Software and research: the Institute's Blog

Bug hunting: Seg fault in lattice disorder Monte Carlo code (written in C) Wr

Latest version published on 20 September, 2018.

By Susanne Wallace, Anna Brown, Lewis Irvine, William Saunders and Paul Secular. As part of the Bath debugging workshop we attempted to find the cause of a segfault in a lattice disorder Monte Carlo code written in C. We were working without a known solution as recent unrelated additions to the code had fixed the bug without revealing why. We were able to find the cause of the segfault using memory checking and debugging tools to narrow down the location of the bug, with print statements to finish.

Research Software Engineering conference 2018 #RSE18

Latest version published on 27 September, 2018.

By Tim Powell, Research Software Engineer at the STFC Hartree Centre. This post was first published at the STFC Hartree Centre blog. On 3rd September the peaceful campus of Birmingham University came alive with bubbling groups of research software engineers, talking in excited tones about their latest optimisation tool and favourite python library, as the third annual conference of Research Software Engineers was started!

My experience of JupyterCon 2018

Latest version published on 18 September, 2018.

By Nikoleta Glynatsi, Software Sustainability Institute Fellow. Project Jupyter is a non profit organisation created to provide services for interactive computing across dozens of programming languages. Project Jupyter is most known for their Jupyter Notebooks but develops and supports several computing products, such as JupyterHub and JupyterLab.

PickCells and exploratory image analysis in cell biology

Latest version published on 17 September, 2018.

By Mike Jackson, Software Architect, The Software Sustainability Institute. PickCells is an image analysis platform developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh.

Code is Science at GCCBOSC

Latest version published on 12 September, 2018.

By Yo Yehudi, University of Cambridge. GCCBOSC this year was a combination of two open source bioinformatics conferences: GCC, the Galaxy Community Conference, and BOSC, the Bioinformatics Open Source Conference. Galaxy is a highly-successful bioinformatics workflow management tool, and BOSC is run by the Open Bioinformatics Foundation (OBF), an organisation dedicated to open-source biology and bioinformatics related software.

EuroPython 2018

Latest version published on 28 August, 2018.

By Raniere Silva, Software Sustainability Institute. EuroPython is the biggest conference dedicated to Python in Europe, with around 1200+ participants every year, run entirely by volunteers. It is also sister event to many national events around the continent, such as PyCon UK. This year, EuroPython was hosted in Edinburgh and, like in previous years, some of the talks were related with research software written in Python. We attended to learn how people are carrying out better research with Python.

Unexpected changes to storage of local variables when compiling Fortran with OpenMP

Latest version published on 23 August, 2018.

By Ryan Pepper and James C. Womack. During the Bath Numerical Debugging Workshop, we participated in a bug hunting session where people brought along real-world bugs which we attempted to tackle.

Software engineering in practice

Latest version published on 10 September, 2018.

By Becky Arnold, University of Sheffield. Jos Martin, senior engineering manager at MathWorks, gave a talk on software engineering in practice on the 27th of June at the University of Sheffield.

Software Deposit Guidance for Researchers

Latest version published on 9 August, 2018.

By Mike Jackson, Software Architect. The Software Sustainability Institute has published a set of guides about depositing research software into digital repositories. These guides cover the main aspects of software deposit.

Lessons from a workshop on “Debugging Numerical Software”

Latest version published on 8 August, 2018.

By Eike Mueller, University of Bath. If you are anything like me, you write code which contains bugs (in my case: lots of bugs). You probably also use code or tools written by others, which might contain even more bugs (e.g. in compilers, scripts, external numerical libraries etc.).