Optimizing iterative data-flow scientific applications using directed cyclic graphs

Data-flow programming models have become a popular choice for writing parallel applications as an alternative to traditional work-sharing parallelism. They are better suited to write applications with irregular parallelism that can present load imbalance. However, these programming models suffer from overheads related to task creation, scheduling and dependency management, limiting performance and scalability when tasks become too small. At the same time, many HPC applications implement iterative methods or multi-step simulations that create the same directed acyclic graphs of tasks on each iteration. By giving application programmers a way to express that a specific loop is creating the same task pattern on each iteration, we can create a single task directed acyclic graph (DAG) once and transform it into a cyclic graph. This cyclic graph is then reused for successive iterations, minimizing task creation and dependency management overhead. This paper presents the taskiter, a new construct we propose for the OmpSs-2 and OpenMP programming models, allowing the use of directed cyclic task graphs (DCTG) to minimize runtime overheads. Moreover, we present a simple immediate successor locality-aware heuristic that minimizes task scheduling overhead by bypassing the runtime task scheduler. We evaluate the implementation of the taskiter and the immediate successor heuristic in 8 iterative benchmarks. Using small task granularities, we obtain a geometric mean speedup of 2.56x over the reference OmpSs-2 implementation, and a 3.77x and 5.2x speedup over the LLVM and GCC OpenMP runtimes, respectively.This work was supported in part by the European Union’s Horizon 2020/EuroHPC Research and Innovation Programme (DEEP-SEA) under Grant 955606; in part by the Spanish State Research Agency—Ministry of Science and Innovation, Generalitat de Catalunya, under Project PCI2021121958 and Project 2021-SGR-01007; in part by the Spanish Ministry of Science and Technology under Contract PID2019-107255GB; and in part by Severo Ochoa under Grant CEX2021-001148-S/MCIN/AEI/10.13039/501100011033.Peer ReviewedPostprint (published version

Matrix Factorization at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies

We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausability), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to TB-sized problems in particle physics, climate modeling and bioimaging. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark's data-parallel model. We perform scaling experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance

Managing Overheads in Asynchronous Many-Task Runtime Systems

Asynchronous Many-Task (AMT) runtime systems are based on the idea of dividing an algorithm into small units of work, known as tasks. The runtime system is then responsible for scheduling and executing these tasks in an efficient manner by taking into account the resources provided to it and the associated data dependencies between the tasks. One of the primary challenges faced by AMTs is managing such fine-grained parallelism and the overheads associated with creating, scheduling and executing tasks. This work develops methodologies for assessing and managing overheads associated with fine-grained task execution in HPX, our exemplar Asynchronous Many-Task runtime system. Known optimization techniques, viz. active message coalescing, task inlining and parallel loop iteration chunking are applied to HPX. Active message coalescing, where messages bound to the same destination are aggregated into a single message, is presented as a solution to minimize overheads associated with fine-grained communications. Methodologies and metrics for analyzing fine-grained communication overheads are developed. The metrics identified and implemented in this research aid in evaluating network efficiency by giving us an intrinsic view of the underlying network overhead that would be difficult to measure using conventional methods. Task inlining, a method that allows runtime systems to manage the overheads introduced by a large number of tasks by merging tasks together into one thread of execution, is presented as a technique for minimizing fine-grained task overheads. A runtime policy that dynamically decides whether to inline a task is developed and evaluated on different processor architectures. A methodology to derive a largely machine independent constant that allows controlling task granularity is developed. Finally, the machine independent constant derived in the context of task inlining is applied to chunking of parallel loop iterations, which confirms its applicability to reduce overheads, in the context of finding the optimal chunk size of the combined loop iterations

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications

Many scientific problems require multiple distinct computational tasks to be executed in order to achieve a desired solution. We introduce the Ensemble Toolkit (EnTK) to address the challenges of scale, diversity and reliability they pose. We describe the design and implementation of EnTK, characterize its performance and integrate it with two distinct exemplar use cases: seismic inversion and adaptive analog ensembles. We perform nine experiments, characterizing EnTK overheads, strong and weak scalability, and the performance of two use case implementations, at scale and on production infrastructures. We show how EnTK meets the following general requirements: (i) implementing dedicated abstractions to support the description and execution of ensemble applications; (ii) support for execution on heterogeneous computing infrastructures; (iii) efficient scalability up to O(10^4) tasks; and (iv) fault tolerance. We discuss novel computational capabilities that EnTK enables and the scientific advantages arising thereof. We propose EnTK as an important addition to the suite of tools in support of production scientific computing

