GPU peer-to-peer techniques applied to a cluster interconnect

Modern GPUs support special protocols to exchange data directly across the PCI Express bus. While these protocols could be used to reduce GPU data transmission times, basically by avoiding staging to host memory, they require specific hardware features which are not available on current generation network adapters. In this paper we describe the architectural modifications required to implement peer-to-peer access to NVIDIA Fermi- and Kepler-class GPUs on an FPGA-based cluster interconnect. Besides, the current software implementation, which integrates this feature by minimally extending the RDMA programming model, is discussed, as well as some issues raised while employing it in a higher level API like MPI. Finally, the current limits of the technique are studied by analyzing the performance improvements on low-level benchmarks and on two GPU-accelerated applications, showing when and how they seem to benefit from the GPU peer-to-peer method.Comment: paper accepted to CASS 201

Optimized Broadcast for Deep Learning Workloads on Dense-GPU InfiniBand Clusters: MPI or NCCL?

Dense Multi-GPU systems have recently gained a lot of attention in the HPC arena. Traditionally, MPI runtimes have been primarily designed for clusters with a large number of nodes. However, with the advent of MPI+CUDA applications and CUDA-Aware MPI runtimes like MVAPICH2 and OpenMPI, it has become important to address efficient communication schemes for such dense Multi-GPU nodes. This coupled with new application workloads brought forward by Deep Learning frameworks like Caffe and Microsoft CNTK pose additional design constraints due to very large message communication of GPU buffers during the training phase. In this context, special-purpose libraries like NVIDIA NCCL have been proposed for GPU-based collective communication on dense GPU systems. In this paper, we propose a pipelined chain (ring) design for the MPI_Bcast collective operation along with an enhanced collective tuning framework in MVAPICH2-GDR that enables efficient intra-/inter-node multi-GPU communication. We present an in-depth performance landscape for the proposed MPI_Bcast schemes along with a comparative analysis of NVIDIA NCCL Broadcast and NCCL-based MPI_Bcast. The proposed designs for MVAPICH2-GDR enable up to 14X and 16.6X improvement, compared to NCCL-based solutions, for intra- and inter-node broadcast latency, respectively. In addition, the proposed designs provide up to 7% improvement over NCCL-based solutions for data parallel training of the VGG network on 128 GPUs using Microsoft CNTK.Comment: 8 pages, 3 figure

