Partial differential equation (PDE) solvers are extensively utilized across numerous scientific and engineering fields. However, achieving high performance and scalability often necessitates intricate and low-level programming, particularly when leveraging deterministic sparsity patterns in structured grids. In this paper, we propose an innovative domain-specific language (DSL), Mat2Stencil, with its compiler, for PDE solvers on structured grids. Mat2Stencil introduces a structured sparse matrix abstraction, facilitating modular, flexible, and easy-to-use expression of solvers across a broad spectrum, encompassing components such as Jacobi or Gauss-Seidel preconditioners, incomplete LU or Cholesky decompositions, and multigrid methods built upon them. Our DSL compiler subsequently generates matrix-free code consisting of generalized stencils through multi-stage programming. The code allows spatial loop-carried dependence in the form of quasi-affine loops, in addition to the Jacobi-style stencil’s embarrassingly parallel on spatial dimensions. We further propose a novel automatic parallelization technique for the spatially dependent loops, which offers a compile-time deterministic task partitioning for threading, calculates necessary inter-thread synchronization automatically, and generates an efficient multi-threaded implementation with fine-grained synchronization. Implementing 4 benchmarking programs, 3 of them being the pseudo-applications in NAS Parallel Benchmarks with 6.3% lines of code and 1 being matrix-free High Performance Conjugate Gradients with 16.4% lines of code, we achieve up to 1.67× and on average 1.03× performance compared to manual implementations.

Out-of-core systems rely on high-performance cache sub-systems to reduce the number of I/O operations. Although the page cache in modern operating systems enables transparent access to memory and storage devices, it suffers from efficiency and scalability issues on cache misses, forcing out-of-core systems to design and implement their own cache components, which is a non-trivial task. This study proposes TriCache, a cache mechanism that enables in-memory programs to efficiently process out-of-core datasets without requiring any code rewrite. It provides a virtual memory interface on top of the conventional block interface to simultaneously achieve user transparency and sufficient out-of-core performance. A multi-level block cache design is proposed to address the challenge of per-access address translations required by a memory interface. It can exploit spatial and temporal localities in memory or storage accesses to render storage-to-memory address translation and page-level concurrency control adequately efficient for the virtual memory interface. Our evaluation shows that in-memory systems operating on top of TriCache can outperform Linux OS page cache by more than one order of magnitude, and can deliver performance comparable to or even better than that of corresponding counterparts designed specifically for out-of-core scenarios.

Machine learning applications on Spark suffers from poor scalability. In this paper, we reveal that the key reasons is the non-scalable reduction, which is restricted by the non-splittable object programming interface in Spark. This insight guides us to propose Sparker, Spark with Efficient Reduction. By providing a split aggregation interface, Sparker is able to perform split aggregation with scalable reduction while being backward compatible with existing applications. We implemented Sparker in 2,534 lines of code. Sparker can improve the aggregation performance by up to 6.47 × and can improve the end-to-end performance of MLlib model training by up to 3.69 × with a geometric mean of 1.81 × .

Apache Spark is a widely deployed big data analytics framework that offers such attractive features as resiliency, load-balancing, and a rich ecosystem. However, there is still plenty of room for improvement in its performance. Although a data-parallel system in a native programming language significantly improves performance, it may require re-implementing many functionalities of Spark to become a full-featured system. It is desirable for native big data systems to just write a compute engine in native languages to ensure high efficiency, and reuse other mature features provided by Spark rather than re-implement everything. But the interaction between the JVM and the native world risks becoming a bottleneck. This paper proposes Chukonu, a native big data framework that re-uses critical big data features provided by Spark. Owing to our novel DAG-splitting approach, the potential Spark integration overhead is alleviated, and its even outperforms existing pure native big data frameworks. Chukonu splits DAG programs into run-time parts and compile-time parts: The run-time parts are delegated to Spark to offload the complexities due to feature implementations. The compile-time parts are natively compiled. We propose a series of optimization techniques to be applied to the compile-time parts, such as operator fusion, vectorization, and compaction, to significantly reduce the Spark integration overhead. The results of evaluation show that Chukonu has a speedup of up to 71.58X (geometric mean 6.09X) over Apache Spark, and up to 7.20X (geometric mean 2.30X) over pure-native frameworks on six commonly-used big data applications. By translating the physical plan produced by SparkSQL into Chukonu programs, Chukonu accelerates Spark-SQL's TPC-DS performance by 2.29X.

Fault tolerance is increasingly important in high-performance computing due to the substantial growth of system scale and decreasing system reliability. In-memory/diskless checkpoint has gained extensive attention as a solution to avoid the IO bottleneck of traditional disk-based checkpoint methods. However, applications using previous in-memory checkpoint suffer from little available memory space. To provide high reliability, previous in-memory checkpoint methods either need to keep two copies of checkpoints to tolerate failures while updating old checkpoints or trade performance for space by flushing in-memory checkpoints into disk. In this paper, we propose a novel in-memory checkpoint method, called self-checkpoint, which can not only achieve the same reliability of previous in-memory checkpoint methods, but also increase the available memory space for applications by almost 50 percent. To validate our method, we apply self-checkpoint method to an important problem: High-Performance Linpack (HPL) with fault tolerance. We implement a scalable and fault tolerant HPL based on this new method, called SKT-HPL, and validate it on two large-scale systems. Experimental results with 24,576 processes show that SKT-HPL achieves over 95 percent of the performance of the original HPL. Compared to the state-of-the-art in-memory checkpoint method, it improves the available memory size by 47 percent and the performance by 5 percent.

Interest has recently grown in efficiently analyzing unstructured data such as social network graphs and protein structures. A fundamental graph algorithm for doing such task is the Breadth-First Search (BFS) algorithm, the foundation for many other important graph algorithms such as calculating the shortest path or finding the maximum flow in graphs. In this paper, we share our experience of designing and implementing the BFS algorithm on Sunway TaihuLight, a newly released machine with 40,960 nodes and 10.6 million accelerator cores. It tops the Top500 list of June 2016 with a 93.01 petaflops Linpack performance [1]. Designed for extremely large-scale computation and power efficiency, processors on Sunway TaihuLight employ a unique heterogeneous many-core architecture and memory hierarchy. With its extremely large size, the machine provides both opportunities and challenges for implementing high-performance irregular algorithms, such as BFS. We propose several techniques, including pipelined module mapping, contention-free data shuffling, and group-based message batching, to address the challenges of efficiently utilizing the features of this large scale heterogeneous machine. We ultimately achieved 23755.7 giga-traversed edges per second (GTEPS), which is the best among heterogeneous machines and the second overall in the Graph500s June 2016 list [2].

Fault tolerance is increasingly important in high performance computing due to the substantial growth of system scale and decreasing system reliability. In-memory/diskless checkpoint has gained extensive attention as a solution to avoid the IO bottleneck of traditional disk-based checkpoint methods. However, applications using previous in-memory checkpoint suffer from little available memory space. To provide high reliability, previous in-memory checkpoint methods either need to keep two copies of checkpoints to tolerate failures while updating old checkpoints or trade performance for space by flushing in-memory checkpoints into disk.