15 degrees, rain and HPC: Summer in Edinburgh (week 3)

The first and probably most important task due for our third week in Edinburgh was the Week 3 report. It’s not only about presenting our project after about two weeks of work but also updating the time schedule and preparing the final report. The finished Week 3 reports will be compiled into one document and be available to the public in the near future.

I had already started it during the previous week as it was due on Tuesday morning of the third week but, of course, there was still some work to do. Adding pictures, do some proof-reading, adjust the formatting, re-phrase some sentences, and remove redundant statements.
However, just after I handed in the final version on Monday, the submitted time schedule started to fall apart slowly.

In the previous weeks, I had four different test cases but only one of them included some actual interactions between the simulated molecules: Two spheres slowly approaching each other, bumping into each other and then drifting apart slowly. As you can easily imagine, that’s a pretty simplistic test and far away from any realistic application of FFEA – a tool for simulating large numbers of proteins. Also, at this scale, the current parallelisation had hardy any noticeable effect on the runtime no matter whether I used the “per-blob parallelisation” (pb) or the “with-blob parallelisation” (wb).

Runtimes of the simulation of two spheres with Van der Waals interactions colliding

As a result, I asked Albert and Ben for a more realistic test to study the performance of the current parallelisation approaches.
They reacted promptly by providing a larger example: Seven “blobs” (the shapes that represent the proteins) with Van der Waals interactions. In fact, it was so large that the simulation still wasn’t finished after more than three days of calculation. That kind of of runtime is not very useful in the early stages of a project where you have to do lots of runs to get an idea of how the codes work and which approaches you should pursue! So, we tried to simplify the test to reduce the runtime – down to four blobs and less time steps. My goal was a somewhat realistic test that still completed in less than an hour.

As I kept changing the different parameters of the simulation, I witnessed an odd behaviour: For one million time steps, the program finished within just a moment, for ten millions it kept running for several hours until I cancelled the calculation. Calculation time is rarely a linear function but this seemed quite extreme!
I found the reason quite accidentally – I just turned off the Van der Waals interactions to study their impact. Doing so allowed me to disable the restart feature as well. And suddenly, the runtimes behaved exactly as expected. As it turned out, the restart feature looks at the output trajectories and starts at the last completed trajectory frame. The test file I had received contained trajectory output from previous runs for the first million time steps and therefore didn’t do any calculation up to this point. That’s why it was so fast. Without the restart, it took pretty much exactly an hour – exactly what I had been looking for all the time.
Quite an easy explanation, maybe even obvious now, but before I knew about the restart feature and the old trajectories, it puzzled me a lot! Now, I was finally able to run the test for the different parallelisation strategies and get an idea of how they performed.
Since I wanted to get reliable results, I used a script to run each simulation multiple times over the course of the weekend. I’ll show you the results in my Week 4 blog post!
Despite exchanging a lot of emails with Ben and Albert, we also met for a telco with them on Friday and discussed our progress during the week, our problems and the goals for the upcoming week.

Interior of St Margaret’s Chapel

For the weekend, Anna, Ondrej, and his girlfriend decided to visit Glasgow, Scotland’s largest city. Edinburgh is the capital but in fact it’s only the second-largest city in the country. I decided to use the time to discover Edinburgh Castle on my own, taking my time for the visit and making the most out of the admission fee! After all, it’s not inexpensive and it’s HUGE! In addition to the castle itself, there are exhibitions about the Honours of Scotland and the Stone of Destiny, certain Scottish regiments of the British Army, the Prisons of War exhibition and of course the National War Museum which is probably worth a visit itself
Despite arriving before 9:30 am (which is when the castle opens), there was already a queue forming, but it didn’t cause much of a delay. I started my visit by joining one of the tour guides that give a brief introduction to the castle and its history. It definitely helped to get an idea where everything is without relying on the map too much! Afterwards, I started next to the gates again and went up to the central square, trying to leave nothing out.
A (literally) small highlight was St Margaret’s Chapel, the oldest building in Edinburgh. It’s tiny and looks exceptionally plain from the outside but the interior is lovely. It’s still used for baptisms and weddings despite being smaller than the average living room. In fact, there was a wedding on the day I visited!
Another notable event was the firing of the One O’ Clock Gun that used to be an audible time signal for the ships in the harbour. It’s fired every day except on Sundays and a few holidays and it’s a great spectacle!

View near Mons Meg

It would take very long to describe everything I saw from Mons Meg to the quarters of Mary Queen of Scots during her stay at Edinburgh to the National War Memorial to the Honours of Scotland and the Stone of Destiny, but I tried to organize my photos in an order that resembles a walk from the gates up to the Great Hall and then to the prison cells, so I suggest having a look at those to learn what I saw there, maybe while having a look at the map of the castle! I also added lots of comments and explanations but feel free to ask me if you have a question.

In the end, I left at 5 pm (just one hour before the castle closed to the public), spending 7.5 hours in the castle! And I still didn’t see the National War Museum but I was getting tired and hungry!
However, spending almost a month with Anna and Ondra definitely left its marks. I realized it when I caught myself thinking “The bus isn’t coming… Hm, it’s not that far! I’ll just walk home!” And I actually walked home. Okay, 2.25 km (1.4 miles) is not THAT far but it felt like a huge change to me – I used to be far too lazy for that kind of stuff!

For me, it was a very successful but also exhausting day. I got to see almost all of the castle without ever feeling rushed, found the perfect souvenir for myself (a necklace with a small yet elegant thistle motif to remind me of my stay here) and treated myself to a nice dinner and a cider.