79,268 research outputs found
Portability of Prolog programs: theory and case-studies
(Non-)portability of Prolog programs is widely considered as an important
factor in the lack of acceptance of the language. Since 1995, the core of the
language is covered by the ISO standard 13211-1. Since 2007, YAP and SWI-Prolog
have established a basic compatibility framework. This article describes and
evaluates this framework. The aim of the framework is running the same code on
both systems rather than migrating an application. We show that today, the
portability within the family of Edinburgh/Quintus derived Prolog
implementations is good enough to allow for maintaining portable real-world
applications.Comment: Online proceedings of the Joint Workshop on Implementation of
Constraint Logic Programming Systems and Logic-based Methods in Programming
Environments (CICLOPS-WLPE 2010), Edinburgh, Scotland, U.K., July 15, 201
VXA: A Virtual Architecture for Durable Compressed Archives
Data compression algorithms change frequently, and obsolete decoders do not
always run on new hardware and operating systems, threatening the long-term
usability of content archived using those algorithms. Re-encoding content into
new formats is cumbersome, and highly undesirable when lossy compression is
involved. Processor architectures, in contrast, have remained comparatively
stable over recent decades. VXA, an archival storage system designed around
this observation, archives executable decoders along with the encoded content
it stores. VXA decoders run in a specialized virtual machine that implements an
OS-independent execution environment based on the standard x86 architecture.
The VXA virtual machine strictly limits access to host system services, making
decoders safe to run even if an archive contains malicious code. VXA's adoption
of a "native" processor architecture instead of type-safe language technology
allows reuse of existing "hand-optimized" decoders in C and assembly language,
and permits decoders access to performance-enhancing architecture features such
as vector processing instructions. The performance cost of VXA's virtualization
is typically less than 15% compared with the same decoders running natively.
The storage cost of archived decoders, typically 30-130KB each, can be
amortized across many archived files sharing the same compression method.Comment: 14 pages, 7 figures, 2 table
On the Implementation of GNU Prolog
GNU Prolog is a general-purpose implementation of the Prolog language, which
distinguishes itself from most other systems by being, above all else, a
native-code compiler which produces standalone executables which don't rely on
any byte-code emulator or meta-interpreter. Other aspects which stand out
include the explicit organization of the Prolog system as a multipass compiler,
where intermediate representations are materialized, in Unix compiler
tradition. GNU Prolog also includes an extensible and high-performance finite
domain constraint solver, integrated with the Prolog language but implemented
using independent lower-level mechanisms. This article discusses the main
issues involved in designing and implementing GNU Prolog: requirements, system
organization, performance and portability issues as well as its position with
respect to other Prolog system implementations and the ISO standardization
initiative.Comment: 30 pages, 3 figures, To appear in Theory and Practice of Logic
Programming (TPLP); Keywords: Prolog, logic programming system, GNU, ISO,
WAM, native code compilation, Finite Domain constraint
PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies
The current landscape of scientific research is widely based on modeling and
simulation, typically with complexity in the simulation's flow of execution and
parameterization properties. Execution flows are not necessarily
straightforward since they may need multiple processing tasks and iterations.
Furthermore, parameter and performance studies are common approaches used to
characterize a simulation, often requiring traversal of a large parameter
space. High-performance computers offer practical resources at the expense of
users handling the setup, submission, and management of jobs. This work
presents the design of PaPaS, a portable, lightweight, and generic workflow
framework for conducting parallel parameter and performance studies. Workflows
are defined using parameter files based on keyword-value pairs syntax, thus
removing from the user the overhead of creating complex scripts to manage the
workflow. A parameter set consists of any combination of environment variables,
files, partial file contents, and command line arguments. PaPaS is being
developed in Python 3 with support for distributed parallelization using SSH,
batch systems, and C++ MPI. The PaPaS framework will run as user processes, and
can be used in single/multi-node and multi-tenant computing systems. An example
simulation using the BehaviorSpace tool from NetLogo and a matrix multiply
using OpenMP are presented as parameter and performance studies, respectively.
The results demonstrate that the PaPaS framework offers a simple method for
defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced
Research Computing, July 22--26, 2018, Pittsburgh, PA, US
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Kronos: a workflow assembler for genome analytics and informatics.
BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos
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