HPC Benchmarks

Discussing HPC benchmarks feels always like opening a can of worms to me. Each benchmark requires a thorough understanding of the software and performance can be tuned massively by using the right compiler settings. And to make matters worse: in many cases, these workloads can be run much faster on a GPU or MIC, making CPU benchmarking in some situations irrelevant.

NAMD (NAnoscale Molecular Dynamics) is a molecular dynamics application designed for high-performance simulation of large biomolecular systems. It is rather memory bandwidth limited, as even with the advantage of an AVX-512 binary, the Xeon 8160 does not defeat the AVX2-equipped AMD EPYC 7601.

LAMMPS is classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. GROMACS (for GROningen MAchine for Chemical Simulations) primarily does simulations for biochemical molecules (bonded interactions). Intel compiled the AMD version with the Intel compiler and AVX2. The Intel machines were running AVX-512 binaries.

For these three tests, the CPU benchmarks results do not really matter. NAMD runs about 8 times faster on an NVIDIA P100. LAMMPS and GROMACS run about 3 times faster on a GPU, and also scale out with multiple GPUs.

Monte Carlo is a numerical method that uses statistical sampling techniques to approximate solutions to quantitative problems. In finance, Monte Carlo algorithms are used to evaluate complex instruments, portfolios, and investments. This is a compute bound, double precision workload that does not run faster on a GPU than on Intel's AVX-512 capable Xeons. In fact, as far as we know the best dual socket Xeons are quite a bit faster than the P100 based Tesla. Some of these tests are also FP latency sensitive.

Black-Scholes is another popular mathematical model used in finance. As this benchmark is also double precision, the dual socket Xeons should be quite competitive compared to GPUs.

So only the Monte Carlo and Black Scholes are really relevant, showing that AVX-512 binaries give the Intel Xeons the edge in a limited number of HPC applications. In most HPC cases, it is probably better to buy a much more affordable CPU and to add a GPU or even a MIC.

The Caveats

Intel drops three big caveats when reporting these numbers, as shown in the bullet points at the bottom of the slide.

Firstly is that these are single node measurements: One 32-core EPYC vs 20/24-core Intel processors. Both of these CPUs, the Gold 6148 and the Platinum 8160, are in the ball-park pricing of the EPYC. This is different to the 8160/8180 numbers that Intel has provided throughout the rest of the benchmarking numbers.

The second is the compiler situation: in each benchmark, Intel used the Intel compiler for Intel CPUs, but compiled the AMD code on GCC, LLVM and the Intel compiler, choosing the best result. Because Intel is going for peak hardware performance, there is no obvious need for Intel to ensure compiler parity here. Compiler choice, as always, can have a substantial effect on a real-world HPC can of worms. 

The third caveat is that Intel even admits that in some of these tests, they have different products oriented to these workloads because they offer faster memory. But as we point out on most tests, GPUs also work well here.

Database Performance & Variability Conclusion: Competition Is Good
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  • hsupengjun - Sunday, December 03, 2017 - link

    Wow, the first few pages are sooo biased, but damn, are they rightfully so. Reply
  • ajc9988 - Tuesday, January 16, 2018 - link

    @Ian Cutress & Johan De Gelas - Could you please update this by running your own numbers AFTER the full implementation of Spectre and Meltdown fixes. That would be so helpful in showing how much these have effected both platforms and whether your conclusions remain after the fixes. Thank you! Reply
  • FentonW - Wednesday, January 17, 2018 - link

    What this doesn't really address is Memory configurations.
    RAM configurations are very much limited with intel given the 2 DIMMS per channel configuration and 6 channels vs 8 with AMD.

    With Intel you can only get 384GB with 16GB DIMMS, compared to 512GB with AMD.
    If you need 512GB then you have to use 32GB DIMMS on intel which again pushes the price up considerably.
    Which is why customers often choose a Broadwell system over Skylake, to keep memory costs down.
    Reply

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