Parallel Programing Project 1
4eme année cyber sécurité
Longest Common Subsequence
Travail réalisé par : Groupe :
DOUAHABI Mohamed Cybersécurité tp B
Professeur :
[Link] Mohamed
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Table des matières
I. Introduction : ............................................................................................................................3
II. Sequential LCS Algorithm : .....................................................................................................4
1. Background and significance : ............................................................................................... 4
2. Dynamic Programing Foundations: ....................................................................................... 4
3. Computational Complexity Analysis: .................................................................................... 4
4. Code review: .......................................................................................................................... 4
III. UPC, MPI, and CUDA Parallel Implementations : ..................................................................6
1. Introduction to Parallelization :.............................................................................................. 6
2. Parallelization Benefits : ........................................................................................................ 7
3. Role of UPC, MPI, and CUDA: ............................................................................................. 7
4. CUDA implementation: ..................................................................................................... 8
5. MPI implementation: ....................................................................................................... 10
IV. Comparative Analysis of LCS Implementations: UPC, MPI, and CUDA: ........................... 12
V. Conclusion:............................................................................................................................ 13
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I. Introduction :
Local sequence alignment, a major challenge in bioinformatics and file comparison
programs, is of great importance for understanding biological sequences and identifying
similarities in diverse datasets. In this project, our main objective is to determine the
length of the longest common sequence (LCS) between two input sequences. The LCS
problem, a classic algorithmic challenge, extends beyond its genomics roots to
applications in file versioning and plagiarism detection. A subsequence, representing
non-contiguous elements of a sequence, is fundamental to the LCS problem and is
illustrated by cases such as DNA sequences and file contents. We examine the
importance of subsequences and their role in recognizing patterns and relationships
between these sequences.
To guide the reader through the intricacies of our investigation, the report follows a
structured roadmap. It begins with an exploration of the sequential LCS algorithm based
on dynamic programming, highlighting its theoretical foundations and computational
complexity. We then extend our exploration to parallel implementations using UPC,
MPI and CUDA, with the aim of optimizing the algorithm's performance.
The experimental setup and methodology are detailed, including hardware
configuration, input parameters, and performance measurements. Following the results
and performance analysis, an overview of the efficiency and scalability of each parallel
implementation is presented. Finally, we discuss the main results, limitations, and
potential for future research, and highlight the broader significance of our work in the
context of local array alignment and parallel programming.
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II. Sequential LCS Algorithm :
1. Background and significance :
Local sequence alignment is a fundamental problem in bioinformatics and file comparison,
essential for understanding biological sequences and identifying patterns in the data.
In this section, we briefly review the importance of local sequence alignment and reaffirm
the main objective of our project: to determine the length of the longest common sequence
(LCS) between two input sequences.
2. Dynamic Programing Foundations:
The core of our research lies in the sequential LCS algorithm based on dynamic
programming. Dynamic programming offers an efficient solution to the LCS problem by
decomposing it into smaller, overlapping sub-problems. We look at the theoretical
underpinnings of the algorithm, exploring the concept of recurrence relations. These
relations define the optimal substructure of the LCS problem, enabling us to construct
solutions from solutions to smaller sub-problems. The algorithm's pseudocode will be
presented, providing a clear representation of its implementation.
3. Computational Complexity Analysis:
Efficiency is a critical aspect of any algorithm, and in this section we analyze the
computational complexity of the sequential LCS algorithm. More specifically, we focus on
time complexity, highlighting how the algorithm's execution time evolves as a function of
the size of the input data. This analysis lays the foundations for our exploration of parallel
implementations, where optimizing computational efficiency becomes paramount.
4. Code review:
a. Phase 1 to calculate LCS Length:
• The function lcs takes two sequences, X and Y, along with their lengths (m and
n).
• It initializes a 2D array L to store the lengths of the LCS.
• The nested loops iterate over all combinations of indices i and j to fill in the table
L in a bottom-up manner.
• The base case handles situations where either sequence is empty, setting the LCS
length to 0.
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• If characters in X and Y match, the length of LCS is extended by one.
• If characters don't match, the length of LCS is determined by taking the
maximum of lengths obtained by excluding one character from either sequence.
b. Phase 2 Algorithm to construct LCS sequence:
• This section initializes an empty sequence S and sets indices “I” and “j” to the
lengths of sequences X and Y.
• The while loop continues as long as both sequences have elements (indices “I”
and “j” are greater than 0).
• If characters at the current positions match, the character from sequence X is
added to the end of the sequence S.
• The loop progresses by adjusting the indices “I” and “j” based on the values
stored in the L table.
• The loop continues until either of the sequences is exhausted.
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III. UPC, MPI, and CUDA Parallel Implementations :
1. Introduction to Parallelization :
Parallelization is a fundamental concept in high-performance computing (HPC), which
aims to improve computational speed and efficiency by dividing tasks into smaller,
independent units that can be processed simultaneously. This approach is particularly
relevant in the context of computationally intensive algorithms, such as the Longest
Common Sequence (LCS) algorithm, where large datasets or complex calculations can
benefit from parallel execution on multiple processors.
Parallelization involves breaking down a computing task into smaller sub-tasks that can be
executed simultaneously, taking advantage of the parallel processing capabilities of modern
computer architectures. This is achieved by using multiple processing units, which can be
CPU cores, GPUs or even distributed computing resources.
In the case of the LCS algorithm, parallelization can be approached using different parallel
programming models, each adapted to specific architectures and computing requirements.
Unified Parallel C (UPC), Message Passing Interface (MPI) and Compute Unified Device
Architecture (CUDA) are three such models, addressing shared memory, distributed
memory and GPU-based parallelism respectively.