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

On the Enhancement of Remote GPU Virtualization in High Performance Clusters

Graphics Processing Units (GPUs) are being adopted in many computing facilities given their extraordinary computing power, which makes it possible to accelerate many general purpose applications from different domains. However, GPUs also present several side effects, such as increased acquisition costs as well as larger space requirements. They also require more powerful energy supplies. Furthermore, GPUs still consume some amount of energy while idle and their utilization is usually low for most workloads. In a similar way to virtual machines, the use of virtual GPUs may address the aforementioned concerns. In this regard, the remote GPU virtualization mechanism allows an application being executed in a node of the cluster to transparently use the GPUs installed at other nodes. Moreover, this technique allows to share the GPUs present in the computing facility among the applications being executed in the cluster. In this way, several applications being executed in different (or the same) cluster nodes can share one or more GPUs located in other nodes of the cluster. Sharing GPUs should increase overall GPU utilization, thus reducing the negative impact of the side effects mentioned before. Reducing the total amount of GPUs installed in the cluster may also be possible. In this dissertation we enhance one framework offering remote GPU virtualization capabilities, referred to as rCUDA, for its use in high-performance clusters. While the initial prototype version of rCUDA demonstrated its functionality, it also revealed concerns with respect to usability, performance, and support for new GPU features, which prevented its used in production environments. These issues motivated this thesis, in which all the research is primarily conducted with the aim of turning rCUDA into a production-ready solution for eventually transferring it to industry. The new version of rCUDA resulting from this work presents a reduction of up to 35% in execution time of the applications analyzed with respect to the initial version. Compared to the use of local GPUs, the overhead of this new version of rCUDA is below 5% for the applications studied when using the latest high-performance computing networks available.Las unidades de procesamiento gráfico (Graphics Processing Units, GPUs) están siendo utilizadas en muchas instalaciones de computación dada su extraordinaria capacidad de cálculo, la cual hace posible acelerar muchas aplicaciones de propósito general de diferentes dominios. Sin embargo, las GPUs también presentan algunas desventajas, como el aumento de los costos de adquisición, así como mayores requerimientos de espacio. Asimismo, también requieren un suministro de energía más potente. Además, las GPUs consumen una cierta cantidad de energía aún estando inactivas, y su utilización suele ser baja para la mayoría de las cargas de trabajo. De manera similar a las máquinas virtuales, el uso de GPUs virtuales podría hacer frente a los inconvenientes mencionados. En este sentido, el mecanismo de virtualización remota de GPUs permite que una aplicación que se ejecuta en un nodo de un clúster utilice de forma transparente las GPUs instaladas en otros nodos de dicho clúster. Además, esta técnica permite compartir las GPUs presentes en el clúster entre las aplicaciones que se ejecutan en el mismo. De esta manera, varias aplicaciones que se ejecutan en diferentes nodos de clúster (o los mismos) pueden compartir una o más GPUs ubicadas en otros nodos del clúster. Compartir GPUs aumenta la utilización general de la GPU, reduciendo así el impacto negativo de las desventajas anteriormente mencionadas. De igual forma, este mecanismo también permite reducir la cantidad total de GPUs instaladas en el clúster. En esta tesis mejoramos un entorno de trabajo llamado rCUDA, el cual ofrece funcionalidades de virtualización remota de GPUs para su uso en clusters de altas prestaciones. Si bien la versión inicial del prototipo de rCUDA demostró su funcionalidad, también reveló dificultades con respecto a la usabilidad, el rendimiento y el soporte para nuevas características de las GPUs, lo cual impedía su uso en entornos de producción. Estas consideraciones motivaron la presente tesis, en la que toda la investigación llevada a cabo tiene como objetivo principal convertir rCUDA en una solución lista para su uso entornos de producción, con la finalidad de transferirla eventualmente a la industria. La nueva versión de rCUDA resultante de este trabajo presenta una reducción de hasta el 35% en el tiempo de ejecución de las aplicaciones analizadas con respecto a la versión inicial. En comparación con el uso de GPUs locales, la sobrecarga de esta nueva versión de rCUDA es inferior al 5% para las aplicaciones estudiadas cuando se utilizan las últimas redes de computación de altas prestaciones disponibles.Les unitats de processament gràfic (Graphics Processing Units, GPUs) estan sent utilitzades en moltes instal·lacions de computació donada la seva extraordinària capacitat de càlcul, la qual fa possible accelerar moltes aplicacions de propòsit general de diferents dominis. No obstant això, les GPUs també presenten alguns desavantatges, com l'augment dels costos d'adquisició, així com major requeriment d'espai. Així mateix, també requereixen un subministrament d'energia més potent. A més, les GPUs consumeixen una certa quantitat d'energia encara estant inactives, i la seua utilització sol ser baixa per a la majoria de les càrregues de treball. D'una manera semblant a les màquines virtuals, l'ús de GPUs virtuals podria fer front als inconvenients esmentats. En aquest sentit, el mecanisme de virtualització remota de GPUs permet que una aplicació que s'executa en un node d'un clúster utilitze de forma transparent les GPUs instal·lades en altres nodes d'aquest clúster. A més, aquesta tècnica permet compartir les GPUs presents al clúster entre les aplicacions que s'executen en el mateix. D'aquesta manera, diverses aplicacions que s'executen en diferents nodes de clúster (o els mateixos) poden compartir una o més GPUs ubicades en altres nodes del clúster. Compartir GPUs augmenta la utilització general de la GPU, reduint així l'impacte negatiu dels desavantatges anteriorment esmentades. A més a més, aquest mecanisme també permet reduir la quantitat total de GPUs instal·lades al clúster. En aquesta tesi millorem un entorn de treball anomenat rCUDA, el qual ofereix funcionalitats de virtualització remota de GPUs per al seu ús en clústers d'altes prestacions. Si bé la versió inicial del prototip de rCUDA va demostrar la seua funcionalitat, també va revelar dificultats pel que fa a la usabilitat, el rendiment i el suport per a noves característiques de les GPUs, la qual cosa impedia el seu ús en entorns de producció. Aquestes consideracions van motivar la present tesi, en què tota la investigació duta a terme té com a objectiu principal convertir rCUDA en una solució preparada per al seu ús entorns de producció, amb la finalitat de transferir-la eventualment a la indústria. La nova versió de rCUDA resultant d'aquest treball presenta una reducció de fins al 35% en el temps d'execució de les aplicacions analitzades respecte a la versió inicial. En comparació amb l'ús de GPUs locals, la sobrecàrrega d'aquesta nova versió de rCUDA és inferior al 5% per a les aplicacions estudiades quan s'utilitzen les últimes xarxes de computació d'altes prestacions disponibles.Reaño González, C. (2017). On the Enhancement of Remote GPU Virtualization in High Performance Clusters [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86219TESISPremios Extraordinarios de tesis doctorale

