Categories
GPUs molecular dynamics

GROMACS 4.6: Running on GPUs

I mentioned before that I would write something on running GROMACS on GPUs. Let’s imagine we want to simulate a solvated lipid bilayer containing 6,000 lipids for 5 µs. The total number of MARTINI coarse-grained beads is around 137,000 and the box dimensions are roughly 42x42x11 nm. Although this is smaller than the benchmark we […]

Categories
distributed computing

Windows Azure for research

I recently attended the first training event in UK by Microsoft on how to use Windows Azure for research. A perspective I wrote for the Software Sustainability Institute has been posted on their website.

Categories
GPUs molecular dynamics

GROMACS 4.6: Scaling of a very large coarse-grained system

So if I have a particular system I want to simulate, how many processing cores can I harness to run a single GROMACS version 4.6 job? If I only use a few then the simulation will take a long time to finish, if I use too many the cores will end up waiting for communications […]

Categories
computing molecular dynamics

GROMACS 4.6

GROMACS is a scientific code designed to simulate the dynamics of small boxes of stuff, that usually contain a protein, water, perhaps a lipid bilayer and a range of other molecules depending on the study. It assumes that all the atoms can be represented as points with a mass and an electrical charge and that all […]

Categories
distributed computing

Crowd-sourced computer networks

Crowd-sourced computer networks Blog post on something I’ve been interested in for a while; how to create and use networks of everyday computers to solve interesting problems in biology. Links to the website of the Software Sustainability Institute.

Categories
computing software carpentry teaching

More posts on the Oxford Software Carpentry Boot Camp

Mike Jackson from the Software Sustainability Institute was one of our instructors last week and has written two interesting blog posts. The first summarises the workshop whilst in the second he lists the feedback that was collected at the end of the two days.

Categories
computing software carpentry teaching

Top Tips for hosting a Software Carpentry Boot Camp

I’ve written a post for the Software Sustainability Institute (who kindly provided the instructors for our boot camp) describing my top tips for hosting a Software Carpentry Boot Camp.

Categories
computing software carpentry teaching

Software Carpentry Feedback

As well as asking the attendees how they thought the workshop had gone, I sent them a questionnaire before the workshop. The idea was to see what their expectations were and if the workshop then met them. For example we asked “How would you describe your expertise in the following tools?” and the results are on […]

Categories
computing software carpentry teaching

Improving Software Carpentry workshops

Aron Ahmadia who helped run the Software Carpentry course has written a nice blog where he e.g. discusses some of the ways the course could be improved.

Categories
computing software carpentry teaching

Running my first Software Carpentry workshop

“Can you email me that script you used to do your analysis?” “Sure. It isn’t very well commented but you should be able to work out what it’s doing. I’ve tested it on a few things and it seems to work.” Sound familiar? Of course, the story normally ends happily but…. Teaching some of the […]