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David Bader's Research Group's Projects

arkouda icon arkouda

Arkouda: NumPy-like arrays at massive scale backed by Chapel (a python/chapel package)

bioperf icon bioperf

BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications

cellbuzz icon cellbuzz

CellBuzz: The Sony-Toshiba-IBM Cell Broadband Engine is a heterogeneous multicore architecture that consists of a traditional microprocessor (PPE) with eight SIMD co-processing units (SPEs) integrated on-chip. This repository contains Cell B.E. optimized libraries and software for FFT, MPEG, compression, and encryption.

custinger icon custinger

This repository contains the cuStinger data structure used for dynamic graph representation.

custingeralg icon custingeralg

This repository contains streaming graph algorithms using the cuStinger data structure.

cycle-detection icon cycle-detection

Cycle-Detection: A Parallel Algorithm for Cycle Detection in Planar Partitioned Digraphs

darpa-ssca2 icon darpa-ssca2

DARPA UHPC Graph Theory Benchmark (Scalable Synthetic Compact Application #2)

dcjuc icon dcjuc

Maximum Parsimonious Tree Construction

exactmp icon exactmp

ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony

graphct icon graphct

GraphCT: a Graph Characterization Toolkit for the Cray XMT

grappa icon grappa

GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

gtfold icon gtfold

GTfold is a fast, scalable multicore code for predicting RNA secondary structure and is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.

gtgraph icon gtgraph

GTgraph: A suite of synthetic random graph generators

hornet icon hornet

Hornet data structure for sparse dynamic graphs and matrices

imageu icon imageu

ImageU: Parallel Combinatorial Algorithms

mst icon mst

MST: Parallel Minimum Spanning Forest

parjedi icon parjedi

ParJedi: Parallel Code for the State Assignment of large Finite State Machines

pasqual icon pasqual

Pasqual: a Parallel de Novo Genome Sequence Assembler

pmedian icon pmedian

PMedian: Parallel Selection and Median Finding

psort icon psort

PSort: Parallel Sorting using Sampling with Randomized and Deterministic Approaches

psrs icon psrs

PSRS: Parallel Sorting using Regular Sampling

rake icon rake

Rake: Parallel Expression Evaluation using Tree Contraction

simple icon simple

SIMPLE is a framework for implementation of parallel algorithms using our methodology for developing high performance programs running on clusters of SMP nodes. Our methodology is based on a small kernel (SIMPLE) of collective communication primitives that make efficient use of the hybrid shared and message passing environment. We illustrate the power of our methodology by presenting experimental results for sorting integers, two-dimensional fast Fourier transforms (FFT), and constraint-satisfied searching.

snap-graph icon snap-graph

SNAP (Small-world Network Analysis and Partitioning) is an extensible parallel framework for exploratory analysis and partitioning of large-scale networks.

sorting icon sorting

Performance evaluation of sequential integer sorting algorithms

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