Fig 1.
Lookup table memory layouts supported by Arioc.
The H lookup table is a hash table that contains J-table offsets; the J table contains reference-sequence locations. (a) H and J tables both reside in page-locked system RAM; all memory accesses from the GPU traverse the PCIe bus. (b) A copy of the H table resides in device RAM on each GPU; only J-table data traverses the PCIe bus. (c) The H and J tables are partitioned across device RAM on all available GPUs; GPU peer-to-peer memory accesses use the NVlink interconnect.
Table 1.
Computers used for Arioc performance testing.
(See S1 Text for GPU peer-to-peer memory topology).
Table 2.
Whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS) runs used for Arioc performance testing.
Fig 2.
Speed versus sensitivity for three GPU memory-layout techniques.
Speed (reads/second) is greater when GPU peer-to-peer memory interconnect is used, for a range of sensitivity (% concordant) settings. Speeds are highest when the H and J tables are partitioned across device RAM on all available GPUs and GPU peer-to-peer memory accesses use the direct P2P memory interconnect. Speeds are lower with H in device RAM on each GPU and J in page-locked system memory. Speeds are lowest when H and J both reside in page-locked system RAM. H table: 25GB; J table: 52GB. Data from SRR6020688 (S1 Data).
Fig 3.
Sensitivity (as overall percentage of concordantly mapped pairs), overall elapsed time, and dollar cost for WGS and WGBS alignment on Amazon Web Services virtual machine instances.
WGS results for SRR6020688 (human, 419,380,558 150nt pairs); WGBS results for SRR6020687 (human, 534,647,118 150nt pairs). Arioc: EC2 p3dn.24xlarge instance ($31.212/hour). Bowtie 2, Bismark: EC2 m5.12xlarge instance ($2.304/hour).