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superresolved.com • View topic - how to restart computation after interruption

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
 
Posts: 1
Joined: Fri Dec 13, 2013 3:24 pm

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
 
Posts: 42
Joined: Wed Jul 18, 2012 2:54 pm

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
william2014
 
Posts: 3
Joined: Thu Nov 13, 2014 10:20 am

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
 
Posts: 9
Joined: Mon Apr 14, 2014 9:24 pm

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
william2014
 
Posts: 3
Joined: Thu Nov 13, 2014 10:20 am

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.
hoha
 
Posts: 9
Joined: Mon Apr 14, 2014 9:24 pm

Re: how to restart computation after interruption

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

edrosten
 
Posts: 42
Joined: Wed Jul 18, 2012 2:54 pm

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.
hoha
 
Posts: 9
Joined: Mon Apr 14, 2014 9:24 pm

Re: how to restart computation after interruption

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

edrosten
 
Posts: 42
Joined: Wed Jul 18, 2012 2:54 pm

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 3786 times



Rewards,
Haydee.
hoha
 
Posts: 9
Joined: Mon Apr 14, 2014 9:24 pm

Re: how to restart computation after interruption

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

edrosten
 
Posts: 42
Joined: Wed Jul 18, 2012 2:54 pm

Re: how to restart computation after interruption

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

Swader
 
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