RSE team activities up to June 2022
The RSE team in ITS Research has had a busy few years since we started sharing our work in this blog. In this post we look at some highlights of recent activity and what we have to look forward to.
rse¶
Speeding up and Parallelising R packages (using Rcpp and C++)
Polytomous variables can be used to model data that has two or more possible outcomes. For example, a survey with multiple-choice questions is polytomous. The R package, poLCA, does statistical clustering of polytomous variables. For example, grouping together survey results that are similar to each other.
Assessing code quality with the NAG Fortran compiler
The NAG Fortran compiler, like other compilers, has diagnostic capabilities which can help us write correct and portable Fortran programs. In this post we'll look at these, comparing with those of the GCC and Intel compilers, and see how the compiler can be a valuable tool when developing or maintaining Fortran code.
Using compiler options to help debug programs
Once we've written a program more advanced than our "Hello, world!" example, we're going to make mistakes. In this post, we'll look at how we can use the very compilers we're using to compile our program to pick up on some of these mistakes.
Introducing Sherman Lo, RSE
Hello! I am Sherman and I have just joined the RSE team at Queen Mary. Glad to meet you all!
My background is in computational statistics and machine learning. I have completed projects in rainfall prediction, defect detection for 3D printing and Markov chains using Monte Carlo. These projects involved collaboration with various scientists, such as meteorologists, engineers and statisticians.
One year of code review club with the William Harvey Research Institute
Over the past year, researchers from QMUL's William Harvey Research Institute (WHRI) have engaged on a collaborative code review club. Through this collaborative effort the group aims to peer review the computational components of their research and provide code quality assurance to all involved researchers. Additionally, the Research Software Engineering group of ITS Research has been assisting the group with knowledge transfer and by participating in the review process.
Introductory computing skills for researchers: Software Carpentry with RSLondon
Research Software London is a community to support the use and development of research software in London and the South East. Since 2019, RSLondon has run a number of Software Carpentry workshops to teach introductory computing skills to researchers. ITSR have been involved in these efforts, providing instructors and helpers at each of these workshops.
Comparison of Python Distributions on Apocrita
When it comes to picking a distribution, Python programmers are spoilt for choice. We're going to compare two of the most popular (CPython and Anaconda) and one that promises big performance improvements with relatively little hassle (Intel Distribution for Python).
Jigsaws with GIMP and Python
Jigsaw puzzles proved wildly popular during lockdown, but they weren't all done on the dining room table on rainy afternoons. The puzzle faced by researchers from the School of English and Drama (SED), lead by Dr Richard Coulton and in collaboration with the Natural History Museum, was to piece together a set of beautiful botanical watercolours brought back from China by the East India Company surgeon James Cuninghame. Cuninghame purchased these works, by an unknown local artist, in Xiamen in 1699. Sometime in the first half of the eighteenth century, perhaps because of their large size, these watercolours were cut up and glued into what you ungenerously, call a scrap book. The British Library has lovingly digitised this book in a series of publicly-available high resolution images funded by Oak Spring Garden Foundation, who also sponsored the current project.
Using Apocrita's GPUs with OpenMP
On Apocrita we can use OpenMP to execute code on GPU devices. This post looks at how to compile such programs and submit them to run on the GPU nodes. The post assumes that you have code, already developed and tested, which is ready for deployment, and that you have been granted access to the GPU nodes.