HPC: Fluid Dynamics with OpenFOAM

Computational Fluid Dynamics is a very important part of the HPC world. Several readers told us that we should look into OpenFOAM, and my lab was able to work with the professionals of Actiflow. Actiflow specializes in combining aerodynamics and product design. Calculating aerodynamics involves the use of CFD software, and Actiflow uses OpenFOAM  to accomplish this. To give you an idea what these skilled engineers can do, they worked with Ferrari to improve the underbody airflow of the Ferrari 599 and increase its downforce.

We were allowed to use one of their test cases as a benchmark, however we are not allowed to discuss the specific solver. All tests were done on OpenFOAM 2.2.1 and openmpi-1.6.3. The reason why we still run with OpenFOAM 2.2.1 is that our current test case does not work well with higher versions.

We also found AVX code inside OpenFoam 2.2.1, so we assume that this is one of the cases where AVX improves FP performance. 

OpenFOAM

As this is AVX code, the clock speed of our Xeon processors can be lower than Intel's official specifications, and turbo boost speeds are also lower. Despite the fact that on Broadwell the only cores that reduce their clock when running AVX code are the AVX-active cores themseves (the others can continue at higher speeds), OpenFOAM does not run appreciably faster on the top of the line Xeon E5 v4 than it did on the E5 v3.

It is not as if OpenFOAM does not scale: 22% more cores delivers 13% higher performance (E5-2699v4 vs E5-2695v4). No, our first impression is that the new Xeon v4 needs to lower the clockspeed more than the old one. The official specifications tell us that both the Xeon E5-2699 v4 and v3 should run AVX code at up to 2.6 GHz with all cores enabled. The reality is however that Broadwell runs at a lower clock on average. 

Spark Benchmarking NAMD
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  • xrror - Tuesday, April 5, 2016 - link

    Even at 3.3Ghz though, they shouldn't be that slow. I'm taking a guess - if this was a student lab, and they bothered to specifically order xeon (or opteron back in the day) workstations - I'm guessing this was a CAD/CAM lab or something running a boatload of expensive licenced software (like, autodesk, solidworks, etc) and some of that stuff is horrible at thrashing on the hard drive, constantly.

    And I doubt your school could spring the cash for SSD drives in them (because Workstation SKU == you pay dearly OEM workstation 'certified' drive cost).

    This is all guesses though. And not trying to defend - it does suck when you have what should be a sweet machine choking for whatever reason, and you're there trying to get your assignments done and you just want to smash the screen cause it just chhhuuuuuuggggsss... ;p
  • SkipPerk - Friday, April 8, 2016 - link

    I have seen this many times, even in the for-profit sector. I once saw a compute cluster that was choking on server with slow storage. They had a 10 gb network and fast Xeon machines running on flash, but the primary storage was too slow. When they get a proper SAN it was an order of magnitude improvement.

    Back in the day storage was often the bottleneck, but it still comes up today.
  • someonesomewherelse - Thursday, September 1, 2016 - link

    We ran everything in virtual machines with the actual disk images not stored locally.... and the lans in the classrooms were 100mbit, idk about the connection from the classroom to the server with the image. How's that for slow?

    I would have loved it if our stuff was as 'slow' as yours. The wifi in the classrooms was very fast too..... especially since I doubt anyone bothered with turning of their torrents (well I mean it's completely understandable, you are going to watch the new episode of your favorite show once you are back home and not everyone had (well has, but most people can get it now) fth with at least 100Mbit line (ideally symmetrical, but some isps are too gready with ul speeds so 300/50 is cheaper than 100/100...... and good luck getting 1000/1000 on a residential package (the hw isn't the problem since you can get 1000/1000 with a commercial (aka over priced) package..... using the same hw... basically I would just need to sign a new contract, send it back, and enjoy the faster line in 1 business day or less)...well at least there are no bw caps (if I didn't read foreign boards bw caps on non mobile connections would be something I'd think no isp could do and not lose all customers) and there's we have no dmca (or something similar) and afaik no plans for one either (if they tried to pass such a law I can imagine that you'd have enough support for a referendum which you would win with a huge mayority), even better, the methods used to catch people downloading torrents are illegal anyway so any evidence obtained with them or derived from them is inadmissible anyway and just by presenting it you have admitted to several crimes which the police and prosecution are obliged to investigate/prosecute.... copyright infringment however is a civil matter).
  • donwilde1 - Tuesday, April 5, 2016 - link

    One of the more interesting Intel features, in my opinion, is that Broadwell carries an on-board encryption engine with its own interpreter similar to a small-memory, embedded JVM. This enables full Trusted Boot capability, which I view as a necessity in today's hackable world. Would you consider a follow-on article on this? The project was a clean-room development called BeiHai, done in China.
  • JamesAnthony - Wednesday, April 6, 2016 - link

    From what I can tell in looking over the benchmarks, there is not much of an increase in performance at all in core vs core performance speeds going from the V1 CPUs to the V4 CPUs
    As if you look at the benchmarks, and calculate that you are comparing 16 cores to 44 cores, the 44 core setup is not 2.75x faster.

    So while your overall speed goes up, your work accomplished per core is not increasing at the same rate.

    Why does this matter? Well thanks to software licensing costs, as you add cores it gets very expensive quickly. So if your software costs (which can easily exceed the hardware costs very quickly) go up with each core you add, but the work done does not, you quickly wind up in a negative cost / performance ratio.

    For quite a few people the E5-2667 v2 CPU with 8 cores at 3.5 GHz (Turbo 4) comes out around the best value for the software licensing cost.

    So while Intel puts out processors that overall can do more work than the previous ones, the move to per core software licensing is making it a negative value proposition. This is why people keep wanting higher clock speed lower core count processors, but we seem stuck around 3.5 GHz for many years.
  • SkipPerk - Friday, April 8, 2016 - link

    Although you are right for workstations, so much demand is for generic virtualized machines. Many buyers are fine with 2 ghz with as many cores as they can get. They load as little RAM as the spec requires and throw out the cheapest single core, dual thread 2 GB RAM VM they can. This is how call centers work, not to mention many low-level office jobs. They do not care about performance because this is more than enough.

    I have had specialty applications where prosumer 6-core or 8-core CPUs were the better deal (usually liquid cooled and overclocked), but not many buyers are licensing insanely expensive analytical software by the core.
  • SeanJ76 - Sunday, April 10, 2016 - link

    @Xeon chips!! TOTAL GARBAGE!
  • legolasyiu - Wednesday, April 20, 2016 - link

    The ASUS Workstation/Server board with V4 boards are very stable and they have 10% OC. I am very interested how the processor with those boards.
  • Bulat Ziganshin - Saturday, May 7, 2016 - link

    >This increases AES (symmetric) encryption performance by 20-25%

    PCLMULQDQ implements part of Galois Field multiplication and bdw actually improved only GCM part of AES-GCM algo. neither AES nor other popular symmetric encryption algos became faster
  • oceanwave1000 - Monday, May 9, 2016 - link

    This article mentioned that the Broadwell EP e5-v4 family has 3 die configurations. I got the 306mm2 and 454mm2. Did anyone catch the third one?

    Thanks.

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