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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  • steepedrostee - Thursday, August 8, 2019 - link

    if i had to guess who is more full of crapola, i would think you
  • Smell This - Thursday, August 8, 2019 - link


    Pooper Lake?

    Cascade is obviously, The Mistake By The Lake

    Chipzillah will certainly strike back but it reminds me of the old 'virgin' joke. "My first wife was an OB/GYN, and all she wanted to do was look at it. My second wife was a psychiatrist, and all she wanted to do was talk about it, and ...

    My third wife was an Intel Fan Girl, and all she could say was, "Wait until next year!"

    HA!
  • RSAUser - Thursday, August 8, 2019 - link

    Do we finally have a contender to run Crysis on max?
  • Tunnah - Thursday, August 8, 2019 - link

    I'd normally just ignore this but this really needs proofreading, There's multiple mistakes on every page, becomes a bit difficult to follow.
  • cerealspiller - Thursday, August 8, 2019 - link

    Well, 50% of the sentences in your post have a grammatical error, so I will just try to ignore it.
  • GreenReaper - Friday, August 9, 2019 - link

    He's a reader, not a writer. ;-)
  • Oliseo - Thursday, August 8, 2019 - link

    Pot. Meet Kettle.
  • steepedrostee - Thursday, August 8, 2019 - link

    wow amd !
  • umano - Thursday, August 8, 2019 - link

    Intel people will welcome "Rome" like gladiators "Ave, Caesar, morituri te salutant"
    I am really happy for Amd and I really hope their sells will be a lot more than they could ever dream.
    Because they become more than competitive with the most rightful strategy, just deliver an awesome product. The fact they think that they will just double their shares shows how sick the market(s) are. The epyc is faster, greener and way way cheaper.
  • 29a - Thursday, August 8, 2019 - link

    "AMD does not blow fuses on cheaper SKUs to create artificial 'value' for buying more expensive SKUs"

    I like this guy, more reviews from him. He's not afraid to bite the hand that feeds him.

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