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

生物物理模拟帮助生物医学研究人员在设计新药、合成组织、医疗设备和手术干预时了解生物系统的物理限制。然而，为现代并行计算机硬件编写高性能的生物物理仿真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学模拟软件来解决这一问题，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特定语言（DSL）开发此软件。DSL是一种简洁的编程语言，其语法设计用于自然地表达狭窄问题域的语义。生物物理学仿真DSL将用于提高仿真软件开发人员的生产力，并通过使DSL实现利用通用编译器和通用语言无法访问的高级特定领域优化来提高所得软件的效率和性能。从生物物理仿真DSL家族中构建的仿真技术将用于解决开发新的神经假体，对抗病毒感染，有效药物发现和了解药物副作用等重要生物学问题。此外，本研究将使研究生和本科生了解特定领域语言在一般计算和生物物理模拟中所起的作用。生物物理模拟DSL将使用通用DSL基础设施开发。这个基础设施将利用多态嵌入，多阶段编译和并行执行模式，以实现高层次的，隐式并行DSL在一个共同的主机语言。DSL基础设施将通过提供并行性和特定于领域的优化的可重用框架来简化DSL开发。完成后，该基础设施将允许其他应用领域的科学家创建和使用自己的高性能DSL，与本研究使用基础设施开发生物物理模拟DSL的方式相同。其结果将是许多领域的新一代DSL，这些DSL在现代异构并行硬件（如多核微处理器、GPU和分布式系统）上提供高生产力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.