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google / deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
BSD 3-Clause "New" or "Revised" License
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can deepconsensus run on an arm machine？ #24

Closed shengxinzhuan closed 2 years ago

shengxinzhuan commented 2 years ago

hello，deepconsensus team! Thanks for make an amazing job for hifi sequencing. It is useful to work on an x86 cpu or gpu machine. However when I try to install it on an arm hpc, I was fail for installing the base requirements pacakage. Do you have the plan to move the deepconsensus on the arm machine ?

pichuan commented 2 years ago

@shengxinzhuan we have not tested it, but can you tell us what error messages you're getting? Which base requirements were failing?

shengxinzhuan commented 2 years ago

@pichuan maybe I should try again for install these pacakges. If I success, I will share the experience. If I fail again, I will give back the message. Thanks!

shengxinzhuan commented 2 years ago

@pichuan hello, I try again, but it fail because the intel-tensorflow do not found. Any pacakages can replace it? Looking for reply

pichuan commented 2 years ago

@shengxinzhuan try use tensorflow instead of intel-tensorflow.

armintoepfer commented 2 years ago

Quick note about data pre-processing, PacBio's released binaries for pbmm2, actc, and ccs only support x86. There are no fundamental reasons for not supporting ARM, except that there hasn't been demand so far. The bigger question, what is the minimum required ARM version to get sufficient performance.

danielecook commented 2 years ago

Closing this issue for now. If you have any further questions feel free to reopen. Thanks.