Last week, in order to avoid working on more important things I started a small project I had wanted to do since quite a while. As mentioned before I am really not happy with C++ as a language to write simulations in. Unfortunately according to the Great Language Shootout all the nice languages are way too slow to be seriously considered.
However - as aptly explained on the shootout page - comparing the speed of programming languages and even the speed of implementations of programming languages is not very meaningful. Results will vary widely dependent on application area.
Therefore the only reasonable thing to do is to implement a benchmark which is representative of the kind of program one is interested in in all candidate languages. Which is exactly what I have started to do.
I have defined a reference model and implemented it in (very very basic) C++ and (C++ish) D (and CUDA which strictly speaking doesn't belong here. More on that in a later blog post - hopefully. I'm really bad at actually writing posts that I have announced before...).
To my great delight it turned out that the D program ran only about 10% longer than my basic C++ version. In principle this is clearly a small enough loss in speed to be compensated for by the nice improvements D offers over C++. I was really disappointed though (you can see how much I would like to abandon C++) when I found out a bit later that PGO (profile guided optimization) gives my C++ program another 20% boost. Add to that the fact that 64-bit D is still some way off and that value types are second class citizens in D and I'm not really sure whether I will do my next project in D or not. In any case it was nice to see the progress they have made. I am optimistic that my C++-days are numbered...
As for the shootout - I will try to find the time to add "proper" implementations in D and C++ (which hopefully will not perform much differently). I hope I will also be able to cover other interesting or up-and-coming languages, such as OCaml or Bitc. If anyone of my three readers feels willing and able to help out - just head over to the project page, read the model definition and hack away. I will be happy to post code/results.
Sunday 31 October 2010
Thursday 28 October 2010
Expensive data
As a theoretical biologist a lot of my research involves burning a *lot* of CPU time on computer simulations of evolving animal populations.
Usually I run a program for thousands of generations, each of which consists of hundreds to thousands of time steps during each of which hundreds of individuals interact with each other and their environment. This has to be replicated a dozen or so times with different seeds of the random number generator. The whole thing has then to be repeated for each combination of parameters I'm interested in.
To give an idea of the scale: Running 10k generations (which has been argued to be far too little) of the simulation I am currently working on on a typical node of my university's cluster (newish multi-core Opterons) takes about 3-5 hours. One standard sweep of the parameter space has 64 parameter combinations (which leaves out so many fascinating possibilities that it hurts) times 10 replicates each, thus 640 runs (each of those sets produces 4-5 GB of data, by the way).
In a typical project I tend to rewrite and change the simulation program many times, first of all to find bugs but then also as part of an iterative process where I create the program and run it, look at the results, think about them, adjust my opinion about the model/question/approach, change the program, run it, etc.
For the latest incarnation of my current project (the 4th or 5th major one) I have now done 25 of the above mentioned parameter sets. That means for just one part of the project I have already used more than 7 CPU-years and produced more than 100GB of data. And that is by far not going to be the end of it...
Usually I run a program for thousands of generations, each of which consists of hundreds to thousands of time steps during each of which hundreds of individuals interact with each other and their environment. This has to be replicated a dozen or so times with different seeds of the random number generator. The whole thing has then to be repeated for each combination of parameters I'm interested in.
To give an idea of the scale: Running 10k generations (which has been argued to be far too little) of the simulation I am currently working on on a typical node of my university's cluster (newish multi-core Opterons) takes about 3-5 hours. One standard sweep of the parameter space has 64 parameter combinations (which leaves out so many fascinating possibilities that it hurts) times 10 replicates each, thus 640 runs (each of those sets produces 4-5 GB of data, by the way).
In a typical project I tend to rewrite and change the simulation program many times, first of all to find bugs but then also as part of an iterative process where I create the program and run it, look at the results, think about them, adjust my opinion about the model/question/approach, change the program, run it, etc.
For the latest incarnation of my current project (the 4th or 5th major one) I have now done 25 of the above mentioned parameter sets. That means for just one part of the project I have already used more than 7 CPU-years and produced more than 100GB of data. And that is by far not going to be the end of it...
Sunday 24 October 2010
Hiking in movies
One of the things I love about The Hobbit and The Lord of the Rings is that while reading those books you can really *feel* how it is to travel. In particular you can feel how it is to travel by foot.
I have done some hiking myself and at least for me there is a special magic to exploring a landscape on your own two feet that is not evoked by any other form of travel. I'm not sure what it is - it includes moments like reaching the highest point of a pass and finally being able to see the valley on the other side, or looking back after an hour of walking and realizing the distance you made - but there is much more to it and I can't easily describe it in a few sentences.
Whatever it is, I think Tolkien managed to transport it quite well in his novels (actually it is said that Tolkien himself loved to make long walks through the English countryside). In Peter Jackson's movies on the other hand it is missing almost entirely. There is certainly no lack of trying - we see great panoramas of landscapes, helicopter flights through snow-covered mountains; we follow the heroes as they walk through brush, moorland, grassland, forest and all other kinds of temperate biome you could imagine. We see them walking, stumbling and climbing.
But still - at least for me this always looks like actors dropped in a scenic landscape (which it of course is) - that is, slightly soulless and artificial. I don't even think the movies are bad in general, I think given the economical constraints (mass appeal required to get back the gigantic investment) they are even close to a best-case scenario. But in this particular aspect they fail almost completely.
But now comes the funny thing. The other day I checked some video clips we made when we had been hiking in the Peak District with the kids the last time. Nothing special really - greyish weather, us, sheep, some hills. But there it was - even in these short amateurish clips, made with a cheap flip camera, I found the "spirit of hiking" was clearly recognizable!