Optimizing the Performance of Multi-threaded Linear Algebra Libraries Based on Task Granularity

Linear algebra libraries play a very important role in many HPC applications. As larger datasets are created everyday, it also becomes crucial for the multi-threaded linear algebra libraries to utilize the compute resources properly. Moving toward exascale computing, the current programming models would not be able to fully take advantage of the advances in memory hierarchies, computer architectures, and networks. Asynchronous Many-Task(AMT) Runtime systems would be the solution to help the developers to manage the available parallelism. In this Dissertation we propose an adaptive solution to improve the performance of a linear algebra library based on a set of compile-time and runtime characteristics including the machine architecture, the expression being evaluated, the number of cores to run the application on, the type of the operation, and also the size of the matrices, to get as close as possible to the highest performance. Our focus is on machine learning applications, where we are potentially dealing with very large matrices, which could make creating temporaries very expensive. For this purpose we selected Blaze C++ library, a high performance template-based math library that gives us this option to access the expression tree at compile time, along with HPX, a C++ standard library for concurrency and parallelism, as our runtime system. HPX, as an AMT runtime system, offers scalibility and fine-grained parallelism through creating lightweight threads for fast context switching between the threads. Finding the optimum task granularity is a challenge in AMTs. Creating too many small tasks would result in performance degradation due to scheduling overhead of the tasks, and creating too few tasks would lead to under-utilization of the resources. Our work focuses on finding the optimum task granularity for each specific problem. We tried two different approaches to model the relationship between the performance and the grain size, in order to find a range of grain sizes that could lead us to the maximum performance. First, we used polynomial functions to model how throughput changes in terms of the grain size, and number of cores. Although this method was successful in finding the range of grain sizes for maximum throughput, it was not physical. This motivated us to go deeper and try to develop an analytical model for execution time in terms of grain size for balanced parallel for loops. Based on the analytical model we propose a method to predict the range of grain size for minimum execution time. Moreover, since the parameters of the proposed model only depend on the system architecture, we suggest to use a parallel for-loop benchmark to find these parameters on a system, and use it to find the range of grain size for minimum execution time for arbitrary balanced parallel for-loop applications ran on the same machine. Having the mentioned models, we changed the current implementation of the HPX backend for Blaze by adding two parameters to represent the unit of work, and the number of units included in each task, for fine grained control of the parallelism, which is possible through HPX runtime system. Also, a complexity estimation function has been added to Blaze to estimate the number of floating point operations occurring in each unit of work. The model parameters estimated through the parallel for-loop benchmark could also be plugged into Blaze at compile time, in order to find the optimum range of grain size at runtime based on the matrix sizes and complexity of the operations. In the next step, we used the identified range of grain size to extend the previous implementation of splittable tasks, as an algorithm to control task granularity. We modified the current implementation by scheduling the tasks on idle cores directly instead of waiting for them to be stolen, and integrating the lower-bound of the analytical model as the threshold to stop splitting, in order to adapt the threshold to the system architecture and the application being executed

MxTasks: a novel processing model to support data processing on modern hardware

The hardware landscape has changed rapidly in recent years. Modern hardware in today's servers is characterized by many CPU cores, multiple sockets, and vast amounts of main memory structured in NUMA hierarchies. In order to benefit from these highly parallel systems, the software has to adapt and actively engage with newly available features. However, the processing models forming the foundation for many performance-oriented applications have remained essentially unchanged. Threads, which serve as the central processing abstractions, can be considered a "black box" that hardly allows any transparency between the application and the system underneath. On the one hand, applications are aware of the knowledge that could assist the system in optimizing the execution, such as accessed data objects and access patterns. On the other hand, the limited opportunities for information exchange cause operating systems to make assumptions about the applications' intentions to optimize their execution, e.g., for local data access. Applications, on the contrary, implement optimizations tailored to specific situations, such as sophisticated synchronization mechanisms and hardware-conscious data structures. This work presents MxTasking, a task-based runtime environment that assists the design of data structures and applications for contemporary hardware. MxTasking rethinks the interfaces between performance-oriented applications and the execution substrate, streamlining the information exchange between both layers. By breaking patterns of processing models designed with past generations of hardware in mind, MxTasking creates novel opportunities to manage resources in a hardware- and application-conscious way. Accordingly, we question the granularity of "conventional" threads and show that fine-granular MxTasks are a viable abstraction unit for characterizing and optimizing the execution in a general way. Using various demonstrators in the context of database management systems, we illustrate the practical benefits and explore how challenges like memory access latencies and error-prone synchronization of concurrency can be addressed straightforwardly and effectively

