Approachable Error Bounded Lossy Compression

Compression is commonly used in HPC applications to move and store data. Traditional lossless compression, however, does not provide adequate compression of floating point data often found in scientific codes. Recently, researchers and scientists have turned to lossy compression techniques that approximate the original data rather than reproduce it in order to achieve desired levels of compression. Typical lossy compressors do not bound the errors introduced into the data, leading to the development of error bounded lossy compressors (EBLC). These tools provide the desired levels of compression as mathematical guarantees on the errors introduced. However, the current state of EBLC leaves much to be desired. The existing EBLC all have different interfaces requiring codes to be changed to adopt new techniques; EBLC have many more configuration options than their predecessors, making them more difficult to use; and EBLC typically bound quantities like point wise errors rather than higher level metrics such as spectra, p-values, or test statistics that scientists typically use. My dissertation aims to provide a uniform interface to compression and to develop tools to allow application scientists to understand and apply EBLC. This dissertation proposal presents three groups of work: LibPressio, a standard interface for compression and analysis; FRaZ/LibPressio-Opt frameworks for the automated configuration of compressors using LibPressio; and work on tools for analyzing errors in particular domains

Analyse des synchronisations dans un programme parallèle ordonnancé par vol de travail. Applications à la génération déterministe de nombres pseudo-aléatoires.

We present two contributions to the field of parallel programming.The first contribution is theoretical: we introduce SIPS analysis, a novel approach to estimate the number of synchronizations performed during the execution of a parallel algorithm.Based on the concept of logical clocks, it allows us: on one hand, to deliver new bounds for the number of synchronizations, in expectation; on the other hand, to design more efficient parallel programs by dynamic adaptation of the granularity.The second contribution is pragmatic: we present an efficient parallelization strategy for pseudorandom number generation, independent of the number of concurrent processes participating in a computation.As an alternative to the use of one sequential generator per process, we introduce a generic API called Par-R, which is designed and analyzed using SIPS.Its main characteristic is the use of a sequential generator that can perform a ``jump-ahead'' directly from one number to another on an arbitrary distance within the pseudorandom sequence.Thanks to SIPS, we show that, in expectation, within an execution scheduled by work stealing of a "very parallel" program (whose depth or critical path is subtle when compared to the work or number of operations), these operations are rare.Par-R is compared with the parallel pseudorandom number generator DotMix, written for the Cilk Plus dynamic multithreading platform.The theoretical overhead of Par-R compares favorably to DotMix's overhead, what is confirmed experimentally, while not requiring a fixed generator underneath.Nous présentons deux contributions dans le domaine de la programmation parallèle.La première est théorique : nous introduisons l'analyse SIPS, une approche nouvelle pour dénombrer le nombre d'opérations de synchronisation durant l'exécution d'un algorithme parallèle ordonnancé par vol de travail.Basée sur le concept d'horloges logiques, elle nous permet,: d'une part de donner de nouvelles majorations de coût en moyenne; d'autre part de concevoir des programmes parallèles plus efficaces par adaptation dynamique de la granularité.La seconde contribution est pragmatique: nous présentons une parallélisation générique d'algorithmes pour la génération déterministe de nombres pseudo-aléatoires, indépendamment du nombre de processus concurrents lors de l'exécution.Alternative à l'utilisation d'un générateur pseudo-aléatoire séquentiel par processus, nous introduisons une API générique, appelée Par-R qui est conçue et analysée grâce à SIPS.Sa caractéristique principale est d'exploiter un générateur séquentiel qui peut "sauter" directement d'un nombre à un autre situé à une distance arbitraire dans la séquence pseudo-aléatoire.Grâce à l'analyse SIPS, nous montrons qu'en moyenne, lors d'une exécution par vol de travail d'un programme très parallèle (dont la profondeur ou chemin critique est très petite devant le travail ou nombre d'opérations), ces opérations de saut sont rares.Par-R est comparé au générateur pseudo-aléatoire DotMix, écrit pour Cilk Plus, une extension de C/C++ pour la programmation parallèle par vol de travail.Le surcout théorique de Par-R se compare favorablement au surcoput de DotMix, ce qui apparait aussi expériemntalement.De plus, étant générique, Par-R est indépendant du générateur séquentiel sous-jacent

Scaling up an end-user dependability framework for spreadsheets

The WYSIWYT (What You See is What You Test) methodology applies formal analysis and testing techniques to the spreadsheet paradigm. So far the methodology has been applied to a research spreadsheet prototype, Forms/3. However, this prototype lacks the mathematical libraries, referential functions, ranges, and macros of commercial spreadsheets like Excel and Lotus 1-2-3. Study subjects are also accustomed to the grid-like interface of commercial spreadsheet packages and many spreadsheets of interest are available in the Excel file format. This project addresses these areas by implementing WYSIWYT in Microsoft Excel and Gnumeric

