Improving the performance of the Parallel Ice Sheet Model on a large-scale, distributed supercomputer

In this thesis, we describe our work to understand and improve the performance and scalability of the Parallel Ice Sheet Model (PISM) on the Ranger supercomputer. PISM enables the simulation of large-scale ice sheets, such as those found in Greenland and Antarctica, which are of particular interest to climate scientists due to their potential to contribute to sea-level rise. PISM has a unique parallel architecture that is designed to take advantage of the computational resources available on state-of-the-art supercomputers. The problem, however, is that even though PISM can run without modifcation on a supercomputer, it is generally unable to do so efficiently. We observed that PISM exhibits rapidly diminishing performance gains as the number of processors is increased, even experiencing an increase in execution time with large processor counts. PISM\u27s inability to make efficient use of the resources available on today\u27s supercomputers presents a challenge to researchers, particularly as larger and higher resolution data sets become available. In this work, we analyzed the reasons for PISM\u27s poor performance and developed techniques to address these issues, resulting in an increase in performance by as much as a factor of 20

Survey of storage systems for high-performance computing

In current supercomputers, storage is typically provided by parallel distributed file systems for hot data and tape archives for cold data. These file systems are often compatible with local file systems due to their use of the POSIX interface and semantics, which eases development and debugging because applications can easily run both on workstations and supercomputers. There is a wide variety of file systems to choose from, each tuned for different use cases and implementing different optimizations. However, the overall application performance is often held back by I/O bottlenecks due to insufficient performance of file systems or I/O libraries for highly parallel workloads. Performance problems are dealt with using novel storage hardware technologies as well as alternative I/O semantics and interfaces. These approaches have to be integrated into the storage stack seamlessly to make them convenient to use. Upcoming storage systems abandon the traditional POSIX interface and semantics in favor of alternative concepts such as object and key-value storage; moreover, they heavily rely on technologies such as NVM and burst buffers to improve performance. Additional tiers of storage hardware will increase the importance of hierarchical storage management. Many of these changes will be disruptive and require application developers to rethink their approaches to data management and I/O. A thorough understanding of today's storage infrastructures, including their strengths and weaknesses, is crucially important for designing and implementing scalable storage systems suitable for demands of exascale computing

A Lightweight I/O Scheme to Facilitate Spatial and Temporal Queries of Scientific Data Analytics

In the era of petascale computing, more scientific applications are being deployed on leadership scale computing platforms to enhance the scientific productivity. Many I/O techniques have been designed to address the growing I/O bottleneck on large-scale systems by handling massive scientific data in a holistic manner. While such techniques have been leveraged in a wide range of applications, they have not been shown as adequate for many mission critical applications, particularly in data post-processing stage. One of the examples is that some scientific applications generate datasets composed of a vast amount of small data elements that are organized along many spatial and temporal dimensions but require sophisticated data analytics on one or more dimensions. Including such dimensional knowledge into data organization can be beneficial to the efficiency of data post-processing, which is often missing from exiting I/O techniques. In this study, we propose a novel I/O scheme named STAR (Spatial and Temporal AggRegation) to enable high performance data queries for scientific analytics. STAR is able to dive into the massive data, identify the spatial and temporal relationships among data variables, and accordingly organize them into an optimized multi-dimensional data structure before storing to the storage. This technique not only facilitates the common access patterns of data analytics, but also further reduces the application turnaround time. In particular, STAR is able to enable efficient data queries along the time dimension, a practice common in scientific analytics but not yet supported by existing I/O techniques. In our case study with a critical climate modeling application GEOS-5, the experimental results on Jaguar supercomputer demonstrate an improvement up to 73 times for the read performance compared to the original I/O method

ArrayBridge: Interweaving declarative array processing with high-performance computing

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.Comment: 12 pages, 13 figure

Helmholtz Portfolio Theme Large-Scale Data Management and Analysis (LSDMA)

