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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  • Cooe - Thursday, August 8, 2019 - link

    Hexus got around ≈31,000 iirc.
  • Ryan Smith - Thursday, August 8, 2019 - link

    Funny enough, from what I've heard from other people who have tested it, it actually doesn't run all that well with dual EPYCs. Too many cores that are too fast, to the point that initialization times are starting to hold back performance.
  • Ian Cutress - Thursday, August 8, 2019 - link

    I got a message from the Cinebench team at one point. They don't spawn/kill/respawn for each little segment: it's kept alive and just fed more data. CB20 is also designed to scale, given that CB15 freaked out above 32 cores or so
  • prisonerX - Wednesday, August 7, 2019 - link

    Where is our resident Intel shill? Selling his INTC stock in a panic perhaps?
  • abufrejoval - Wednesday, August 7, 2019 - link

    comiserating with the ARM server guys
  • Lord of the Bored - Thursday, August 8, 2019 - link

    Not gonna lie, I scrolled straight to the comments to see the Intel fanboy spinning this. Instead I got a wall of... Call of Duty references, I think?
  • PeachNCream - Friday, August 9, 2019 - link

    The fact that AMD released a product that breaks even HStewart's ability to defend shill for Intel should say something pretty epic about Epyc.
  • Lord of the Bored - Saturday, August 10, 2019 - link

    You ain't lyin' there. Seems the name was chosen well.
  • Korguz - Saturday, August 10, 2019 - link

    i bet, he would STILL but the intel cpu too. even though it costs more, slower and probably uses more power.
  • Samus - Thursday, August 8, 2019 - link

    I was just thinking if Trump doesn't crash the market with his shenanigans then AMD could be an incredibly good buy in the next few months. The first time they've been a good buy in awhile.

    Although a lot of my daytrader friends have always claimed AMD was a good short-term buy, which is partially true, but if they can keep momentum and Intel doesn't try strongarming them out of OEMs (you know, like they used too...)

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