Scaling up an end-user dependability framework for spreadsheets

The WYSIWYT (What You See is What You Test) methodology applies formal analysis and testing techniques to the spreadsheet paradigm. So far the methodology has been applied to a research spreadsheet prototype, Forms/3. However, this prototype lacks the mathematical libraries, referential functions, ranges, and macros of commercial spreadsheets like Excel and Lotus 1-2-3. Study subjects are also accustomed to the grid-like interface of commercial spreadsheet packages and many spreadsheets of interest are available in the Excel file format. This project addresses these areas by implementing WYSIWYT in Microsoft Excel and Gnumeric

Space and Earth Sciences, Computer Systems, and Scientific Data Analysis Support, Volume 1

This Final Progress Report covers the specific technical activities of Hughes STX Corporation for the last contract triannual period of 1 June through 30 Sep. 1993, in support of assigned task activities at Goddard Space Flight Center (GSFC). It also provides a brief summary of work throughout the contract period of performance on each active task. Technical activity is presented in Volume 1, while financial and level-of-effort data is presented in Volume 2. Technical support was provided to all Division and Laboratories of Goddard's Space Sciences and Earth Sciences Directorates. Types of support include: scientific programming, systems programming, computer management, mission planning, scientific investigation, data analysis, data processing, data base creation and maintenance, instrumentation development, and management services. Mission and instruments supported include: ROSAT, Astro-D, BBXRT, XTE, AXAF, GRO, COBE, WIND, UIT, SMM, STIS, HEIDI, DE, URAP, CRRES, Voyagers, ISEE, San Marco, LAGEOS, TOPEX/Poseidon, Pioneer-Venus, Galileo, Cassini, Nimbus-7/TOMS, Meteor-3/TOMS, FIFE, BOREAS, TRMM, AVHRR, and Landsat. Accomplishments include: development of computing programs for mission science and data analysis, supercomputer applications support, computer network support, computational upgrades for data archival and analysis centers, end-to-end management for mission data flow, scientific modeling and results in the fields of space and Earth physics, planning and design of GSFC VO DAAC and VO IMS, fabrication, assembly, and testing of mission instrumentation, and design of mission operations center

An adaptor for C++ callbacks with C and Fortran libraries

This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract Object-oriented programming using C++ is increasingly being adopted in the development of scientific codes. A recurrent issue in this regard is the interaction of newly developed codes with existing legacy libraries written in C or Fortran. Often, one needs to pass raw function pointers to such libraries’ procedures for callback purposes. This is problematic as it conflicts with one of the cornerstones of object-oriented programming: the association of functions and data through objects. Curr... Title of program: Adapt2rfp Catalogue Id: AENU_v1_0 Nature of problem Object-oriented programming using C++ is increasingly being adopted in the development of scientific codes. A recurrent issue in this regard, is the interaction of newly developed codes with existing legacy libraries written in C or Fortran. Often, one needs to pass raw function pointers to such libraries' procedures for callback purposes. This is problematic as it conflicts with one of the cornerstones of object-oriented programming, the association of functions and data through objects. Curren ... Versions of this program held in the CPC repository in Mendeley Data AENU_v1_0; Adapt2rfp; 10.1016/j.cpc.2012.10.01

A Hybrid-parallel Architecture for Applications in Bioinformatics

Since the advent of Next Generation Sequencing (NGS) technology, the amount of data from whole genome sequencing has been rising fast. In turn, the availability of these resources led to the tapping of whole new research fields in molecular and cellular biology, producing even more data. On the other hand, the available computational power is only increasing linearly. In recent years though, special-purpose high-performance devices started to become prevalent in today’s scientific data centers, namely graphics processing units (GPUs) and, to a lesser extent, field-programmable gate arrays (FPGAs). Driven by the need for performance, developers started porting regular applications to GPU frameworks and FPGA configurations to exploit the special operations only these devices may perform in a timely manner. However, applications using both accelerator technologies are still rare. Major challenges in joint GPU/FPGA application development include the required deep knowledge of associated programming paradigms and the efficient communication both types of devices. In this work, two algorithms from bioinformatics are implemented on a custom hybrid-parallel hardware architecture and a highly concurrent software platform. It is shown that such a solution is not only possible to develop but also its ability to outperform implementations on similar- sized GPU or FPGA clusters in terms of both performance and energy consumption. Both algorithms analyze case/control data from genome- wide association studies to find interactions between two or three genes with different methods. Especially in the latter case, the newly available calculation power and method enables analyses of large data sets for the first time without occupying whole data centers for weeks. The success of the hybrid-parallel architecture proposal led to the development of a high- end array of FPGA/GPU accelerator pairs to provide even better runtimes and more possibilities