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Pagoda Project

The Pagoda Project researches and develops cutting-edge software for implementing high-performance applications and software infrastructure under the Partitioned Global Address Space (PGAS) model.

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UPC++

UPC++ is a C++ PGAS library that supports low-overhead, fine-grained communication, including Remote Memory Access (RMA) and Remote Procedure Call (RPC).

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GASNet-EX

GASNet is a communication middleware library providing network-independent, high-performance Remote Memory Access and Active Messages.
It powers UPC, UPC++, Legion, Chapel, Fortran and other models.

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Unified Parallel C (UPC)

UPC is a PGAS extension to C designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware.

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ExaBiome

ExaBiome is developing exascale algorithms and software to assemble genome sequences. The MetaHipMer Genome Assembler uses UPC, UPC++ and GASNet to achieve robust scaling on modern supercomputers.

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SIMCov

SIMCov is a parallel 3-D agent-based cellular-level model of COVID-19 viral progression in human lungs, written using UPC++.

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Berkeley Container Library (BCL)

The Berkeley Container Library is a cross-platform C++ library of distributed data structures. It has backends for GASNet-EX, UPC++, MPI RMA and OpenSHMEM.

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BQSKit

The Berkeley Quantum Synthesis Toolkit is a superoptimizing quantum compiler and research vehicle that combines ideas from several projects into an accessible and extensible software suite.

    

The CLaSS Group is recruiting! Available positions include:
C++ Programmer/Software Engineer
HPC Application Developer

 

 The CLaSS Group mission is to research, design, and implement new models, features and optimizations of parallel programming languages and their execution environments for leading-edge High Performance Computing (HPC) systems. Research topics include but are not limited to design, implementation and optimization of parallel programming languages, compilers, operating systems, and advanced communication and run-time libraries. This builds on the group’s long history of leadership in this area with the development of the GASNet communication library, UPC programming language, UPC++ library, data-centric programming models, Operating Systems / Runtimes, and the software stack for quantum computers.

Research

Pagoda Project

The Pagoda Project researches and develops cutting-edge software for implementing high-performance applications and software infrastructure under the Partitioned Global Address Space (PGAS) model. The project is primarily funded by the Exascale Computing Project, and interacts with partner projects in industry, government and academia. The Pagoda software stack consists of a communication portability layer, GASNet, and productivity layers: UPC++ and Berkeley UPC.

GASNet

GASNet is a language-independent, networking middleware layer that provides network-independent, high-performance communication primitives including Remote Memory Access (RMA) and Active Messages (AM). It has been used to implement parallel programming models and libraries such as UPC, UPC++, Co-Array Fortran, Legion, Chapel, and many others. The interface is primarily intended as a compilation target and for use by runtime library writers (as opposed to end users), and the primary goals are high performance, interface portability, and expressiveness.

UPC++

UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming, and is designed to interoperate smoothly and efficiently with MPI, OpenMP, CUDA and AMTs. It leverages GASNet-EX to deliver low-overhead, fine-grained communication, including Remote Memory Access (RMA) and Remote Procedure Call (RPC).

Berkeley UPC

Unified Parallel C (UPC) is a PGAS extension of the C programming language designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware. Berkeley UPC is a portable, high-performance implementation of the UPC language using GASNet for communication.

ExaBiome

The ExaBiome project is developing HipMer, the first high-quality end-to-end de novo genome assembler designed for extreme scale analysis. HipMer is a PGAS application, and the main software dependencies are the UPC language and UPC++ library, both of which use GASNet-EX for communication. HipMer’s high performance is based on several novel algorithmic advancements attained by leveraging the efficiency and programmability of the one-sided communication capabilities of the Unified Parallel C (UPC), and RPC calls from the UPC++ Library, including optimized high-frequency k-mer analysis, communication avoiding de Bruijn graph traversal, advanced I/O optimization, and extensive parallelization across the numerous and complex application phases.

SIMCoV

Spatial Immune Model of Coronavirus (SIMCoV) is a scalable computational model written in UPC++ that simulates hundreds of millions of lung cells, including respiratory epithelial cells and T cells. SIMCoV replicates viral growth dynamics observed in patients and shows that spatially dispersed infections lead to increased viral loads. The model shows how the timing and strength of the T cell response can affect viral persistence, oscillations, and control. By incorporating spatial interactions, SIMCoV provides a parsimonious explanation for the dramatically different viral load trajectories among patients by varying only the number of initial sites of infection, and the magnitude and timing of the T cell immune response.

Berkeley Container Library

The Berkeley Container Library (BCL) is a set of generic, cross-platform, high-performance data structures for irregular applications, including queues, hash tables, Bloom filters and more. BCL is written in C++ using an internal DSL called the BCL Core that provides one-sided communication primitives such as remote get and remote put operations. The BCL Core has backends for MPI, OpenSHMEM, GASNet-EX, and UPC++, allowing BCL data structures to be used natively in programs written using any of these programming environments.

Caffeine

CoArray Fortran Framework of Efficient Interfaces to Network Environments Caffeine is a parallel runtime library that aims to support Fortran compilers with a programming-model-agnostic application binary interface (ABI) to various communication libraries. Current work is on supporting the ABI with the GASNet-EX or with POSIX processes. Future plans include support for an alternative MPI back end.

TOP500

TOP500 Supercomputing Sites The TOP500 project was started in 1993 to provide a reliable basis for tracking and detecting trends in high-performance computing. Twice a year, a list of the sites operating the 500 most powerful computer systems is…

PyFloT

Tuning floating point precision using dynamic program information and temporal locality. The goal of this tool is to help finding a mixed precision solution to reduce execution time while maintaining some notion of correctness.

BQSKit

The Berkeley Quantum Synthesis Toolkit (BQSKit) is a superoptimizing quantum compiler and research vehicle that combines ideas from several projects at LBNL into an easily accessible and quickly extensible software suite.

Past Projects

Projects from current and former CLaSS members that have been replaced by follow-on work or are no longer actively being…

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Publications

Demonstrating UPC++/Kokkos Interoperability in a Heat Conduction Simulation (Extended Abstract)

November 19, 2021

Optimization of Asynchronous Communication Operations through Eager Notifications

November 18, 2021

GASNet-EX Memory Kinds: Support for Device Memory in PGAS Programming Models

November 17, 2021

UPC++: An Asynchronous RMA/RPC Library for Distributed C++ Applications

November 16, 2021

UPC++ v1.0 Programmer’s Guide, Revision 2021.9.0

September 30, 2021

UPC++ v1.0 Specification, Revision 2021.9.0

September 29, 2021

UPC++ as_eager Working Group Draft, Revision 2020.6.2

August 9, 2021

Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection

June 21, 2021

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

May 1, 2021

UPC++ and GASNet: PGAS Support for Exascale Apps and Runtimes

April 15, 2021

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