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Scientists Using Supercomputers To Puzzle Out Dinosaur Movement

Soulskill posted about 10 months ago | from the turns-out-they-sucked-at-ballet dept.

Supercomputing 39

Nerval's Lobster writes "Scientists at the University of Manchester in England figured out how the largest animal ever to walk on Earth, the 80-ton Argentinosaurus, actually walked on earth. Researchers led by Bill Sellers, Rudolfo Coria and Lee Margetts at the N8 High Performance Computing facility in northern England used a 320 gigaflop/second SGI High Performance Computing Cluster supercomputer called Polaris to model the skeleton and movements of Argentinosaurus. The animal was able to reach a top speed of about 5 mph, with 'a slow, steady gait,' according to the team (PDF). Extrapolating from a few feet of bone, paleontologists were able to estimate the beast weighed between 80 and 100 tons and grew up to 115 feet in length. Polaris not only allowed the team to model the missing parts of the dinosaur and make them move, it did so quickly enough to beat the deadline for PLOS ONE Special Collection on Sauropods, a special edition of the site focusing on new research on sauropods that 'is likely to be the "de facto" international reference for Sauropods for decades to come,' according to a statement from the N8 HPC center. The really exciting thing, according to Coria, was how well Polaris was able to fill in the gaps left by the fossil records. 'It is frustrating there was so little of the original dinosaur fossilized, making any reconstruction difficult,' he said, despite previous research that established some rules of weight distribution, movement and the limits of dinosaurs' biological strength."

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Surprise Twist! (2)

Gr33nJ3ll0 (1367543) | about 10 months ago | (#45300847)

SGI IS the dinosaur.

320 gigaflops/second (2, Interesting)

Anonymous Coward | about 10 months ago | (#45300901)

It seems there might be a typo in the article. 320 gigaflops/second is not that much, and can be gotten on a GPU for maybe $100 now. According to this page (http://n8hpc.org.uk/about/facilities), 320 gigaflops/second is the peak performance of each 2-cpu, 16-core sandy bridge node in the cluster, while the entire cluster has a peak performance of 110 teraflops/second. It is possible that this simulation just uses a single node on the cluster, but then it would be hardly worth mentioning the use of the cluster at all.

Re:320 gigaflops/second (5, Insightful)

bob_super (3391281) | about 10 months ago | (#45300951)

You don't understand. Gigaflops per second is an acceleration unit.

Run the sim for a while and you get a very very fast cluster indeed...

Re:320 gigaflops/second (1)

drakaan (688386) | about 10 months ago | (#45301037)

Acceleration units are for old people. Quickening units are way better. Try 1 Gigaflop per second per second!

Nope, the 320 GFLOPS is per node (1)

gentryx (759438) | about 10 months ago | (#45306005)

...and the cluster consists of 332 nodes. So according to the lab's homepage [n8hpc.org.uk] the whole cluster is able to deliver 110 TFLOPS (Tera Floating-point operations per second). You'd need to buy a couple of GPUs to equal that.

I don't understand what you mean by acceleration unit. Each node delivers that performance instantly. There is no change over time.

Re:Nope, the 320 GFLOPS is per node (1)

bob_super (3391281) | about 10 months ago | (#45306135)

from OP: 320 gigaflops/second
That's 320 Giga-Floating-point operations per second per second. Because the ps in "flops" is "per second".
Quantity per second squared is an acceleration.

Like an ATM Machine, really.

Re:Nope, the 320 GFLOPS is per node (1)

gentryx (759438) | about 10 months ago | (#45306245)

Oh, a joke... [troll.me] Sorry, didn't get it. Some people interpret GFLOPS as Giga Floating Point OPerationS. Which is IMHO sic(k).

Re:Nope, the 320 GFLOPS is per node (1)

DMUTPeregrine (612791) | about 10 months ago | (#45306781)

GFLOPS = Billion Floating Point Operations per Second
GFLOPS per second = Billion Floating Point Operations per Second per Second. It's an acceleration unit, and a mistake.

