Galley: A New Parallel File System for Parallel Applications

Most current multiprocessor file systems are designed to use multiple disks in parallel, using the high aggregate bandwidth to meet the growing I/O requirements of parallel scientific applications. Most multiprocessor file systems provide applications with a conventional Unix-like interface, allowing the application to access those multiple disks transparently. This interface conceals the parallelism within the file system, increasing the ease of programmability, but making it difficult or impossible for sophisticated application and library programmers to use knowledge about their I/O to exploit that parallelism. In addition to providing an insufficient interface, most current multiprocessor file systems are optimized for a different workload than they are being asked to support. In this work we examine current multiprocessor file systems, as well as how those file systems are used by scientific applications. Contrary to the expectations of the designers of current parallel file systems, the workloads on those systems are dominated by requests to read and write small pieces of data. Furthermore, rather than being accessed sequentially and contiguously, as in uniprocessor and supercomputer workloads, files in multiprocessor file systems are accessed in regular, structured, but non-contiguous patterns. Based on our observations of multiprocessor workloads, we have designed Galley, a new parallel file system that is intended to efficiently support realistic scientific multiprocessor workloads. In this work, we introduce Galley and discuss its design and implementation. We describe Galley\u27s new three-dimensional file structure and discuss how that structure can be used by parallel applications to achieve higher performance. We introduce several new data-access interfaces, which allow applications to explicitly describe the regular access patterns we found to be common in parallel file system workloads. We show how these new interfaces allow parallel applications to achieve tremendous increases in I/O performance. Finally, we discuss how Galley\u27s new file structure and data-access interfaces can be useful in practice

GekkoFS: A temporary burst buffer file system for HPC applications

Many scientific fields increasingly use high-performance computing (HPC) to process and analyze massive amounts of experimental data while storage systems in today’s HPC environments have to cope with new access patterns. These patterns include many metadata operations, small I/O requests, or randomized file I/O, while general-purpose parallel file systems have been optimized for sequential shared access to large files. Burst buffer file systems create a separate file system that applications can use to store temporary data. They aggregate node-local storage available within the compute nodes or use dedicated SSD clusters and offer a peak bandwidth higher than that of the backend parallel file system without interfering with it. However, burst buffer file systems typically offer many features that a scientific application, running in isolation for a limited amount of time, does not require. We present GekkoFS, a temporary, highly-scalable file system which has been specifically optimized for the aforementioned use cases. GekkoFS provides relaxed POSIX semantics which only offers features which are actually required by most (not all) applications. GekkoFS is, therefore, able to provide scalable I/O performance and reaches millions of metadata operations already for a small number of nodes, significantly outperforming the capabilities of common parallel file systems.Peer ReviewedPostprint (author's final draft

A Study of Client-based Caching for Parallel I/O

The trend in parallel computing toward large-scale cluster computers running thousands of cooperating processes per application has led to an I/O bottleneck that has only gotten more severe as the the number of processing cores per CPU has increased. Current parallel file systems are able to provide high bandwidth file access for large contiguous file region accesses; however, applications repeatedly accessing small file regions on unaligned file region boundaries continue to experience poor I/O throughput due to the high overhead associated with accessing parallel file system data. In this dissertation we demonstrate how client-side file data caching can improve parallel file system throughput for applications performing frequent small and unaligned file I/O. We explore the impacts of cache page size and cache capacity using the popular FLASH I/O benchmark and explore a novel cache sharing approach that leverages the trend toward multi-core processors. We also explore a technique we call progressive page caching that represents cache data using dynamic data structures rather than fixed-size pages of file data. Finally, we explore a cache aggregation scheme that leverages the high-level file I/O interfaces provided by the PVFS file system to provide further performance enhancements. In summary, our results indicate that a correctly configured middleware-based file data cache can dramatically improve the performance of I/O workloads dominated by small unaligned file accesses. Further, we demonstrate that a well designed cache can offer stable performance even when the selected cache page granularity is not well matched to the provided workload. Finally, we have shown that high-level file system interfaces can significantly accelerate application performance, and interfaces beyond those currently envisioned by the MPI-IO standard could provide further performance benefits