Design of robust scheduling methodologies for high performance computing

Scientific applications are often large, complex, computationally-intensive, and irregular. Loops are often an abundant source of parallelism in scientific applications. Due to the ever-increasing computational needs of scientific applications, high performance computing (HPC) systems have become larger and more complex, offering increased parallelism at multiple hardware levels. Load imbalance, caused by irregular computational load per task and unpredictable computing system characteristics (system variability), often degrades the performance of applications. Besides, perturbations, such as reduced computing power, network latency availability, or failures, can severely impact the performance of the applications. System variability and perturbations are only expected to increase in future extreme-scale computing systems. Extrapolating the current failure rate to Exascale would result in a failure every 20 minutes. Such failure rate and perturbations would render the computing systems unusable. This doctoral thesis improves the performance of computationally-intensive scientific applications on HPC systems via robust load balancing. Robust scheduling ensures and maintains improved load balanced execution under unpredictable application and system characteristics. A number of dynamic loop self-scheduling (DLS) techniques have been introduced and successfully used in scientific applications between the 1980s and 2000s. These DLS techniques are not fault-tolerant as they were originally introduced. In this thesis, we identify three major research questions to achieve robust scheduling (1) How to ensure that the DLS techniques employed in scientific applications today adhere to their original design goals and specifications? (2) How to select a DLS technique that will achieve improved performance under perturbations? (3) How to tolerate perturbations during execution and maintain a load balanced execution on HPC systems? To answer the first question, we reproduced the original experiments that introduced the DLS techniques to verify their present implementation. Simulation is used to reproduce experiments on systems from the past. Realistic simulation induces a similar analysis and conclusions to the analysis of the native results. To this end, we devised an approach for bridging the native and simulative executions of parallel applications on HPC systems. This simulation approach is used to reproduce scheduling experiments on past and present systems to verify the implementation of DLS techniques. Given the multiple levels of parallelism offered by the present HPC systems, we analyzed the load imbalance in scientific applications, from computer vision, astrophysics, and mathematical kernels, at both thread and process levels. This analysis revealed a significant interplay between thread level and process level load balancing. We found that dynamic load balancing at the thread level propagates to the process level and vice versa. However, the best application performance is only achieved by two-level dynamic load balancing. Next, we examined the performance of applications under perturbations. We found that the most robust DLS technique does not deliver the best performance under various perturbations. The most efficient DLS technique changes by changing the application, the system, or perturbations during execution. This signifies the algorithm selection problem in the DLS. We leveraged realistic simulations to address the algorithm selection problem of scheduling under perturbations via a simulation assisted approach (SimAS), which answers the second question. SimAS dynamically selects DLS techniques that improve the performance depending on the application, system, and perturbations during the execution. To answer the third question, we introduced a robust dynamic load balancing (rDLB) approach for the robust self-scheduling of scientific applications under failures (question 3). rDLB proactively reschedules already allocated tasks and requires no detection of perturbations. rDLB tolerates up to P −1 processor failures (P is the number of processors allocated to the application) and boosts the flexibility of applications against nonfatal perturbations, such as reduced availability of resources. This thesis is the first to provide insights into the interplay between thread and process level dynamic load balancing in scientific applications. Verified DLS techniques, SimAS, and rDLB are integrated into an MPI-based dynamic load balancing library (DLS4LB), which supports thirteen DLS techniques, for robust dynamic load balancing of scientific applications on HPC systems. Using the methods devised in this thesis, we improved the performance of scientific applications by up to 21% via two-level dynamic load balancing. Under perturbations, we enhanced their performance by a factor of 7 and their flexibility by a factor of 30. This thesis opens up the horizons into understanding the interplay of load balancing between various levels of software parallelism and lays the ground for robust multilevel scheduling for the upcoming Exascale HPC systems and beyond