Exploring Parallel HPC

HPC benchmarking, just like server software benchmarking, requires a lot of research. We are definitely not HPC experts, so we will limit ourselves to one HPC benchmark.

Developed by the Theoretical and Computational Biophysics Group at the University of Illinois Urbana-Champaign, NAMD is a set of parallel molecular dynamics codes for extreme parallelization on thousands of cores. NAMD is also part of SPEC CPU2006 FP.

To be fair, NAMD is mostly single precision. And, as you probably know, the Titan RTX was designed to excel at single precision workloads; so the NAMD benchmark is a good match for the Titan RTX. Especially now that the NAMD authors reveal that: 

Performance is markedly improved when running on Pascal (P100) or newer CUDA-capable GPUs. 

Still, it is an interesting benchmark as the NAMD binary is compiled with Intel ICC and optimized for AVX.  For our testing, we used the "NAMD_2.13_Linux-x86_64-multicore" binary. This binary supports AVX instructions, but only the "special” AVX-512 instructions for the Intel Xeon Phi. Therefore, we also compiled an AVX-512 ICC optimized binary. This way we can really measure how well the AVX-512 crunching power of the Xeon compares to NVIDIA’s GPU acceleration.  

We used the most popular benchmark load, apoa1 (Apolipoprotein A1). The results are expressed in simulated nanoseconds per wall-clock day. We measure at 500 steps.

NAMD Molecular Dynamics 2.13

Using AVX-512 boosts performance in this benchmark by 46%. But again, this software runs so much faster on a GPU, which is of course understandable. At best, the Xeon has 28 cores running at 2.3 GHz. Each cycle 32 single precision floating operations can be done. All in all, the Xeon can do 2 TFLOPs (2.3 G*28*32). So a dual Xeon setup can do 4 TFLOPs at the most. The Titan RTX, on the other hand, can do 16 TFLOPs, or 4 times as much. The end result is that NAMD runs 3 times faster on the Titan than on the dual Intel Xeon

Inference: ResNet-50 Analyzing Intel's Cascade Lake in the New Era of AI
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  • Drumsticks - Monday, July 29, 2019 - link

    It's an interesting, valuable take on the challenges of responding to many of the ML workloads of today with a general purpose CPU, thanks! A third party review of Intel's latest against Nvidia, and even throwing AMD in to the mix, is pretty helpful as the two companies have been going at it for a while now.

    Intel has a lot of stuff going that should make the next few years quite interesting. If they manage to follow through on the Nervana Coprocessor/NNP-I that Toms talked about, or on their discrete GPUs, they'll have a potent lineup. The execution definitely isn't guaranteed, especially given the software reliance these products will have, but if Intel really can manage to transform their product stack, and do it in the next few years, they'll be well on their way to competing in a much larger market, and defending their current one.

    OTOH, if they fail with all of them, it'll definitely be bad news for their future. They obviously won't go bankrupt (they'll continue to be larger than AMD for the foreseeable future), but it'll be exponentially harder if not impossible to get back into those markets they missed.
  • JohanAnandtech - Monday, July 29, 2019 - link

    Thanks! Indeed, Nervana coprocessors are indeed Intel's most promising technology in this area.
  • p1esk - Monday, July 29, 2019 - link

    No one in their right mind would think "gee, should I get CPU or GPU for my DL app?" More concerning for Intel should be the fact that I bought a Threadripper for my latest DL build.
  • Smell This - Monday, July 29, 2019 - link

    You gotta Radeon VII ?

    I'm thinking Intel, and to a lesser extent, nVidia, is waiting for the next shoe(s) to drop in **Big Compute** --- Cascade Lake has been left at the starting gate.

    An AMD Radeon Instinct 'cluster' on a dense specialized 'chiplet' server with hundreds of CPU cores/threads is where this train is headed ...
  • JohanAnandtech - Monday, July 29, 2019 - link

    Spinning up a GPU based instance on Amazon is much more expensive than a CPU one. So for development purposes, this question is asked.
  • p1esk - Tuesday, July 30, 2019 - link

    Then you should be answering precisely that question: which instance should I spin up? Your article does not help with that because the CPU you test is more expensive than the GPU.
  • JohnnyClueless - Monday, July 29, 2019 - link

    Really surprised Intel, and to a lesser extent AMD, are even trying to fight this battle with nVidia on these terms. It’s a lot like going to a gun fight and developing an extra sharp samurai sword rather than bringing the usual switchblade knife. The sword may be awesome, but it’s always going to be the wrong tool for the gun fight.

    IMO, a better approach to capture market share in DL/AI/HPC might be to develop a low core count (by 2019 standards) CPU that excelled at sequential single threaded performance. Something like 6-10 GHz. That would provide a huge and tangible boost to any workload that is at least partially single core frequency limited, and that is most DL/AI/HPC workloads. Leave the parallel computing to chips and devices designed to excel at such workloads!
  • Eris_Floralia - Monday, July 29, 2019 - link

    Still living in early 2000s?
  • FunBunny2 - Monday, July 29, 2019 - link

    "Something like 6-10 GHz. "

    IIRC, all the chip tried to get near that, but couldn't. it's not nice to fool Mother Nature.
  • Santoval - Monday, July 29, 2019 - link

    "Something like 6-10 GHz."
    Google "Dennard scaling" (which ended in ~2005) to find out why this is impossible, at least with silicon based MOSFET transistors (including the GAA-FET based ones of the next decade). Wikipedia has a very informative page with multiple links to various sources for even more. The gist of the end of Dennard scaling is that single core clocks higher than ~5 GHz (at a reasonable TDP of up to ~100W) are explicitly forbidden at *any* node.

    When Dennard scaling ended -in combination with the slowing down of Moore's Law- there was another, related consequence : Koomey's law started to slow down. Koomey's law is all about power efficiency, i.e. how many computations you can extract from each Wh or kWh.

    Before the early 2000s the number of computations per x unit of energy doubled on average every 1.57 years. In 2011 Koomey himself re-evaluated his law and got an average doubling of computations every 2.6 years for the previous decade, a substantial collapse of power efficiency. Since 2011 Koomey's law has obviously slowed down further.

    To make a long story short Moore's law puts a limit to the number of transistors we can fit in each mm^2, and that limit is not too far away. Dennard scaling once allowed us to raise clocks with each new node at the same TDP, and this is ancient history in computing terms. Koomey's law, finally, puts a limit to the power efficiency of our CPUs/GPUs, and this continues to slow down due to the slowing down of Moore's Law (when Moore's Law ends Koomey's law will also end, thus all three fundamental computing laws will be "dead").

    Unless we ditch silicon (and even CMOS transistors, if required) and adopt a new computing paradigm we will have neither 6 - 10 GHz clocked CPUs in a couple of decades nor will we able to speed up CPUs, GPUs and computers at all.

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