Sorry for the late reply. Later, I just left the computer running on > E-cores, which took longer. Now I further tested the new kojak.exe you sent > me, but it still doesn't change the default CPU usage. > > I believe this "feature" is due to how Windows handles task > prioritization. I finally resolved it by adjusting the priority and > affinity of Kojak.exe in the Windows Task Manager. > > Thanks for your help and advice! > > Best, > Zeyu Wang > > On Wednesday, May 29, 2024 at 10:52:42 PM UTC-4 David Shteynberg wrote: > >> Hi Zeyu, >> >> Thanks for testing this! I recompiled another executable that should use >> more of the CPU during the search. Can you please test it to see if this >> suits your needs? Naturally, if you set the number of threads too high it >> might degrade the overall performance of your machine during the Kojak >> search. >> >> >> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download >> >> It would interesting to compare the performance of before and after this >> change. I am testing this on i9-13900H. >> >> Cheers, >> -David >> >> On Tue, May 28, 2024 at 9:21 PM Zeyu Wang <wangze...@gmail.com> wrote: >> >>> 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. >>> 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/637fa2e7-7f6d-4811-9537-858bd6bb540bn%40googlegroups.com >>> <https://groups.google.com/d/msgid/spctools-discuss/637fa2e7-7f6d-4811-9537-858bd6bb540bn%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-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/f6f97166-aaf6-4f83-a185-e2f01d63f48an%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/f6f97166-aaf6-4f83-a185-e2f01d63f48an%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-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-WD15aaZca3Kd%2B31dR1iGwzuB8wXpe5tDJ%3DL9%3DdGYn8w%40mail.gmail.com.
