Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

[Zeyu Wang]

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  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  wrote:

> Hi David,
>
> Thank you! Here are the two kojak parameter files I tested (the 
> original and the customized).  Link: Kojak_Troubleshooting 
> 
>  .
>
> 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  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/UP05640_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 
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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

[Zeyu Wang]

Hi David,

Thank you! I will replace the previous Kojak.exe (official build) with this 
new gcc compiled version and have a try.  

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  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  wrote:

> Hi David,
>
> Thank you! Here are the two kojak parameter files I tested (the 
> original and the customized).  Link: Kojak_Troubleshooting 
> 
>  .
>
> 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  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/UP05640_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
>  
> 
> .
>
> -- 
> You received this message because you are subscribed to the Google 
>

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

['David Shteynberg' via spctools-discuss]

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  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  wrote:
>>>
 Hi David,

 Thank you! Here are the two kojak parameter files I tested (the
 original and the customized).  Link: Kojak_Troubleshooting
 
  .

 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  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/UP05640_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
 
 .

 --
 You received this message because you are subscribed to the Google
 Groups "spctools-discuss" group.
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>>> To view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com
 

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

[Zeyu Wang]

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  wrote:
>>
>>> Hi David,
>>>
>>> Thank you! Here are the two kojak parameter files I tested (the original 
>>> and the customized).  Link: Kojak_Troubleshooting 
>>> 
>>>  .
>>>
>>> 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  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/UP05640_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
>>>  
>>> 
>>> .
>>>
>>> -- 
>>> 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
>>>  
>>> 
>>> .
>>>
>>

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