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2. Parallelization Benefits :
• Speed up: The primary objective of parallelization is to achieve a significant reduction
in computation time by distributing tasks over several processors. This is particularly
crucial in scenarios where sequential execution would be impractical due to data volume
or computational complexity.
• Efficiency Gains: Parallelization makes better use of resources, ensuring that idle
processing units are actively used. This efficiency gain is crucial for solving problems
that require substantial computing resources.
• Scalability: Parallel algorithms are designed to adapt efficiently to increasing
computing resources. As the number of processors or cores increases, the performance
improvement should ideally be proportional, guaranteeing scalability for larger datasets
or more complex calculations.
3. Role of UPC, MPI, and CUDA:
• UPC: UPC is designed for shared-memory parallelism, where several processors share
a common address space. It simplifies parallel programming on shared-memory
architectures, by facilitating coordination between processors.
• MPI: MPI is designed for distributed memory parallelism, where several processors
have their own independent memory spaces. MPI facilitates communication and
synchronization between processors, enabling efficient parallelism between machine
clusters.
• CUDA: CUDA is specifically designed for GPGPU (General-Purpose GPU)
parallelism, using the massively parallel architecture of GPUs. It offloads certain
computational tasks to the GPU, which can process them in parallel with the CPU.
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4. CUDA implementation:
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• Memory Management:
To facilitate seamless interaction between the CPU and GPU, dynamic memory
allocation is employed using cudaMallocManaged. This ensures efficient memory
sharing and data consistency between the CPU and GPU, eliminating the need for
explicit data transfers.
• Thread Coordination and Shared Memory:
Threads within GPU blocks are organized using threadIdx and blockIdx to efficiently
handle different portions of the LCS problem. Shared memory is utilized to enable
communication and synchronization between threads, enhancing overall parallel
execution.
• Performance Evaluation:
Execution times are measured using the gettimeofday function, allowing for accurate
timing assessments. Comparative analysis with the CPU implementation provides
insights into the efficiency gains achieved through GPU parallelization.
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• Code Optimization Strategies:
To enhance performance, the CUDA kernel incorporates optimizations such as loop
unrolling and shared memory utilization. These strategies aim to maximize parallelism
and minimize redundant computations.
• Output:
In evaluating the performance of the Longest Common Subsequence (LCS) algorithm
for the input sequences "AGGTAB" and "GXTXAYB," the anticipated length of the
LCS is 4, corresponding to the common subsequence "GTAB." The CPU
implementation yields the expected result of 4, demonstrating the accuracy of the
sequential approach. Following corrections in the GPU implementation, which initially
produced an unexpected result, the revised version now aligns with the anticipated LCS
length of 4. This successful alignment underscores the effectiveness of parallelization
using GPU acceleration, achieving both efficiency and accuracy in LCS computation.
5. MPI implementation:
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• This C++ MPI code demonstrates a parallelized solution to a dynamic programming
problem for finding the length of the longest common subsequence of two randomly
generated strings s1 and s2 .
• The code utilizes Message Passing Interface (MPI) for parallel processing, distributing
the computation across multiple processes. The parallelized solution divides the
problem into blocks, each handled by a different MPI process.
• The results are then combined to obtain the final answer. Additionally, the code includes
a sequential solution for comparison, and the execution times of both parallel and
sequential approaches are measured. The primary objective is to showcase the efficiency
of parallel computing using MPI in solving a common algorithmic problem.
IV. Comparative Analysis of LCS Implementations: UPC, MPI, and
CUDA:
When comparing implementations of the Longest Common Subsequence (LCS)
algorithm across Unified Parallel C (UPC), Message Passing Interface (MPI), and
CUDA, considerations center on computational complexity and time efficiency.
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UPC, tailored for shared-memory systems, excels in scenarios with distributed data
among threads, minimizing communication overhead.
MPI, designed for distributed-memory systems, efficiently manages parallel tasks
across processes.
CUDA, harnessing GPU parallelization, stands out for substantial acceleration with
extensive data parallelism.
The choice depends on factors like task granularity, memory architecture, and the
specific nature of the LCS problem. While UPC and MPI suit distributed environments,
CUDA excels with GPU parallelism. Profiling and benchmarking are vital for
determining the most efficient approach based on algorithm characteristics and available
hardware resources.
V. Conclusion:
In conclusion, our project on the Longest Common Subsequence (LCS) algorithm explores
both sequential and parallel implementations, utilizing Unified Parallel C (UPC), Message
Passing Interface (MPI), and Compute Unified Device Architecture (CUDA). We began by
emphasizing the significance of LCS in bioinformatics and file comparison, showcasing its
applications in diverse fields. The sequential LCS algorithm, based on dynamic
programming, laid the foundation, focusing on theoretical foundations, computational
complexity, and detailed code review.
The parallel implementations with UPC, MPI, and CUDA were meticulously presented,
highlighting the benefits of parallelization in terms of speed-up, efficiency gains, and
scalability. Each parallel paradigm's role was discussed, with UPC catering to shared-
memory systems, MPI for distributed-memory systems, and CUDA leveraging GPU
parallelism. The CUDA implementation featured memory management, thread
coordination, shared memory utilization, performance evaluation, and optimization
strategies, demonstrating its efficiency through comparative analysis.
Our comparative analysis underscored the strengths of each parallel paradigm, with UPC
excelling in scenarios with distributed data among threads, MPI efficiently managing
parallel tasks across processes, and CUDA standing out for substantial acceleration with
extensive data parallelism. The choice among these paradigms depends on factors like task
granularity, memory architecture, and the specific nature of the LCS problem.
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