Re:320 gigaflops/second (1)

Trax3001BBS (2368736) | about 10 months ago | (#45304103)

It seems there might be a typo in the article. 320 gigaflops/second is not that much, and can be gotten on a GPU for maybe $100 now. According to this page (http://n8hpc.org.uk/about/facilities), 320 gigaflops/second is the peak performance of each 2-cpu, 16-core sandy bridge node in the cluster, while the entire cluster has a peak performance of 110 teraflops/second.

Ah now http://www.sciencedaily.com/ [sciencedaily.com] claims it's the equivalent of 30,000 desktop computers :}
http://www.sciencedaily.com/releases/2013/10/131030125538.htm [sciencedaily.com]

Re:320 gigaflops/second (0)

Anonymous Coward | about 10 months ago | (#45305993)

Which desktop computer?

My 4 year old Apple Cube, or my 1 year old cobbled together Frankenstein windows machine?

Interpolation... (1)

bob_super (3391281) | about 10 months ago | (#45300927)

So, starting with a few partial chunks of data, and guessing the shape of the others based on overall dinosaurs knowledge, we got a very high precision simulation.

At least when we get an election poll, it usually is delivered with a calculated uncertainty margin.

Re:Interpolation... (0)

Anonymous Coward | about 10 months ago | (#45300993)

Just like all the old misassembled dino skeletons, but this one's an animated 3D model you can port over to Team Fortres.

Re:Interpolation... (1)

mwehle (2491950) | about 10 months ago | (#45302111)

Just like all the old misassembled dino skeletons, but this one's an animated 3D model you can port over to Team Fortres.

Yeah, that was kind of my reaction - the summary is written as if this model is a marvel of accuracy, but any claims about the dinosaur's movements will necessarily remain conjecture. Precision != accuracy.

Re:Interpolation... (0)

Anonymous Coward | about 10 months ago | (#45305219)

They are likely using the current knowledge about bones and tissues (hopefully taking into account the oxygen difference), and sprinkle a generous amount of physics on top of it. I'd bet their models are tested against current animals quite well.

Re:Interpolation... (1)

clarkn0va (807617) | about 10 months ago | (#45301013)

Extrapolating from a few feet of bone, paleontologists were able to estimate

Science at its best! Honestly though, I don't need a few feet of bone to estimate that this very same dinosaur was an excellent conversationalists and patron of the high arts.

Wait, what?! (4, Funny)

LeninZhiv (464864) | about 10 months ago | (#45300935)

You're telling me that SCIENTISTS, actual scientists, are turning to COMPUTERS, to do their work?

What is the world coming to?

Accuracy? (1)

camperdave (969942) | about 10 months ago | (#45301043)

Extrapolating from a few feet of bone, paleontologists were able to estimate the beast weighed between 80 and 100 tons and grew up to 115 feet in length.

A few feet of bone... like what? A femur, perhaps? So, from a couple of feet of femur, they can determine the size and shape of the entire animal? How do they know it was a brontosaur*-style vs a tyrannosaur style animal? How do they know this is the bone of a separate species and isn't the bone of an animal suffering from a glandular defect? Extrapolating the characteristics of a species from one very incomplete sample... I sense a large percentage of handwaving, guesswork and artistic license taking place here.

*Yes, I know it's not called a brontosaur anymore. Poor things went extinct twice.

Big numbers (1)

Ceriel Nosforit (682174) | about 10 months ago | (#45301053)

N8 HPC currently operate Polaris, an SGI High Performance Computing cluster, with 332 compute nodes. Each node has two of the latest Intel Sandy Bridge processors and these nodes have a capacity of 320 GigaFLOPS/second. By using all of the nodes of Polaris together, a peak performance of 110 TeraFLOPS/second. Unlocking this peak performance has been helped by our use of a fast InfiniBand interconnect joining the nodes together.

- http://n8hpc.org.uk/about/facilities [n8hpc.org.uk]

So my GPU isn't three times faster. Oh well. Can't win 'em all.

I am going to call BS... (5, Interesting)

PortHaven (242123) | about 10 months ago | (#45301089)

I am always amazed at how much under-estimation of dinosaurs there is. Remember when we thought Tyranosaurus Rex was slow? Now, we estimate that it runs at what? up to 35 mph?