Implementing Transparent Compression and Leveraging Solid State Disks in a High Performance Parallel File System

In recent years computers have been increasing in compute density and speed at a dramatic pace. This increase allows for massively parallel programs to run faster than ever before. Unfortunately, many such programs are being held back by the relatively slow I/O subsystems that they are forced to work with. Storage technology simply has not followed the same curve of progression in the computing world. Because the storage systems are so slow in comparison the processors are forced to idle while waiting for data; a potentially performance crippling condition. This performance disparity is lessened by the advent of parallel file systems. Such file systems allow data to be spread across multiple servers and disks. High speed networking allows for large amounts of bandwidth to and from the file system with relatively low latency. This arrangement allows for very large increases in sustained read and write speeds on large files although performance of the file system can be hampered if an application spends most of its time working on small data sets and files. In recent years there has also been an unprecedented forward shift in high performance I/O systems through the widespread development and deployment of NAND Flash-based solid state disks (SSDs). SSDs offer many advantages over traditional platter-based hard disk drives (HDDs) but also suffer from very specific disadvantages due to their use of Flash memory as a storage medium as well as use of a hardware flash translation layer (FTL). The advantages of SSDs are numerous: faster random and sequential access times, higher I/O operations per second} (IOPS), and much lower power consumption in both idle and load scenarios. SSDs also tend to have a much longer mean time between failure (MTBF); an advantage that can be attributed to their complete lack of moving parts. Two key things prevent SSDs from widespread mass storage deployment: storage capacity and cost per gigabyte. Enterprise level SSDs that utilize single-level cell (SLC) Flash are orders of magnitude more expensive per gigabyte than their enterprise class HDD counterparts (which are also higher capacity per drive). Because of this disparity we propose utilizing relatively small SSDs in conjunction with high capacity HDD arrays in parallel file systems like OrangeFS (previously known as the Parallel Virtual File System, or PVFS). The access latencies and bandwidth of SSDs make them an ideal medium for storing file metadata in a parallel file system. These same characteristics also make them ideal for integration as a persistent server-side cache. We also introduce a method of transparently compressing file data in striped parallel file systems for high-performance streaming reads and writes with increased storage capacity to combat rising checkpoint sizes and bandwidth requirements

Dynamic File-Access Characteristics of a Production Parallel Scientific Workload

Multiprocessors have permitted astounding increases in computational performance, but many cannot meet the intense I/O requirements of some scientific applications. An important component of any solution to this I/O bottleneck is a parallel file system that can provide high-bandwidth access to tremendous amounts of data in parallel to hundreds or thousands of processors. Most successful systems are based on a solid understanding of the characteristics of the expected workload, but until now there have been no comprehensive workload characterizations of multiprocessor file systems. We began the CHARISMA project in an attempt to fill that gap. We instrumented the common node library on the iPSC/860 at NASA Ames to record all file-related activity over a two-week period. Our instrumentation is different from previous efforts in that it collects information about every read and write request and about the mix of jobs running in the machine (rather than from selected applications). The trace analysis in this paper leads to many recommendations for designers of multiprocessor file systems. First, the file system should support simultaneous access to many different files by many jobs. Second, it should expect to see many small requests, predominantly sequential and regular access patterns (although of a different form than in uniprocessors), little or no concurrent file-sharing between jobs, significant byte- and block-sharing between processes within jobs, and strong interprocess locality. Third, our trace-driven simulations showed that these characteristics led to great success in caching, both at the compute nodes and at the I/O nodes. Finally, we recommend supporting strided I/O requests in the file-system interface, to reduce overhead and allow more performance optimization by the file system

