QR Factorization of Tall and Skinny Matrices in a Grid Computing Environment

Previous studies have reported that common dense linear algebra operations do not achieve speed up by using multiple geographical sites of a computational grid. Because such operations are the building blocks of most scientific applications, conventional supercomputers are still strongly predominant in high-performance computing and the use of grids for speeding up large-scale scientific problems is limited to applications exhibiting parallelism at a higher level. We have identified two performance bottlenecks in the distributed memory algorithms implemented in ScaLAPACK, a state-of-the-art dense linear algebra library. First, because ScaLAPACK assumes a homogeneous communication network, the implementations of ScaLAPACK algorithms lack locality in their communication pattern. Second, the number of messages sent in the ScaLAPACK algorithms is significantly greater than other algorithms that trade flops for communication. In this paper, we present a new approach for computing a QR factorization -- one of the main dense linear algebra kernels -- of tall and skinny matrices in a grid computing environment that overcomes these two bottlenecks. Our contribution is to articulate a recently proposed algorithm (Communication Avoiding QR) with a topology-aware middleware (QCG-OMPI) in order to confine intensive communications (ScaLAPACK calls) within the different geographical sites. An experimental study conducted on the Grid'5000 platform shows that the resulting performance increases linearly with the number of geographical sites on large-scale problems (and is in particular consistently higher than ScaLAPACK's).Comment: Accepted at IPDPS10. (IEEE International Parallel & Distributed Processing Symposium 2010 in Atlanta, GA, USA.

Power management and optimization

After many years of focusing on “faster” computers, people have started taking notice of the fact that the race for “speed” has had the unfortunate side effect of increasing the total power consumed, thereby increasing the total cost of ownership of these machines. The heat produced has required expensive cooling facilities. As a result, it is difficult to ignore the growing trend of “Green Computing,” which is defined by San Murugesan as “the study and practice of designing, manufacturing, using, and disposing of computers, servers, and associated subsystems – such as monitors, printers, storage devices, and networking and communication systems – efficiently and effectively with minimal or no impact on the environment”. There have been different approaches to green computing, some of which include data center power management, operating system support, power supply, storage hardware, video card and display hardware, resource allocation, virtualization, terminal servers and algorithmic efficiency. In this thesis, we particularly study the relation between algorithmic efficiency and power consumption, obtaining performance models in the process. The algorithms studied primarily include basic linear algebra routines, such as matrix and vector multiplications and iterative solvers. Our studies show that it if the source code is optimized and tuned to the particular hardware used, there is a possibility of reducing the total power consumed at only slight costs to the computation time. The data sets utilized in this thesis are not significantly large and consequently, the power savings are not large either. However, as these optimizations can be scaled to larger data sets, it presents a positive outlook for power savings in much larger research environments

Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime

A 100-million-atom biomolecular simulation with NAMD is one of the three benchmarks for the NSF-funded sustainable petascale machine. Simulating this large molecular system on a petascale machine presents great challenges, including handling I/O, large memory footprint and getting good strong-scaling results. In this paper, we present parallel I/O techniques to enable the simula-tion. A new SMP model is designed to efficiently utilize ubiquitous wide multicore clusters by extending the CHARM++ asynchronous message-driven runtime. We exploit node-aware techniques to op-timize both the application and the underlying SMP runtime. Hi-erarchical load balancing is further exploited to scale NAMD to the full Jaguar PF Cray XT5 (224,076 cores) at Oak Ridge Na-tional Laboratory, both with and without PME full electrostatics, achieving 93 % parallel efficiency (vs 6720 cores) at 9 ms per step for a simple cutoff calculation. Excellent scaling is also obtained on 65,536 cores of the Intrepid Blue Gene/P at Argonne National Laboratory. 1

Performance analysis of single board computer clusters

The past few years have seen significant developments in Single Board Computer (SBC) hardware capabilities. These advances in SBCs translate directly into improvements in SBC clusters. In 2018 an individual SBC has more than four times the performance of a 64-node SBC cluster from 2013. This increase in performance has been accompanied by increases in energy efficiency (GFLOPS/W) and value for money (GFLOPS/$). We present systematic analysis of these metrics for three different SBC clusters composed of Raspberry Pi 3 Model B, Raspberry Pi 3 Model B+ and Odroid C2 nodes respectively. A 16-node SBC cluster can achieve up to 60GFLOPS, running at 80W. We believe that these improvements open new computational opportunities, whether this derives from a decrease in the physical volume required to provide a fixed amount of computation power for a portable cluster; or the amount of compute power that can be installed given a fixed budget in expendable compute scenarios. We also present a new SBC cluster construction form factor named Pi Stack; this has been designed to support edge compute applications rather than the educational use-cases favoured by previous methods. The improvements in SBC cluster performance and construction techniques mean that these SBC clusters are realising their potential as valuable developmental edge compute devices rather than just educational curiosities

Adaptive Parallelism for Coupled, Multithreaded Message-Passing Programs

Hybrid parallel programming models that combine message passing (MP) and shared- memory multithreading (MT) are becoming more popular, especially with applications requiring higher degrees of parallelism and scalability. Consequently, coupled parallel programs, those built via the integration of independently developed and optimized software libraries linked into a single application, increasingly comprise message-passing libraries with differing preferred degrees of threading, resulting in thread-level heterogeneity. Retroactively matching threading levels between independently developed and maintained libraries is difficult, and the challenge is exacerbated because contemporary middleware services provide only static scheduling policies over entire program executions, necessitating suboptimal, over-subscribed or under-subscribed, configurations. In coupled applications, a poorly configured component can lead to overall poor application performance, suboptimal resource utilization, and increased time-to-solution. So it is critical that each library executes in a manner consistent with its design and tuning for a particular system architecture and workload. Therefore, there is a need for techniques that address dynamic, conflicting configurations in coupled multithreaded message-passing (MT-MP) programs. Our thesis is that we can achieve significant performance improvements over static under-subscribed approaches through reconfigurable execution environments that consider compute phase parallelization strategies along with both hardware and software characteristics. In this work, we present new ways to structure, execute, and analyze coupled MT- MP programs. Our study begins with an examination of contemporary approaches used to accommodate thread-level heterogeneity in coupled MT-MP programs. Here we identify potential inefficiencies in how these programs are structured and executed in the high-performance computing domain. We then present and evaluate a novel approach for accommodating thread-level heterogeneity. Our approach enables full utilization of all available compute resources throughout an application’s execution by providing programmable facilities with modest overheads to dynamically reconfigure runtime environments for compute phases with differing threading factors and affinities. Our performance results show that for a majority of the tested scientific workloads our approach and corresponding open-source reference implementation render speedups greater than 50 % over the static under-subscribed baseline. Motivated by our examination of reconfigurable execution environments and their memory overhead, we also study the memory attribution problem: the inability to predict or evaluate during runtime where the available memory is used across the software stack comprising the application, reusable software libraries, and supporting runtime infrastructure. Specifically, dynamic adaptation requires runtime intervention, which by its nature introduces additional runtime and memory overhead. To better understand the latter, we propose and evaluate a new way to quantify component-level memory usage from unmodified binaries dynamically linked to a message-passing communication library. Our experimental results show that our approach and corresponding implementation accurately measure memory resource usage as a function of time, scale, communication workload, and software or hardware system architecture, clearly distinguishing between application and communication library usage at a per-process level