Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Optimización del rendimiento y la eficiencia energética en sistemas masivamente paralelos

RESUMEN Los sistemas heterogéneos son cada vez más relevantes, debido a sus capacidades de rendimiento y eficiencia energética, estando presentes en todo tipo de plataformas de cómputo, desde dispositivos embebidos y servidores, hasta nodos HPC de grandes centros de datos. Su complejidad hace que sean habitualmente usados bajo el paradigma de tareas y el modelo de programación host-device. Esto penaliza fuertemente el aprovechamiento de los aceleradores y el consumo energético del sistema, además de dificultar la adaptación de las aplicaciones. La co-ejecución permite que todos los dispositivos cooperen para computar el mismo problema, consumiendo menos tiempo y energía. No obstante, los programadores deben encargarse de toda la gestión de los dispositivos, la distribución de la carga y la portabilidad del código entre sistemas, complicando notablemente su programación. Esta tesis ofrece contribuciones para mejorar el rendimiento y la eficiencia energética en estos sistemas masivamente paralelos. Se realizan propuestas que abordan objetivos generalmente contrapuestos: se mejora la usabilidad y la programabilidad, a la vez que se garantiza una mayor abstracción y extensibilidad del sistema, y al mismo tiempo se aumenta el rendimiento, la escalabilidad y la eficiencia energética. Para ello, se proponen dos motores de ejecución con enfoques completamente distintos. EngineCL, centrado en OpenCL y con una API de alto nivel, favorece la máxima compatibilidad entre todo tipo de dispositivos y proporciona un sistema modular extensible. Su versatilidad permite adaptarlo a entornos para los que no fue concebido, como aplicaciones con ejecuciones restringidas por tiempo o simuladores HPC de dinámica molecular, como el utilizado en un centro de investigación internacional. Considerando las tendencias industriales y enfatizando la aplicabilidad profesional, CoexecutorRuntime proporciona un sistema flexible centrado en C++/SYCL que dota de soporte a la co-ejecución a la tecnología oneAPI. Este runtime acerca a los programadores al dominio del problema, posibilitando la explotación de estrategias dinámicas adaptativas que mejoran la eficiencia en todo tipo de aplicaciones.ABSTRACT Heterogeneous systems are becoming increasingly relevant, due to their performance and energy efficiency capabilities, being present in all types of computing platforms, from embedded devices and servers to HPC nodes in large data centers. Their complexity implies that they are usually used under the task paradigm and the host-device programming model. This strongly penalizes accelerator utilization and system energy consumption, as well as making it difficult to adapt applications. Co-execution allows all devices to simultaneously compute the same problem, cooperating to consume less time and energy. However, programmers must handle all device management, workload distribution and code portability between systems, significantly complicating their programming. This thesis offers contributions to improve performance and energy efficiency in these massively parallel systems. The proposals address the following generally conflicting objectives: usability and programmability are improved, while ensuring enhanced system abstraction and extensibility, and at the same time performance, scalability and energy efficiency are increased. To achieve this, two runtime systems with completely different approaches are proposed. EngineCL, focused on OpenCL and with a high-level API, provides an extensible modular system and favors maximum compatibility between all types of devices. Its versatility allows it to be adapted to environments for which it was not originally designed, including applications with time-constrained executions or molecular dynamics HPC simulators, such as the one used in an international research center. Considering industrial trends and emphasizing professional applicability, CoexecutorRuntime provides a flexible C++/SYCL-based system that provides co-execution support for oneAPI technology. This runtime brings programmers closer to the problem domain, enabling the exploitation of dynamic adaptive strategies that improve efficiency in all types of applications.Funding: This PhD has been supported by the Spanish Ministry of Education (FPU16/03299 grant), the Spanish Science and Technology Commission under contracts TIN2016-76635-C2-2-R and PID2019-105660RB-C22. This work has also been partially supported by the Mont-Blanc 3: European Scalable and Power Efficient HPC Platform based on Low-Power Embedded Technology project (G.A. No. 671697) from the European Union’s Horizon 2020 Research and Innovation Programme (H2020 Programme). Some activities have also been funded by the Spanish Science and Technology Commission under contract TIN2016-81840-REDT (CAPAP-H6 network). The Integration II: Hybrid programming models of Chapter 4 has been partially performed under the Project HPC-EUROPA3 (INFRAIA-2016-1-730897), with the support of the EC Research Innovation Action under the H2020 Programme. In particular, the author gratefully acknowledges the support of the SPMT Department of the High Performance Computing Center Stuttgart (HLRS)