Now, the really interesting thing to ask is of course, why is that so? The non-interesting answer would be that my personal experience (having been on that hike myself) colours my perception and that for everybody else the videos would be just as soulless as the mentioned movie scenes. This is perfectly possible of course, however I find it much more interesting to imagine that there is more to it than just that.
Here are a number of factors that I think might be responsible:
perfection
Pictures in Hollywood movies are perfect and glossy, my clips aren't. Perfection creates distance and a feeling of artificialness.
objective camera
In the movies we see the heroes stoically marching through New Zealand's Best Of. Since the heroes as well as said Best Of (and especially the combination of the two) cost a lot of money and supposedly are what the viewers want to see, the camera is quite busy putting them in the best light. Most of the time therefore we either see the landscape at a wide angle with the group of people somewhere in the middle or we see the latter from the front or the side passing the camera's position. That means we get an uninvolved (helicopter-equipped) spectator's view of what's going on, which is how we would experience a landscape when sitting in a car or a train (or a heli), but *not* how we experience it when walking through it.
speed
When a movie wants to show us that a car for instance is moving very fast, we usually see it approaching (very fast) to the camera's position (preferably at a turn), passing it and then moving away. The camera usually stays fixed at its position and only turns to keep the car in focus.
When filming people walking in contrast directors seem to think that walking per se is a far too boring activity to keep the viewer's attention. Therefore the camera compensates by moving around the person. Approaching it from the back, passing it, approaching it from the front, circling it, etc. This all makes for a busy picture however it does *not* convey the feeling of slowness that is defining for walking. I think essentially walking is usually shown as an activity while in reality it is more of a state.
So, after all this - what do we see in my clip? We see a slow pan of the (greyish, wet, sheep-dotted) landscape. Then a group of people overtakes the camera and slowly (in walking speed that is) moves downwards a small hill, climbs a fence gate and disappears down a path. As I said, really nothing special and more than anything proof of my utter lack of cinematographic ability. Still (for me) it perfectly transports the slowness and smallness of people moving through a landscape by foot.
I have done some hiking myself and at least for me there is a special magic to exploring a landscape on your own two feet that is not evoked by any other form of travel. I'm not sure what it is - it includes moments like reaching the highest point of a pass and finally being able to see the valley on the other side, or looking back after an hour of walking and realizing the distance you made - but there is much more to it and I can't easily describe it in a few sentences.
Whatever it is, I think Tolkien managed to transport it quite well in his novels (actually it is said that Tolkien himself loved to make long walks through the English countryside). In Peter Jackson's movies on the other hand it is missing almost entirely. There is certainly no lack of trying - we see great panoramas of landscapes, helicopter flights through snow-covered mountains; we follow the heroes as they walk through brush, moorland, grassland, forest and all other kinds of temperate biome you could imagine. We see them walking, stumbling and climbing.
But still - at least for me this always looks like actors dropped in a scenic landscape (which it of course is) - that is, slightly soulless and artificial. I don't even think the movies are bad in general, I think given the economical constraints (mass appeal required to get back the gigantic investment) they are even close to a best-case scenario. But in this particular aspect they fail almost completely.
But now comes the funny thing. The other day I checked some video clips we made when we had been hiking in the Peak District with the kids the last time. Nothing special really - greyish weather, us, sheep, some hills. But there it was - even in these short amateurish clips, made with a cheap flip camera, I found the "spirit of hiking" was clearly recognizable!
Now, the really interesting thing to ask is of course, why is that so? The non-interesting answer would be that my personal experience (having been on that hike myself) colours my perception and that for everybody else the videos would be just as soulless as the mentioned movie scenes. This is perfectly possible of course, however I find it much more interesting to imagine that there is more to it than just that.
Here are a number of factors that I think might be responsible:
perfection
Pictures in Hollywood movies are perfect and glossy, my clips aren't. Perfection creates distance and a feeling of artificialness.
objective camera
In the movies we see the heroes stoically marching through New Zealand's Best Of. Since the heroes as well as said Best Of (and especially the combination of the two) cost a lot of money and supposedly are what the viewers want to see, the camera is quite busy putting them in the best light. Most of the time therefore we either see the landscape at a wide angle with the group of people somewhere in the middle or we see the latter from the front or the side passing the camera's position. That means we get an uninvolved (helicopter-equipped) spectator's view of what's going on, which is how we would experience a landscape when sitting in a car or a train (or a heli), but *not* how we experience it when walking through it.
speed
When a movie wants to show us that a car for instance is moving very fast, we usually see it approaching (very fast) to the camera's position (preferably at a turn), passing it and then moving away. The camera usually stays fixed at its position and only turns to keep the car in focus.
When filming people walking in contrast directors seem to think that walking per se is a far too boring activity to keep the viewer's attention. Therefore the camera compensates by moving around the person. Approaching it from the back, passing it, approaching it from the front, circling it, etc. This all makes for a busy picture however it does *not* convey the feeling of slowness that is defining for walking. I think essentially walking is usually shown as an activity while in reality it is more of a state.
So, after all this - what do we see in my clip? We see a slow pan of the (greyish, wet, sheep-dotted) landscape. Then a group of people overtakes the camera and slowly (in walking speed that is) moves downwards a small hill, climbs a fence gate and disappears down a path. As I said, really nothing special and more than anything proof of my utter lack of cinematographic ability. Still (for me) it perfectly transports the slowness and smallness of people moving through a landscape by foot.
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