Now, I wonder what their model would predict the top speed of an Elephant to be? If you look at an Elephant and it's gait you'd think it slow. But it can reach top speeds of 25 mph. Guess what, if you compare an elephant to most other animals in a simulation. You would not conclude that they could hit 25mph. Why? Because elephants don't really run as other animals. They always have one foot on the ground. Their movement doesn't match. So if you said, take an elephant and model it to see if it can run. It would return back that it was incapable of running. When in fact, elephants have a modified gait that they use for higher speeds.

I'd wager the movement is akin to pogo'ing affect. If you've ever run with your knees locked, you'll understand what I mean. It's clearly not as fast as "running" but it can be faster than walking. But whatever, however, you want to describe it. An elephant exceeds the speeds a typical model would show it capable of.

Now, if you take these premises, and create a model. Your conclusions are going to be "fail". Why? Because you have limited knowledge. Take a large saurapod and model it after a running gait. It will show negative results. So you say, hey, let's see how it does with a more elephant like gait. Cause elephants don't really run, but they can charge at up to 25mph. Results fail. You now conclude that said giant beastie is only capable of 5mph walk.

YOU ARE WRONG!!!! Because you've predicted based on a model without understanding other forms of movement. Would 5mph be sustainable for the achievement of accessing food? avoiding predators? etc. In other words, can a 5mph speed sustain a giant saurapod's lifestyle?

Consider for a moment that many lizards when they run seem to not just use their legs, but rather bend their elongated bodies left and right creating a wiggle affect. Rather similar to what a snake does. It is not just the reach of the legs, but the shortening of the torso that affects the speed and movement of some lizards.

And it may very well be likely that a similar body function would allow greater speed. Most extremely slow moving creatures such as turtles, have a tendency to be armored and protected.

My gutt feels like they're missing an unknown aspect of mechanics. And that such creatures could probably reach at least 8-12mph

Re:I am going to call BS... (3, Insightful)

Gavrielkay (1819320) | about 10 months ago | (#45301315)

It is certainly possible that you're right. Of course, it's also possible that people who study this know about your objections and incorporated all that into the model.

If they're right about the size of this animal, it really is hard to imagine its bones and muscles being sturdy enough to handle it moving particularly fast. Also, as far as outrunning predators, what exactly would eat one of these things? Even in the modern world, the largest animals really only have to worry about predators if they are young, sick or vastly outnumbered. A fully grown Argentinosaurus wasn't likely to need to run away from much of anything.

The problem is a tendency to underestimate... (4, Interesting)

PortHaven (242123) | about 10 months ago | (#45302067)

They once thought these animals couldn't even raise their tales.

The length was too long. They were too big.

Yet look at giant Anacondas. Neither slow nor weak and with a vascular system running blood up and down its length. The truth is, nearly every under-assumption of these creatures has been proven wrong.

Look at our large land animals: elephant, rhino, moose, giraffe, polar bear....NONE OF WHICH ARE SLOW

Now, they're never fast as pinnacle predators cats, wolves, etc. But they're never slow. Rather, it is not speed they tend to lack, but agility. They often can charge forward at a brisk pace, but most are not very good at high speed turns.

I'll still wager $5 they're completely mis-analyzing due to mis-conceived models. A penguin fails at a flight model. But it would be pretty darn stupid to then conclude that a penguin's top speed is a mere 2-3mph. Simply because you never thought to consider an aquatic model.

Re:The problem is a tendency to underestimate... (1)

camperdave (969942) | about 10 months ago | (#45304205)

They once thought these animals couldn't even raise their tales.

The length was too long. They were too big.

Well, Tolkein managed to get the Silmarillion published.

Re:The problem is a tendency to underestimate... (1)

PortHaven (242123) | about a year ago | (#45402941)

That he did...but can it be turned into a trilogy?

