HPC: NAMD

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. In contrast with previous FP benchmarks, the NAMD binary is compiled with Intel ICC and optimized for AVX and AVX-512.

The NAMD binary is compiled with Intel ICC, optimized for AVX and mostly single preciscion floating point (fp32).  For our testing, we used the "NAMD_2.13_Linux-x86_64-multicore" binary.  At some point we want to use this test with AOCC or similar AMD optimized binary, but were unable to do so for this review.

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

Even without AVX-512 and optimal AVX optimization, the 7742 is already offering the same kind of performance as an ultra optimized Intel binary on top of the top of the line Xeon 8280. When do an apples-to-apples comparison, the EPYC 7742 is no less than 43% faster. 

AMD claims a 35% advantage (3.8 ns/days vs 2.8 ns/days) and that seems to confirm our own preliminary benchmarking. 

Java Performance: Critical-jOPS First Impressions of 2x 64-Cores
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  • Kevin G - Wednesday, August 7, 2019 - link

    Clock speeds. AMD is being very aggressive on clocks here but the Ryzen 3000 series were still higher. I would expect new Threadripper chips to clock closer to their Ryzen 3000 cousins.

    AMD *might* differentiate Threadripper by cache amounts. While the CPU cores work, they may end up binning Threadripper based upon the amount of cache that wouldn't pass memory tests.

    Last thing would be price. The low end Epyc chips are not that expensive but suffer from low cores/low clocks. Threadripper can offer more for those prices.
  • quorm - Wednesday, August 7, 2019 - link

    Here's hoping we see a 16 core threadripper with a 4ghz base clock.
  • azfacea - Wednesday, August 7, 2019 - link

    half memory channels. half pcie lanes. also i think with epyc AMD spends more on support and system development. i can see 48c 64c threadripper coming 30-40% lower and not affecting epyc
  • twtech - Wednesday, August 7, 2019 - link

    If they gimp the memory access again, it mostly defeats the purpose of TR as a workstation chip. You'd want an Epyc anyway.
  • quorm - Wednesday, August 7, 2019 - link

    Well, on the plus side, the i/o die should solve the asymmetric memory access problem.
  • ikjadoon - Wednesday, August 7, 2019 - link

    Stunning.
  • aryonoco - Wednesday, August 7, 2019 - link

    Between 50% to 100% higher performance while costing between 40% to 50% less. Stunning!

    I remember the sad days of Opteron in 2012 and 2013. If you'd told me that by the end of the decade AMD would be in this position, I'd have wanted to know what you're on.

    Everyone at AMD deserves a massive cheer, from the technical and engineering team all the way to Lisa Su, who is redefining what "execution" means.

    Also thanks for the testing Johan, I can imagine testing this server at home with Europe's recent heatwave would have not been fun. Good to see you writing frequently for AT again, and looking forward to more of your real world benchmarks.
  • twtech - Wednesday, August 7, 2019 - link

    It's as much about Intel having dropped the ball over the past few years as it is about AMD's execution.

    According to Intel's old roadmaps, they ought to be transitioning past 10nm on to 7nm by now, and AMD's recent releases in that environment would have seemed far less impressive.
  • deltaFx2 - Wednesday, August 7, 2019 - link

    Yeah, except I don't remember anyone saying Intel was going great guns because AMD dropped the ball in the bulldozer era. AMD had great bulldozer roadmaps too, it didn't matter much. If bulldozer had met its design targets maybe Nehalem would not be as impressive... See, nobody ever says that. It's almost like if AMD is doing well, it's not because they did a good job but intel screwed up.

    Roadmaps are cheap. Anyone can cobble together a powerpoint slide.
  • Lord of the Bored - Thursday, August 8, 2019 - link

    Well, it is a little of both on both sides.
    Intel's been doing really well in part because AMD bet hard on Bulldozer and it didn't pay out.

    Similarly, when AMD's made really good processors but Intel was on their game, it didn't much matter. The Athlon and the P2/3 traded blows in the Megahertz wars, but in the end AMD couldn't actually break Intel because Intel made crooked business deals*backspace* because AMD was great, but not actually BETTER.

    The Athlon 64 was legendary because AMD was at the top of their game and Intel was riding THEIR Bulldozer into the ground at the same time. If the Pentium Mobile hadn't existed, thus delaying a Netburst replacement, things would be very different right now.

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