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1. Evaluating Asynchronous Parallel I/O on HPC Systems

   https://doi.org/10.1109/IPDPS54959.2023.00030  

   Ravi, John; Byna, Suren; Koziol, Quincey; Tang, Houjun; Becchi, Michela (May 2023, 10.1109/IPDPS54959.2023.00030)

   Parallel I/O is an effective method to optimize data movement between memory and storage for many scientific applications. Poor performance of traditional disk-based file systems has led to the design of I/O libraries which take advantage of faster memory layers, such as on-node memory, present in high-performance computing (HPC) systems. By allowing caching and prefetching of data for applications alternating computation and I/O phases, a faster memory layer also provides opportunities for hiding the latency of I/O phases by overlapping them with computation phases, a technique called asynchronous I/O. Since asynchronous parallel I/O in HPC systems is still in the initial stages of development, there hasn't been a systematic study of the factors affecting its performance.In this paper, we perform a systematic study of various factors affecting the performance and efficacy of asynchronous I/O, we develop a performance model to estimate the aggregate I/O bandwidth achievable by iterative applications using synchronous and asynchronous I/O based on past observations, and we evaluate the performance of the recently developed asynchronous I/O feature of a parallel I/O library (HDF5) using benchmarks and real-world science applications. Our study covers parallel file systems on two large-scale HPC systems: Summit and Cori, the former with a GPFS storage and the latter with a Lustre parallel file system. 

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2. Efficient and Safe I/O Operations for Intermittent Systems

   Yildiz, Eren; Ahmed, Saad; Islam, Bashima; Hester, Josiah; Yildirim, Kasim S. (May 2023, Proceedings of the Eighteenth European Conference on Computer Systems (EuroSys ’23))

   Task-based intermittent software systems always re-execute peripheral input/output (I/O) operations upon power failures since tasks have all-or-nothing semantics. Re-executed I/O wastes significant time and energy and risks memory inconsistency. This paper presents EaseIO, a new task-based intermittent system that remedies these problems. EaseIO programming interface introduces re-execution semantics for I/O operations to facilitate safe and efficient I/O management for intermittent applications. EaseIO compiler front-end considers the programmer-annotated I/O re-execution semantics to preserve the task's energy efficiency and idem-potency. EaseIO runtime introduces regional privatization to eliminate memory inconsistency caused by idempotence bugs. Our evaluation shows that EaseIO reduces the wasted useful I/O work by up to 3× and total execution time by up to 44% by avoiding 76% of the redundant I/O operations, as compared to the state-of-the-art approaches for intermittent computing. Moreover, for the first time, EaseIO ensures memory consistency during DMA-based I/O operations. 

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3. A multiparty session typing discipline for fault-tolerant event-driven distributed programming

   https://doi.org/10.1145/3485501  

   Viering, Malte; Hu, Raymond; Eugster, Patrick; Ziarek, Lukasz (October 2021, Proceedings of the ACM on Programming Languages)

   This paper presents a formulation of multiparty session types (MPSTs) for practical fault-tolerant distributed programming. We tackle the challenges faced by session types in the context of distributed systems involving asynchronous and concurrent partial failures – such as supporting dynamic replacement of failed parties and retrying failed protocol segments in an ongoing multiparty session – in the presence of unreliable failure detection. Key to our approach is that we develop a novel model of event-driven concurrency for multiparty sessions. Inspired by real-world practices, it enables us to unify the session-typed handling of regular I/O events with failure handling and the combination of features needed to express practical fault-tolerant protocols. Moreover, the characteristics of our model allow us to prove a global progress property for well-typed processes engaged in multiple concurrent sessions, which does not hold in traditional MPST systems. To demonstrate its practicality, we implement our framework as a toolchain and runtime for Scala, and use it to specify and implement a session-typed version of the cluster management system of the industrial-strength Apache Spark data analytics framework. Our session-typed cluster manager composes with other vanilla Spark components to give a functioning Spark runtime; e.g., it can execute existing third-party Spark applications without code modification. A performance evaluation using the TPC-H benchmark shows our prototype implementation incurs an average overhead below 10%. 

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4. On Overlapping Communication and File I/O in Collective Write Operation

   https://doi.org/10.1109/IPDPSW50202.2020.00175  

   Feki, Raafat; Gabriel, Edgar (May 2020, 2020 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW))

   null (Ed.)

   Many parallel scientific applications spend a significant amount of time reading and writing data files. Collective I/O operations allow to optimize the file access of a process group by redistributing data across processes to match the data layout on the file system. In most parallel I/O libraries, the implementation of collective I/O operations is based on the two-phase I/O algorithm, which consists of a communication phase and a file access phase. This papers evaluates various design options for overlapping two internal cycles of the two-phase I/O algorithm, and explores using different data transfer primitives for the shuffle phase, including non-blocking two-sided communication and multiple versions of one-sided communication. The results indicate that overlap algorithms incorporating asynchronous I/O outperform overlapping approaches that only rely on non-blocking communication. However, in the vast majority of the testcases one-sided communication did not lead to performance improvements over two-sided communication. 

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5. Predicting and Comparing the Performance of Array Management Libraries

   https://doi.org/10.1109/IPDPS47924.2020.00097  

   Kang, Donghe; Rubel, Oliver; Byna, Suren; Blanas, Spyros (May 2020, 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS))

   Many applications are increasingly becoming I/O-bound. To improve scalability, analytical models of parallel I/O performance are often consulted to determine possible I/O optimizations. However, I/O performance modeling has predominantly focused on applications that directly issue I/O requests to a parallel file system or a local storage device. These I/O models are not directly usable by applications that access data through standardized I/O libraries, such as HDF5, FITS, and NetCDF, because a single I/O request to an object can trigger a cascade of I/O operations to different storage blocks. The I/O performance characteristics of applications that rely on these libraries is a complex function of the underlying data storage model, user-configurable parameters and object-level access patterns. As a consequence, I/O optimization is predominantly an ad-hoc process that is performed by application developers, who are often domain scientists with limited desire to delve into nuances of the storage hierarchy of modern computers.This paper presents an analytical cost model to predict the end-to-end execution time of applications that perform I/O through established array management libraries. The paper focuses on the HDF5 and Zarr array libraries, as examples of I/O libraries with radically different storage models: HDF5 stores every object in one file, while Zarr creates multiple files to store different objects. We find that accessing array objects via these I/O libraries introduces new overheads and optimizations. Specifically, in addition to I/O time, it is crucial to model the cost of transforming data to a particular storage layout (memory copy cost), as well as model the benefit of accessing a software cache. We evaluate the model on real applications that process observations (neuroscience) and simulation results (plasma physics). The evaluation on three HPC clusters reveals that I/O accounts for as little as 10% of the execution time in some cases, and hence models that only focus on I/O performance cannot accurately capture the performance of applications that use standard array storage libraries. In parallel experiments, our model correctly predicts the fastest storage library between HDF5 and Zarr 94% of the time, in contrast with 70% of the time for a cutting-edge I/O model. 

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