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[cudapoa] make maximum number of edges per node configurable #607

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r-mafi opened this issue Nov 30, 2020 · 0 comments
Open

[cudapoa] make maximum number of edges per node configurable #607

r-mafi opened this issue Nov 30, 2020 · 0 comments
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cudapoa GPU-based partial order alignment enhancement New feature or request

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r-mafi commented Nov 30, 2020

CUDAPOA_MAX_NODE_EDGES and CUDAPOA_MAX_NODE_ALIGNMENTS with default value of 50 defined in cudapoa_structs.cuh have a big impact on memory usage per POA. Consequently maximum number of POAs residing on GPU can increase by using smaller values for these two parameters. Changing these macros to template parameters allows achieving higher parallelism, particularly for processing long reads.
As a rule of thumb, the value for these parameters should not exceed maximum number of reads per window.
@r-mafi r-mafi added enhancement New feature or request cudapoa GPU-based partial order alignment labels Nov 30, 2020
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