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

生物物理学模拟帮助生物医学研究人员在设计新药、合成组织、医疗器械和外科干预措施时了解生物系统的物理约束。然而，为现代并行计算机硬件编写高性能的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生物物理模拟软件来解决这个问题，该软件针对复杂的高性能计算机硬件进行了优化。该项目将使用一系列领域专用语言(DSL)开发该软件。DSL是一种简洁的编程语言，其语法旨在自然地表达狭义问题域的语义。生物物理模拟DSL将用于提高模拟软件开发人员的生产力，并通过使DSL实现能够利用通用编译器和通用语言无法访问的高级领域特定优化来提高模拟软件开发人员的生产率和最终软件的效率和性能。从生物物理模拟DSL家族建立的模拟技术将用于解决开发新的神经假体、对抗病毒感染、有效的药物发现和了解药物副作用等重要生物学问题。此外，这项研究将使研究生和本科生了解特定领域的语言在一般计算中所扮演的角色，特别是生物物理模拟。生物物理模拟DSL将使用通用的DSL基础设施来开发。该基础设施将利用多态嵌入、多阶段编译和并行执行模式来用通用宿主语言实现高级的、隐式并行的DSL。DSL基础设施将通过为并行性和特定于域的优化提供可重用的框架来简化DSL开发。建成后，这一基础设施将允许其他应用领域的科学家创建和使用他们自己的高性能DSL，就像本研究使用该基础设施开发用于生物物理模拟的DSL一样。其结果将是多个领域的新一代DSL，这些领域在多核微处理器、GPU和分布式系统等现代异类并行硬件上提供高生产率的应用程序开发和高性能。

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.