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Use dedicated graphics to find repeats (Read 78 times)
Sep 10th, 2019 at 1:58pm

felince tokyo   Offline
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Hi!

I normally use UGENE to locate genome wide direct and inverted repeats in bacterial genomes. I can obtain the results without any problem but I'm finding inconvenient the time it takes to make such calculation (several hours, depending on the genome size). My laptop has an Intel Core i7 8550U with 16 GB of ram and I was wondering if I could speed up this calculation by using the dedicated graphics (Nvidia Geforce MX150). By looking at the options, CUDA seems to be able to work with this graphics chip, but I think it is not being used for this specific calculation. Could you please tell me how to do it?

Thank you  Smiley
 
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Reply #1 - Sep 10th, 2019 at 2:32pm

Olga Golosova   Offline
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Hi Felince!

Thank you very much for the feedback! It was useful.

There is currently no special optimization for a single input sequence except multi-threading. Note that video cards calculations are currently supported for two algorithms only: Smith-Waterman and UGENE Genome Aligner.

Could you please send us some data for which calculation takes several hours?
 
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Reply #2 - Sep 11th, 2019 at 7:09am

felince tokyo   Offline
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Hi Olga, thank you for your response.

This is one of the sequences that I'm analyzing (genbank file):

https://www.ncbi.nlm.nih.gov/nuccore/AP013068

I attached the parameters and the log. As you can see it took more than 4 hours, with the processor at 100% use, although the memory usage was about 3 GB.
 

repeats.jpg (84 KB | 2 )
repeats.jpg
log.jpg (22 KB | 2 )
log.jpg
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Reply #3 - Sep 12th, 2019 at 4:20pm

Olga Golosova   Offline
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Thank you, Felince!

On my computer this task also was calculated for 3 hours.

I think, this task is a good candidate for parallelization on a video card. We'll think about this and maybe add some optimization in future. However, if you'd like the future to come as soon as possible  Smiley, please consider to use our commercial support services.
 
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Reply #4 - Sep 13th, 2019 at 3:17pm

felince tokyo   Offline
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Dear Olga,

Thank you very much for taking this into consideration. It will be great to receive direct support from Ugene developers. depending on how this analysis develops further we might consider about acquiring paid support.
 
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Reply #5 - Sep 13th, 2019 at 3:30pm

Olga Golosova   Offline
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Dear Felince.

Okay, thank you again for the feedback!
 
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