Related papers: DNA sequence alignment: An assignment for OpenMP, …
The aim of the paper is to introduce general techniques in order to optimize the parallel execution time of sorting on a distributed architectures with processors of various speeds. Such an application requires a partitioning step. For…
Heterogeneous face matching is a challenge issue in face recognition due to large domain difference as well as insufficient pairwise images in different modalities during training. This paper proposes a coupled deep learning (CDL) approach…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…
Entity matching is an important and difficult step for integrating web data. To reduce the typically high execution time for matching we investigate how we can perform entity matching in parallel on a distributed infrastructure. We propose…
Sequence alignment is one of the oldest and the most famous problems in bioinformatics. Even after 45 years, for one reason or another, this problem is still actual; current solutions are trade-offs between execution time, memory…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
Online Continual Learning (OCL) methods train a model on a non-stationary data stream where only a few examples are available at a time, often leveraging replay strategies. However, usage of replay is sometimes forbidden, especially in…
MPI is the de facto standard for parallel computing on a cluster of computers. Checkpointing is an important component in any strategy for software resilience and for long-running jobs that must be executed by chaining together time-bounded…
Graphics Processing Units (GPUs) are having a transformational effect on numerical lattice quantum chromodynamics (LQCD) calculations of importance in nuclear and particle physics. The QUDA library provides a package of mixed precision…
A hybrid scheme that utilizes MPI for distributed memory parallelism and OpenMP for shared memory parallelism is presented. The work is motivated by the desire to achieve exceptionally high Reynolds numbers in pseudospectral computations of…
Growing heterogeneity and configurability in HPC architectures has made auto-tuning applications and runtime parameters on these systems very complex. Users are presented with a multitude of options to configure parameters. In addition to…
Sequence-to-Sequence models were introduced to tackle many real-life problems like machine translation, summarization, image captioning, etc. The standard optimization algorithms are mainly based on example-to-example matching like maximum…
MPI+Threads, embodied by the MPI/OpenMP hybrid programming model, is a parallel programming paradigm where threads are used for on-node shared-memory parallelization and MPI is used for multi-node distributed-memory parallelization. OpenMP…
We present a simple and easy to apply methodology for using high-level self-submitting parallel job queues in an MPI environment. Using C++, we implemented a library of functions, MPQueue, both for testing our concepts and for use in real…
Scheduling query execution plans is a particularly complex problem in shared-nothing parallel systems, where each site consists of a collection of local time-shared (e.g., CPU(s) or disk(s)) and space-shared (e.g., memory) resources and…
We present a generic framework for parallel coordinate descent (CD) algorithms that includes, as special cases, the original sequential algorithms Cyclic CD and Stochastic CD, as well as the recent parallel Shotgun algorithm. We introduce…
With multi-core processors a ubiquitous building block of modern supercomputers, it is now past time to enable applications to embrace these developments in processor design. To achieve exascale performance, applications will need ways of…
As multicore computing is now standard, it seems irresponsible for constraints researchers to ignore the implications of it. Researchers need to address a number of issues to exploit parallelism, such as: investigating which constraint…
w-Projection is a wide-field imaging technique that is widely used in radio synthesis arrays. Processing the wide-field big data generated by the future Square Kilometre Array (SKA) will require significant updates to current methods to…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…