Parallel netCDF: A Scientific High-Performance I/O Interface

Dataset storage, exchange, and access play a critical role in scientific applications. For such purposes netCDF serves as a portable and efficient file format and programming interface, which is popular in numerous scientific application domains. However, the original interface does not provide an efficient mechanism for parallel data storage and access. In this work, we present a new parallel interface for writing and reading netCDF datasets. This interface is derived with minimum changes from the serial netCDF interface but defines semantics for parallel access and is tailored for high performance. The underlying parallel I/O is achieved through MPI-IO, allowing for dramatic performance gains through the use of collective I/O optimizations. We compare the implementation strategies with HDF5 and analyze both. Our tests indicate programming convenience and significant I/O performance improvement with this parallel netCDF interface.Comment: 10 pages,7 figure

Deductive Verification of Parallel Programs Using Why3

The Message Passing Interface specification (MPI) defines a portable message-passing API used to program parallel computers. MPI programs manifest a number of challenges on what concerns correctness: sent and expected values in communications may not match, resulting in incorrect computations possibly leading to crashes; and programs may deadlock resulting in wasted resources. Existing tools are not completely satisfactory: model-checking does not scale with the number of processes; testing techniques wastes resources and are highly dependent on the quality of the test set. As an alternative, we present a prototype for a type-based approach to programming and verifying MPI like programs against protocols. Protocols are written in a dependent type language designed so as to capture the most common primitives in MPI, incorporating, in addition, a form of primitive recursion and collective choice. Protocols are then translated into Why3, a deductive software verification tool. Source code, in turn, is written in WhyML, the language of the Why3 platform, and checked against the protocol. Programs that pass verification are guaranteed to be communication safe and free from deadlocks. We verified several parallel programs from textbooks using our approach, and report on the outcome.Comment: In Proceedings ICE 2015, arXiv:1508.0459

Using eSkel to Implement the Multiple Baseline Stereo Application

We give an overview of the Edinburgh Skeleton Library eSkel, a structured parallel programming library which offers a range of skeletal parallel programming constructs to the C/MPI programmer. Then we illustrate the efficacy of such a high level approach through an application of multiple baseline stereo. We describe the application and show different ways to introduce parallelism using algorithmic skeletons. Some performance results will be reported

Session-Based Programming for Parallel Algorithms: Expressiveness and Performance

This paper investigates session programming and typing of benchmark examples to compare productivity, safety and performance with other communications programming languages. Parallel algorithms are used to examine the above aspects due to their extensive use of message passing for interaction, and their increasing prominence in algorithmic research with the rising availability of hardware resources such as multicore machines and clusters. We contribute new benchmark results for SJ, an extension of Java for type-safe, binary session programming, against MPJ Express, a Java messaging system based on the MPI standard. In conclusion, we observe that (1) despite rich libraries and functionality, MPI remains a low-level API, and can suffer from commonly perceived disadvantages of explicit message passing such as deadlocks and unexpected message types, and (2) the benefits of high-level session abstraction, which has significant impact on program structure to improve readability and reliability, and session type-safety can greatly facilitate the task of communications programming whilst retaining competitive performance