how to restart computation after interruption

Bayesian analysis of blinking and bleaching

how to restart computation after interruption

Postby pascalB » Fri Dec 13, 2013 3:47 pm

Hello
The manual states that the result file of the stand-alone program allows restarting of the computation after an interruption.
Could anybody please indicate how to perform this restart ?
Thank you
pascalB
 
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Re: how to restart computation after interruption

Postby edrosten » Fri Jan 03, 2014 10:30 am

Hi,

Normally 3B is run roughly like this:
multispot5_headless --log_ratios markup.png --save_spots output-1.txt some_images/*.tiff

To restart the run you would do:

multispot5_headles --load_checkpoint output-1.txt --save_spots output-2.txt some_images/*.tiff

Note that the input file and output file must be different. Also you don't need to specify the markup a second time. In order to combine the results back into a single file, you can do:

cat output-1.txt output-2.txt > output-all.txt

The restarting and combining can be used as many times as you wish.
edrosten
 
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Re: how to restart computation after interruption

Postby william2014 » Mon Nov 24, 2014 11:08 am

Hi there,
i am currently trying to restart my 3B computation after interruption. we have to run the following command:
multispot5_headles --load_checkpoint output-1.txt --save_spots output-2.txt some_images/*.tiff

I did almost the same thing. Also, my command was:
./multispot5_headless --save_spots test_data/results1.txt --log_ratios test_data/markup1.bmp test_data/img_000000232.fits test_data/img_000000060.fits

Everything was ok. But after an interruption, when i want to restart the computation by running now the following command:

./mutispot5_headless --load--checkpoint test_data/results.txt --save_spots test_data/results2.txt est_data/img_000000232.fits test_data/img_000000060.fits, i get the following error message:

!!GV3::Register String save_spots must be defined. Exception. Terminate calling after throwing an instance of 'GVars3:: gvar was not defined' Aborted.
Could someone help me?
Thanks
william
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Re: how to restart computation after interruption

Postby hoha » Mon Nov 24, 2014 8:02 pm

Hi,

I think your problems seems to be the command:
It is:
./mutispot5_headless --load_checkpoint test_data/results1.txt --save_spots test_data/results2.txt test_data/img_000000232.fits test_data/img_000000060.fits

The red letters are some of the things that your command line was missing.
Remember that you need the results file that in your case I suppose is results1.txt

Let me know if this was helpful.
Haydee.
hoha
 
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Re: how to restart computation after interruption

Postby william2014 » Wed Nov 26, 2014 12:32 pm

Hi Hoha,

thanks, your rewark was helpful. The commandline is now working.

Regards
William
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Re: how to restart computation after interruption

Postby hoha » Wed Nov 26, 2014 4:34 pm

Wonderful!!

Just a thing... I forgot to tell you that the code of multispot5_headless.cc file needs to add an else, if you dont know where or how I to do it let me know.
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Re: how to restart computation after interruption

Postby edrosten » Sat Dec 13, 2014 5:43 pm

hoha wrote:Wonderful!!

Just a thing... I forgot to tell you that the code of multispot5_headless.cc file needs to add an else, if you dont know where or how I to do it let me know.


Sounds like a bug! Can you post some details and I'll fix it.


-Ed
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Re: how to restart computation after interruption

Postby hoha » Fri Dec 19, 2014 7:15 am

Hi Ed,

Yes it's a bug, you only need to add an else next to if(checkpoint_file != "") {.....} it's approx in line 130 in the multispot5_headless.cc file. This fix the problem. This was helpful? Or what details u were talking about?

Regards,
Haydee.
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Re: how to restart computation after interruption

Postby edrosten » Fri Jan 02, 2015 10:47 am

hoha wrote:Yes it's a bug, you only need to add an else next to if(checkpoint_file != "") {.....} it's approx in line 130 in the multispot5_headless.cc file. This fix the problem. This was helpful? Or what details u were talking about?


Hi,

This is helpful, but I'm not sure I follow exactly: I've made some edits to my version so I might not be looking at the same source file as you. Could you attach your fixed version of the file? Also, which version is yours derived from?

Alternatively, if you've been using git or github, you could send me a pull request.

Regards

-Ed
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Re: how to restart computation after interruption

Postby hoha » Fri Jan 09, 2015 3:04 am

Hi edrosten!

I have been using threeB-1.1, but I didn't use any of these version control systems. But if you want we can create a new repository, would you?

P.D. Attached the fixed file.
multispot5_headless.zip
I compressed because I couldn't upload only the file
(2.13 KiB) Downloaded 3005 times



Rewards,
Haydee.
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Re: how to restart computation after interruption

Postby edrosten » Tue Jan 27, 2015 6:52 pm

hoha wrote:Hi edrosten!

I have been using threeB-1.1, but I didn't use any of these version control systems. But if you want we can create a new repository, would you?

P.D. Attached the fixed file.
multispot5_headless.zip



Rewards,
Haydee.


Thanks!

I've added the changes to the source code. I've not compiled a release yet.

-Ed
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Re: how to restart computation after interruption

Postby Swader » Wed Aug 02, 2017 8:04 am

Does restarting lose the progress?
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