A shared-disk parallel cluster file system

Dissertação apresentada para obtenção do Grau de Doutor em Informática Pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaToday, clusters are the de facto cost effective platform both for high performance computing (HPC) as well as IT environments. HPC and IT are quite different environments and differences include, among others, their choices on file systems and storage: HPC favours parallel file systems geared towards maximum I/O bandwidth, but which are not fully POSIX-compliant and were devised to run on top of (fault prone) partitioned storage; conversely, IT data centres favour both external disk arrays (to provide highly available storage) and POSIX compliant file systems, (either general purpose or shared-disk cluster file systems, CFSs). These specialised file systems do perform very well in their target environments provided that applications do not require some lateral features, e.g., no file locking on parallel file systems, and no high performance writes over cluster-wide shared files on CFSs. In brief, we can say that none of the above approaches solves the problem of providing high levels of reliability and performance to both worlds. Our pCFS proposal makes a contribution to change this situation: the rationale is to take advantage on the best of both – the reliability of cluster file systems and the high performance of parallel file systems. We don’t claim to provide the absolute best of each, but we aim at full POSIX compliance, a rich feature set, and levels of reliability and performance good enough for broad usage – e.g., traditional as well as HPC applications, support of clustered DBMS engines that may run over regular files, and video streaming. pCFS’ main ideas include: · Cooperative caching, a technique that has been used in file systems for distributed disks but, as far as we know, was never used either in SAN based cluster file systems or in parallel file systems. As a result, pCFS may use all infrastructures (LAN and SAN) to move data. · Fine-grain locking, whereby processes running across distinct nodes may define nonoverlapping byte-range regions in a file (instead of the whole file) and access them in parallel, reading and writing over those regions at the infrastructure’s full speed (provided that no major metadata changes are required). A prototype was built on top of GFS (a Red Hat shared disk CFS): GFS’ kernel code was slightly modified, and two kernel modules and a user-level daemon were added. In the prototype, fine grain locking is fully implemented and a cluster-wide coherent cache is maintained through data (page fragments) movement over the LAN. Our benchmarks for non-overlapping writers over a single file shared among processes running on different nodes show that pCFS’ bandwidth is 2 times greater than NFS’ while being comparable to that of the Parallel Virtual File System (PVFS), both requiring about 10 times more CPU. And pCFS’ bandwidth also surpasses GFS’ (600 times for small record sizes, e.g., 4 KB, decreasing down to 2 times for large record sizes, e.g., 4 MB), at about the same CPU usage.Lusitania, Companhia de Seguros S.A, Programa IBM Shared University Research (SUR

Dealing with small Files in HPC Environments: automatic Loop-Back Mounting of Disk Images

Processing of large numbers (hundreds of thousands) of small files (i.e., up to a few KB) is notoriously problematic for all modern parallel file systems. While modern storage solutions provide high and scalable bandwidth through parallel storage servers connected with a high-speed network, accessing small files is sequential and latency-bounded. Paradoxically, performance of file access is worse than if the files were stored on a local hard drive. We present a generic solution for large-scale HPC facilities that improves the performance of workflows dealing with large numbers of small file. The files are saved inside a single large file containing a disk image, similarly to an archive. When needed, the image is mounted through the Unix loop-back device, and the contents of the image are available to the user in the form of a usual directory tree. Since mounting of disks under Unix often requires super-user privileges, security concerns and possible ways to address them are considered. A complete Python implementation of image creation, mounting, and unmounting framework is presented. A seamless integration into HPC environments managed by SLURM is discussed on an example of read-only software modules created by administrators, and user-created disk images with read-only application input data. Finally, results of performance benchmarks carried out on the Abel supercomputer facility in Oslo, Norway, are shown

Parallel network file systems using authenticated key exchange protocols

The keyestablishment for secure many-to-many communications is very important nowadays. The problem is inspired by the proliferation of large-scale distributed file systems supporting parallel access to multiple storage devices. In this, a variety of authenticated key exchange protocols that are designed to address the issues. This shows that these protocols are capable of reducing the workload of the metadata server and concurrently supporting forward secrecy and escrow-freeness. All this requires only a small fraction of increased computation overhead at the client. This proposed three authenticated key exchange protocols for parallel network file system (pNFS). The protocols offer three appealing advantages over the existing Kerberos-based protocol. First, the metadata server executing these protocols has much lower workload than that of the Kerberos-based approach. Second, two of these protocols provide forward secrecy: one is partially forward secure (with respect to multiple sessions within a time period), while the other is fully forward secure (with respect to a session). Third, designed a protocol which not only provides forward secrecy, but is also escrow-free