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Group 06

Acceleration of

deep neural network-based nanopore super accuracy basecalling

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Aminda Amarasinghe

E/17/012

Thilini madushani

E/17/201

Achintha Sandakalum

E/17/284

Our Team

Supervisors

Dr. Hasindu Gamaarachchi

Prof. Roshan Ragel

Dr. Damayanthi Hearth

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Agenda

Introduction
Background of the Problem
Methodology
Experiments and Findings
Challenges
Progress & Future plans
Expected Outcomes

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Introduction

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Nanopore DNA Sequencing

Nucleotides within a DNA molecule.

Adenine
Cytosine
Thymine
Guanine

Importance:

Genomics

Agriculture & Food Science

Microbiology

Forensic Science

Different bases Distinct changes in electrical current

C

T

C

A

G

A

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Background of the Problem

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Transition from HMM based basecallers to RNN based basecallers improved the accuracy, But total execution time increased.

Different implementations of RNN based basecallers

Dorado, Slorado

Cublas library for basic linear algebra operations

RNN based Inference process is massively time consuming

Hidden Markov Model based basecallers

RNN based basecallers

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CPU only version

GPU CUDA version

GPU + ONT’s close source koi library

Current implementations of Slorado basecaller

Slorado uses Slow5/Blow5 input file format

It consists of 5 RNN layers

Basecalling involves common time consuming tasks such as matrix operations

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GPU Architecture

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Problem definition

Existing GPU-based implementations it takes several days to complete Nanopore basecalling process.

Practical human genome contains approximately 3 billion base pairs.

Hence current basecalling implementation should be accelerated massively after identifying the bottleneck.

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Methodology

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Understanding the codebase

Finding the bottlenecks using timestamps

Optimising the bottlenecks

Methodology

Testing for the performance improvement & Accuracy

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Experiments and Findings

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Profiling Slorado to find the bottlenecks

forward() :

Performs the forward pass of an LSTM layer using cuBLAS library functions for matrix multiplication

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Bottleneck

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Bottleneck

forward()

matmul_f16()

rnn->weights.t().contiguous()

Transposes the weight matrices of an RNN layer and store in a contiguous memory layout

Time consumption : 58.06%

Performs the matrix multiplication

Time consumption : 29.45%

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Optimizations on Contiguous Memory Allocation

Experiments

Check if contiguous() is Necessary
Check for duplicate copies
Reduce Frequent Dynamic Allocation
Use Standard Containers
Reusing Memory

contiguous() executes 766035 times for hg2_prom_lsk114_subsubsample dataset

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Optimizations

Previous code

File : CRFModel.cpp

Updated code

File : CRFModel.cpp

File : globals.cpp

Optimizations on Contiguous Memory Allocation

Executes in for loop of forward()

Executes only once in forward()

Executes in for loop of forward()

Stores transposed weights in contiguous layout

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Results

Model: dna_r10.4.1_e8.2_400bps_sup@v4.0.0

Input : hg2_prom_lsk114_subsubsample/reads.blow5

	Previous version	Updated version
Time for contiguous() (Sec)	4337.379	0.025
Total time (Sec)	8308.320	4354.287

Reduced time consumption by 52% with the same accuracy

Optimizations on Contiguous Memory Allocation

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Results

Model: dna_r10.4.1_e8.2_400bps_sup@v4.0.0

Input : hg2_prom_lsk114_subsubsample/reads.blow5

Optimizations on Contiguous Memory Allocation

97.55 % Accuracy

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2. Optimization on matrix multiplication

breaks down the matrices into smaller submatrices, or tiles, and performs the multiplication on these tiles.

takes advantage of the cache memory and reduces the number of memory accesses

Algorithm	Time complexity
Naive algorithm	O(n^3)
Strassen’s algorithm	O(n^2.81)
Coppersmith and Winograd’s algorithm	O(n^2.38)

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2. Winograd’s Algorithm for fast matrix multiplication

Recursive approach
Utilizes optimized Cublas basic matrix algebra kernels

cublasSgemm, cublasSgeam, cublasSetMatrix

Optimizing the Matrix Multiplication Using Strassen and Winograd Algorithms with Limited Recursions on Many-Core

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Challenges

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GPU Memory usage

Changing Environment variables in the server

Communicating with other project groups

Defining env variables for the session in bashrc file

Challenges

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Progress & Future Plans

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Next Steps…

Embedding the Winograd matrix multiplication into Slorado basecaller
Further optimizations considering GPU occupancy
Evaluating accuracy against the baseline accuracy

Significant acceleration by optimizing contiguous memory allocation of RNN weights

Implementation of Winograd algorithm based large matrix multiplication

Summarizing current findings into the manuscript

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Project Timeline

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Week 15 of Semester 8

Week 3 of Semester 8

Week 1 of Semester 7

End of Semester 7

,

Week 7 of semester 8

Final presentation

Completed Manuscript

Final Accelerated version

Initial Accelerated version

Mid presentation

Identification of bottlenecks

Understand the problem

Literature Review

proposal presentation

Experiments on optimizations

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Expected Outcomes

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Final Outcomes

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Accelerated Slorado

Open source Slorado basecaller

A manuscript

Evaluation of the findings

Comparable or higher accuracy compared to the baseline accuracy

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Thank You

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Q & A

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GPU	NVIDIA GeForce RTX 3090 Ti
Model	Super Accuracy model
Input dataset	hg2_prom_lsk114_subsubsample/reads.blow5
No of entries	400
Size of the dataset	1.5 GB

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