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Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
This paper investigates co-scheduling algorithms for processing a set of parallel applications. Instead of executing each application one by one, using a maximum degree of parallelism for each of them, we aim at scheduling several…
High-Performance Computing (HPC) and Artificial Intelligence (AI) workloads typically demand substantial memory bandwidth and, to a degree, memory capacity. CXL memory expansion modules, also known as CXL "type-3" devices, enable…
Compute Express Link (CXL) is a promising technology that addresses memory and storage challenges. Despite its advantages, CXL faces performance threats from external interference when co-existing with current memory and storage systems.…
As large language models gain widespread adoption, running them efficiently becomes crucial. Recent works on LLM inference use speculative decoding to achieve extreme speedups. However, most of these works implicitly design their algorithms…
A parallel server system is a stochastic processing network with applications in manufacturing, supply chain, ride-hailing, call centers, etc. Heterogeneous customers arrive in the system, and only a subset of servers can serve any customer…
Algorithms for extracting hydrologic features and properties from digital elevation models (DEMs) are challenged by large datasets, which often cannot fit within a computer's RAM. Depression filling is an important preconditioning step to…
The hypercube queueing model was initially developed to address spatial queueing problems and has found wide applications in emergency services, such as ambulance and police systems. While the model was originally designed for homogeneous…
Modern external memory is represented by several device classes. At present, HDD, SATA SSD and NVMe SSD are widely used. Recently ultra-low latency SSD such as Intel Optane became available on the market. Each of these types exhibits it's…
We present a work-efficient parallel level-synchronous Breadth First Search (BFS) algorithm for shared-memory architectures which achieves the theoretical lower bound on parallel running time. The optimality holds regardless of the shape of…
There are two intertwined factors that affect performance of concurrent data structures: the ability of processes to access the data in parallel and the cost of synchronization. It has been observed that for a large class of…
The concurrency literature presents a number of approaches for building non-blocking, FIFO, multiple-producer and multiple-consumer (MPMC) queues. However, only a fraction of them have high performance. In addition, many queue designs, such…
The dedicated memory of hardware accelerators can be insufficient to store all weights and/or intermediate states of large deep learning models. Although model parallelism is a viable approach to reduce the memory pressure issue,…
Main memory column-stores have proven to be efficient for processing analytical queries. Still, there has been much less work in the context of clusters. Using only a single machine poses several restrictions: Processing power and data…
We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we…
In this paper, we study the communication complexity for the problem of computing a conjunctive query on a large database in a parallel setting with $p$ servers. In contrast to previous work, where upper and lower bounds on the…
Very large volumes of spatial data increasingly become available and demand effective management. While there has been decades of research on spatial data management, few works consider the current state of commodity hardware, having…
Recent Serverless workloads tend to be largescaled/CPU-memory intensive, such as DL, graph applications, that require dynamic memory-to-compute resources provisioning. Meanwhile, recent solutions seek to design page management strategies…
Compute Express Link (CXL) is a rapidly emerging coherent interconnect standard that provides opportunities for memory pooling and sharing. Memory sharing is a well-established software feature that improves memory utilization by avoiding…