On the acceleration of wavefront applications using distributed many-core architectures

In this paper we investigate the use of distributed graphics processing unit (GPU)-based architectures to accelerate pipelined wavefront applications—a ubiquitous class of parallel algorithms used for the solution of a number of scientific and engineering applications. Specifically, we employ a recently developed port of the LU solver (from the NAS Parallel Benchmark suite) to investigate the performance of these algorithms on high-performance computing solutions from NVIDIA (Tesla C1060 and C2050) as well as on traditional clusters (AMD/InfiniBand and IBM BlueGene/P). Benchmark results are presented for problem classes A to C and a recently developed performance model is used to provide projections for problem classes D and E, the latter of which represents a billion-cell problem. Our results demonstrate that while the theoretical performance of GPU solutions will far exceed those of many traditional technologies, the sustained application performance is currently comparable for scientific wavefront applications. Finally, a breakdown of the GPU solution is conducted, exposing PCIe overheads and decomposition constraints. A new k-blocking strategy is proposed to improve the future performance of this class of algorithm on GPU-based architectures

Neurostream: Scalable and Energy Efficient Deep Learning with Smart Memory Cubes

open4siHigh-performance computing systems are moving towards 2.5D and 3D memory hierarchies, based on High Bandwidth Memory (HBM) and Hybrid Memory Cube (HMC) to mitigate the main memory bottlenecks. This trend is also creating new opportunities to revisit near-memory computation. In this paper, we propose a flexible processor-in-memory (PIM) solution for scalable and energy-efficient execution of deep convolutional networks (ConvNets), one of the fastest-growing workloads for servers and high-end embedded systems. Our co-design approach consists of a network of Smart Memory Cubes (modular extensions to the standard HMC) each augmented with a many-core PIM platform called NeuroCluster. NeuroClusters have a modular design based on NeuroStream coprocessors (for Convolution-intensive computations) and general-purpose RISC-V cores. In addition, a DRAM-friendly tiling mechanism and a scalable computation paradigm are presented to efficiently harness this computational capability with a very low programming effort. NeuroCluster occupies only 8 percent of the total logic-base (LoB) die area in a standard HMC and achieves an average performance of 240 GFLOPS for complete execution of full-featured state-of-the-art (SoA) ConvNets within a power budget of 2.5 W. Overall 11 W is consumed in a single SMC device, with 22.5 GFLOPS/W energy-efficiency which is 3.5X better than the best GPU implementations in similar technologies. The minor increase in system-level power and the negligible area increase make our PIM system a cost-effective and energy efficient solution, easily scalable to 955 GFLOPS with a small network of just four SMCs.openAzarkhish, Erfan*; Rossi, Davide; Loi, Igor; Benini, LucaAzarkhish, Erfan*; Rossi, Davide; Loi, Igor; Benini, Luc