9,772 research outputs found
Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method.
Recent advances in selected configuration interaction methods have made them competitive with the most accurate techniques available and, hence, creating an increasingly powerful tool for solving quantum Hamiltonians. In this work, we build on recent advances from the adaptive sampling configuration interaction (ASCI) algorithm. We show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The ASCI search algorithm can be used in several different modes, which includes an integral driven search and a coefficient driven search. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques, we present ASCI results applied to a large range of systems and basis sets to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-ζ benchmark data for the G1 data set. The largest of these calculations is Si2H6 which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets
Extreme Scale De Novo Metagenome Assembly
Metagenome assembly is the process of transforming a set of short,
overlapping, and potentially erroneous DNA segments from environmental samples
into the accurate representation of the underlying microbiomes's genomes.
State-of-the-art tools require big shared memory machines and cannot handle
contemporary metagenome datasets that exceed Terabytes in size. In this paper,
we introduce the MetaHipMer pipeline, a high-quality and high-performance
metagenome assembler that employs an iterative de Bruijn graph approach.
MetaHipMer leverages a specialized scaffolding algorithm that produces long
scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is
end-to-end parallelized using the Unified Parallel C language and therefore can
run seamlessly on shared and distributed-memory systems. Experimental results
show that MetaHipMer matches or outperforms the state-of-the-art tools in terms
of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and
is able to assemble previously intractable grand challenge metagenomes. We
demonstrate the unprecedented capability of MetaHipMer by computing the first
full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion
reads - size 2.6 TBytes.Comment: Accepted to SC1
QCDGPU: open-source package for Monte Carlo lattice simulations on OpenCL-compatible multi-GPU systems
The multi-GPU open-source package QCDGPU for lattice Monte Carlo simulations
of pure SU(N) gluodynamics in external magnetic field at finite temperature and
O(N) model is developed. The code is implemented in OpenCL, tested on AMD and
NVIDIA GPUs, AMD and Intel CPUs and may run on other OpenCL-compatible devices.
The package contains minimal external library dependencies and is OS
platform-independent. It is optimized for heterogeneous computing due to the
possibility of dividing the lattice into non-equivalent parts to hide the
difference in performances of the devices used. QCDGPU has client-server part
for distributed simulations. The package is designed to produce lattice gauge
configurations as well as to analyze previously generated ones. QCDGPU may be
executed in fault-tolerant mode. Monte Carlo procedure core is based on PRNGCL
library for pseudo-random numbers generation on OpenCL-compatible devices,
which contains several most popular pseudo-random number generators.Comment: Presented at the Third International Conference "High Performance
Computing" (HPC-UA 2013), Kyiv, Ukraine; 9 pages, 2 figure
Reconciling Graphs and Sets of Sets
We explore a generalization of set reconciliation, where the goal is to
reconcile sets of sets. Alice and Bob each have a parent set consisting of
child sets, each containing at most elements from a universe of size .
They want to reconcile their sets of sets in a scenario where the total number
of differences between all of their child sets (under the minimum difference
matching between their child sets) is . We give several algorithms for this
problem, and discuss applications to reconciliation problems on graphs,
databases, and collections of documents. We specifically focus on graph
reconciliation, providing protocols based on set of sets reconciliation for
random graphs from and for forests of rooted trees
FSL-BM: Fuzzy Supervised Learning with Binary Meta-Feature for Classification
This paper introduces a novel real-time Fuzzy Supervised Learning with Binary
Meta-Feature (FSL-BM) for big data classification task. The study of real-time
algorithms addresses several major concerns, which are namely: accuracy, memory
consumption, and ability to stretch assumptions and time complexity. Attaining
a fast computational model providing fuzzy logic and supervised learning is one
of the main challenges in the machine learning. In this research paper, we
present FSL-BM algorithm as an efficient solution of supervised learning with
fuzzy logic processing using binary meta-feature representation using Hamming
Distance and Hash function to relax assumptions. While many studies focused on
reducing time complexity and increasing accuracy during the last decade, the
novel contribution of this proposed solution comes through integration of
Hamming Distance, Hash function, binary meta-features, binary classification to
provide real time supervised method. Hash Tables (HT) component gives a fast
access to existing indices; and therefore, the generation of new indices in a
constant time complexity, which supersedes existing fuzzy supervised algorithms
with better or comparable results. To summarize, the main contribution of this
technique for real-time Fuzzy Supervised Learning is to represent hypothesis
through binary input as meta-feature space and creating the Fuzzy Supervised
Hash table to train and validate model.Comment: FICC201
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