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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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It would be very nice if you could add cuda option to DeepSignal #24

Closed vahidAK closed 4 years ago

vahidAK commented 4 years ago

Hi @PengNi , One thing I noticed that could be a good enhancement to deepsignal is cuda option. We have 7 GPUs and when I run deppsignal on gpu server it distributes job on all gpus and just uses part of their ram and processing power, so it would be very useful if you could add options to select the gpu number and amount of threads and ram for each gpu in deepsignal.

Thanks, Vahid

PengNi commented 4 years ago

Hi @vahidAK , you can try add CUDA_VISIBLE_DEVICES=0 before the deepsignal command, like CUDA_VISIBLE_DEVICES=0 deepsignal call_mods ... (0 is the GPU number). That's what we did in our experiments.

vahidAK commented 4 years ago

Hi @PengNi Great! thanks a lot