SHF: Large: Domain Specific Language Infrastructure for Biological Simulation Software

SHF：大型：生物模拟软件的领域特定语言基础设施

• 批准号: 1111943
• 负责人: Oyekunle Olukotun
• 金额: $ 177.07万
• 依托单位: Stanford University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-15 至 2016-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1111943&HistoricalAwards=false
• 关键词: SHF; Large; Domain; Specific; Language

Biophysics simulation helps biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions. However, writing high-performance biophysics simulation software for modern parallel computer hardware is a challenging problem. This research project will solve this problem by developing a new generation of biophysics simulation software that is optimized for complex high-performance computer hardware. The project will develop this software using a family of domain specific languages (DSLs). A DSL is a concise programming language with a syntax that is designed to naturally express the semantics of a narrow problem domain. Biophysics simulation DSLs will be used to improve the productivity of simulation software developers and the efficiency and performance of the resulting software by enabling the DSL implementation to take advantage of high-level domain-specific optimizations that are inaccessible to general-purpose compilers and general-purpose languages. The simulation technology built from the family of biophysics simulation DSLs will be used to solve the important biological problems of developing new neuroprosthetics, combating viral infections, effective drug discovery, and understanding drug side effects. In addition, this research will expose students at the graduate and undergraduate level to the role that domain-specific languages play in computing in general and biophysics simulation in particular.The biophysics simulation DSLs will be developed with a general DSL infrastructure. This infrastructure will make use of polymorphic embeddings, multi-stage compilation, and parallel execution patterns to implement the high-level, implicitly parallel DSLs in a common host language. The DSL infrastructure will simplify DSL development by providing a reusable framework for parallelism and domain-specific optimization. When completed, this infrastructure will allow scientists in other application domains to create and use their own high-performance DSLs, in the same manner that this research uses the infrastructure to develop DSLs for biophysics simulation. The result will be a new generation of DSLs in a number of domains that provide high-productivity application development and high-performance on modern heterogeneous parallel hardware such as multicore microprocessors, GPUs and distributed systems.

生物物理学模拟有助于生物医学研究人员在设计新型药物，合成组织，医疗设备和手术干预措施时了解生物系统的物理限制。但是，为现代平行计算机硬件编写高性能生物物理模拟软件是一个具有挑战性的问题。该研究项目将通过开发新一代的生物物理模拟软件来解决此问题，该软件已针对复杂的高性能计算机硬件进行了优化。该项目将使用特定域（DSL）系列开发此软件。 DSL是一种简洁的编程语言，其语法旨在自然地表达狭窄的问题域的语义。生物物理学模拟DSL将用于提高仿真软件开发人员的生产率以及通过启用DSL实施来利用综合用途编译器和通用语言无法访问的高级域特异性优化，并利用高级域特异性优化，来提高模拟软件开发人员的生产率以及所得软件的效率和性能。由生物物理学模拟家族构建的仿真技术将用于解决发展新的神经假想，打击病毒感染，有效的药物发现并了解药物副作用的重要生物学问题。此外，这项研究将使学生在毕业生和本科水平上揭露域特异性语言在一般计算中的作用，尤其是生物物理学模拟。生物物理学模拟DSL将通过一般的DSL基础架构开发。该基础架构将利用多态性嵌入，多阶段汇编和并行执行模式，以在通用主机语言中实现高级的，隐式平行的DSL。 DSL基础架构将通过为并行性和特定于域特异性优化提供可重复使用的框架来简化DSL的开发。完成后，该基础架构将允许其他应用领域中的科学家创建和使用自己的高性能DSL，就像本研究使用基础架构开发用于生物物理学模拟的DSL相同的方式。结果将是许多域中的新一代DSL，这些域提供了高生产率的应用程序开发和对现代异质并行硬件（例如多核算微处理器，GPU和分布式系统）的高性能。