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1
Introduction
2
Science Questions
3
Large Machines
4
Exoscale Computing
5
Specialization
6
Deep Learning Algorithms
7
Cost of Data Movement
8
Decoupling between GPU and CPU
9
Parallel algorithms
10
Metagenome assembly
11
Local assembly
12
Parallelization
13
Applications
14
Architectures
15
Hashing
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Distributed Algorithm
17
Multicore Camera Counting
18
Minimizers
19
Alignment
20
GPU Optimized
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Metahammer
22
Generalized Nbody
23
Long Read Overlap
24
Long Read Alignment
25
Communication Avoiding Algorithms
26
Bulk Synchronous Algorithms
27
Takeaways
28
QA
Description:
Explore genomic data analysis at scale in this comprehensive lecture from the Society for Industrial and Applied Mathematics. Delve into the challenges and opportunities of mapping genomic analysis problems to petascale and exascale architectures. Learn about high-performance tools for analyzing microbial data, including alignment, profiling, clustering, and assembly. Discover common computational patterns and motifs that inform parallelization strategies and architectural requirements. Examine two general approaches to genomic analysis: asynchronous one-sided communication in UPC++ and bulk-synchronous collectives. Gain insights into specialized algorithms, GPU optimization, distributed algorithms, and communication-avoiding techniques. Understand the impact of growing genomic datasets on memory and computational requirements, and explore solutions for large-scale parallel platforms.

Genomic Analysis at Scale - Mapping Irregular Computations to Advanced Architectures

Society for Industrial and Applied Mathematics
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