The Helmholtz Association funded the "Large-Scale Data Management and Analysis" portfolio theme from 2012-2016. Four Helmholtz centres, six universities and another research institution in Germany joined to enable data-intensive science by optimising data life cycles in selected scientific communities. In our Data Life cycle Labs, data experts performed joint R&D together with scientific communities. The Data Services Integration Team focused on generic solutions applied by several communities

Exascale storage systems: an analytical study of expenses

The computational power and storage capability of supercomputers are growing at a different pace, with storage lagging behind; the widening gap necessitates new approaches to keep the investment and running costs for storage systems at bay. In this paper, we aim to unify previous models and compare different approaches for solving these problems. By extrapolating the characteristics of the German Climate Computing Center's previous supercomputers to the future, cost factors are identified and quantified in order to foster adequate research and development. Using models to estimate the execution costs of two prototypical use cases, we are discussing the potential of three concepts: re-computation, data deduplication and data compression

Making the case for reforming the I/O software stack of extreme-scale systems

This work was supported in part by the U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research, under Contract No. DE-AC02-05CH11231. This research has been partially funded by the Spanish Ministry of Science and Innovation under grant TIN2010-16497 “Input/Output techniques for distributed and high-performance computing environments”. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement number 328582

Monitoring, analysis and optimisation of I/O in parallel applications

High performance computing (HPC) is changing the way science is performed in the 21st Century; experiments that once took enormous amounts of time, were dangerous and often produced inaccurate results can now be performed and refined in a fraction of the time in a simulation environment. Current generation supercomputers are running in excess of 1016 floating point operations per second, and the push towards exascale will see this increase by two orders of magnitude. To achieve this level of performance it is thought that applications may have to scale to potentially billions of simultaneous threads, pushing hardware to its limits and severely impacting failure rates. To reduce the cost of these failures, many applications use checkpointing to periodically save their state to persistent storage, such that, in the event of a failure, computation can be restarted without significant data loss. As computational power has grown by approximately 2x every 18 ? 24 months, persistent storage has lagged behind; checkpointing is fast becoming a bottleneck to performance. Several software and hardware solutions have been presented to solve the current I/O problem being experienced in the HPC community and this thesis examines some of these. Specifically, this thesis presents a tool designed for analysing and optimising the I/O behaviour of scientific applications, as well as a tool designed to allow the rapid analysis of one software solution to the problem of parallel I/O, namely the parallel log-structured file system (PLFS). This thesis ends with an analysis of a modern Lustre file system under contention from multiple applications and multiple compute nodes running the same problem through PLFS. The results and analysis presented outline a framework through which application settings and procurement decisions can be made

Improving Parallel I/O Performance Using Interval I/O

Today\u27s most advanced scientific applications run on large clusters consisting of hundreds of thousands of processing cores, access state of the art parallel file systems that allow files to be distributed across hundreds of storage targets, and utilize advanced interconnections systems that allow for theoretical I/O bandwidth of hundreds of gigabytes per second. Despite these advanced technologies, these applications often fail to obtain a reasonable proportion of available I/O bandwidth. The reasons for the poor performance of application I/O include the noncontiguous I/O access patterns used for scientific computing, contention due to false sharing, and the somewhat finicky nature of parallel file system performance. We argue that a more fundamental cause of this problem is the legacy view of a file as a linear sequence of bytes. To address these issues, we introduce a novel approach for parallel I/O called Interval I/O. Interval I/O is an innovative approach that uses application access patterns to partition a file into a series of intervals, which are used as the fundamental unit for subsequent I/O operations. Use of this approach provides superior performance for the noncontiguous access patterns which are frequently used by scientific applications. In addition, the approach reduces false contention and the unnecessary serialization it causes. Interval I/O also significantly increases the performance of atomic mode operations. Finally, the Interval I/O approach includes a technique for supporting parallel I/O for cooperating applications. We provide a prototype implementation of our Interval I/O system and use it to demonstrate performance improvements of as much as 1000% compared to ROMIO when using Interval I/O with several common benchmarks