Re:I am going to call BS... (0)

Anonymous Coward | about a year ago | (#45307305)

Actually the model, as I understand it, is fairly basic in the arguments it makes. What is input is the size of the bones and location of tendons and muscle groups (which should be well understood from comparative anatomy). The model is then left alone with basic rules of physic and learns how to move the dinosaur. From old articles on the subject, I belive they first tried this with the same limited info but with bones sizes and shapes of existing animals to see how the model "learned" the best way to make the skeleton moved and found that it fairly accurately replicated the natural modes of locomotion of existing animals. Only then did they apply it to long dead animals, but in both cases only the same kind of information (or lack thereof) is fed to the computer model. Obviously, better knowledge is available for the mass of current animals, but the basic physics that the model uses is the same whether it is a Brachiosaurus, an elephant or a mouse.

Re:I am going to call BS... (1)

Arker (91948) | about 10 months ago | (#45302017)

My gut tells me that at least one thing they are missing in the mechanics is that these were aquatic animals. The inverse square law has always suggested strongly that it would be very dangerous for these things to try and walk on dry ground - and a broken leg would be fatal for them without exception. But they inhabited supertropical swampland areas and if they kept a good portion of their bulk in the water...

Re:I am going to call BS... (0)

Anonymous Coward | about 10 months ago | (#45302153)

Dinosaurs don't current run at any speed other than what our engines can push.

Re:I am going to call BS... (0)

Anonymous Coward | about 10 months ago | (#45303849)

It certainly makes sense. Before predicting speeds of dinosaurs we need to test speeds of known animals according to our simulation. Only if results are correct and fully tested in many cases, only then we can trust the dinosaur results. That is the normal testing procedure for me, I test for outcome I know is correct and then decide if I can trust any output or the program needs improving.

Food (3, Interesting)

Archangel Michael (180766) | about 10 months ago | (#45301103)

Has anyone figured out how much food these things had to eat to grow that big, how long they had to live?

My questions are about the likelyhood of these things being "common" at those sizes.

More worthwhile projects? (-1)

Anonymous Coward | about 10 months ago | (#45301199)

So the big headline is that paleontologists have applied basic structural modeling to hypothesize maximum speed and dimensions of an extinct sauropod? That's great, guys, just great. I am sure this will have thousands of immediate applications that will help solve humanity's most pressing needs. Oh, it will make Jurassic Park XVI animation rendering that much more realistic?

How's that research on a new cancer drug coming along? Sustainable farming? Understanding climate change? Population growth?

I am sorry to be such a "downer" on geeky news about computers and dinosaurs, but it seems to me there are far more worthwhile (with much greater return) uses of compute power than hypothesizing how an extinct reptile lumbered along millions of years ago.

His feet hurt (1)

TempleOS (3394245) | about 10 months ago | (#45301341)

God said his feet hurt when he stepped.

Elephants can do 25 km/h (0)

Anonymous Coward | about 10 months ago | (#45301507)

For more context: elephants can run up to 25 km/h
http://www.newscientist.com/article/dn3583-elephants-need-for-speed-defies-definition.html

QWOP Dinosaur Edition (2)

decipher_saint (72686) | about 10 months ago | (#45301593)

...which actually sounds pretty good

*stumbles sideways falls over stegosaurus*

Just came here to post exactly this. (1)

gentryx (759438) | about 10 months ago | (#45306033)

I imagine they tried to let the machine figure our how to press the gazillion of buttons to make the dinosaur go by testing thousands of combinations.

Science or S.W.A.G. (scientific wild-assed guess)? (1)

gpronger (1142181) | about 10 months ago | (#45301767)

Extrapolated from one bone???

fill in the gaps (1)

cascadingstylesheet (140919) | about 10 months ago | (#45302503)

The really exciting thing, according to Coria, was how well Polaris was able to fill in the gaps left by the fossil records.

And we know it did so correctly because ... ?

Computer modelers are the new armchair scientists (1)

Ranbot (2648297) | about 10 months ago | (#45302877)

"Extrapolating from a few feet of bone..." There's certainly a place for modeling in science, but there are definitely scientists that are using these models based on very little actual data to give some semblance of authority to what is really a wild guess.

Video or (0)

Anonymous Coward | about 10 months ago | (#45302889)

... it didn't happen.

awesome dinos (0)

Anonymous Coward | about a year ago | (#45315173)

I'd just like to add that dinosaurs are awesome.

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