A survey of the practice of computational science

Abstract

Computing plays an indispensable role in scientific research. Presently, researchers in science have different problems, needs, and beliefs about computation than professional programmers. In order to accelerate the progress of science, computer scientists must understand these problems, needs, and beliefs. To this end, this paper presents a survey of scientists from diverse disciplines, practicing computational science at a doctoral-granting university with very high research activity. The survey covers many things, among them, prevalent programming practices within this scientific community, the importance of computational power in different fields, use of tools to enhance performance and software productivity, computational resources leveraged, and prevalence of parallel computation. The results reveal several patterns that suggest interesting avenues to bridge the gap between scientific researchers and programming tools developers.

Jug: Software for Parallel Reproducible Computation in Python

“…As many scientists now spend a significant fraction of their time performing computational work [28,49], increasing their productivity in this task can have significant effects. Jug is based on Python, a programming language which is widely used for scientific computation.…”

“…However, unlike Make, Jug is written in Python, a general purpose programming language which is widely used in scientific programming [49]. A Task in Jug can consist of any Python function and its arguments.…”

Design considerations for parallel performance tools

“…Prabhu et al [36] present an extensive survey of software practices in computational science. They conclude that cur rent programming systems and tools do not meet the require ments for scientific computing.…”

Software Carpentry: lessons learned

“…While their undergraduate programs may include a generic introduction to programming or a statistics or numerical methods course (in which they are often expected to pick up programming on their own), they are almost never told that version control exists, and rarely if ever shown how to design a maintainable program in a systematic way, or how to turn the last twenty commands they typed into a re-usable script. As a result, they routinely spend hours doing things that could be done in minutes, or don’t do things at all because they don’t know where to start 2, 3 .…”