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
Comments Locked

180 Comments

View All Comments

  • MDD1963 - Friday, August 9, 2019 - link

    of the '1800 servers', how many of those are virtual, just out of curiosity? ('1800 servers' is not quite as impressive if there were, for example, 10 hosts w/ 180 Windows VMs each, for example) U.S.A.F offices are still mostly Windows 10...I'd suspect the are datacenters at each base having a large Windows Server presence as well.. (But, we used Redhat onboard assorted recce aircraft for many years now....; which seems stupid in light of the fact they could easily use CentOS for free; presumably, a Senator's family members work at Redhat, and enjoy the large income from support contracts)
  • eek2121 - Friday, August 9, 2019 - link

    Employers use Windows, data centers use Linux. All the major cloud providers, including Microsoft, have reported that Linux has the highest market share.
  • gylgamesh - Friday, August 9, 2019 - link

    Could you please specify what kind of servers those are and what tasks do they perform, and also which MS Windows OS are they using? Thanks.
  • Slickest - Thursday, August 8, 2019 - link

    I work for one of the largest colleges in the nation, and 90% of our servers are Windows.
  • 69369369 - Thursday, August 8, 2019 - link

    "LUL"

    Go back to Twitch kiddo.
  • azfacea - Thursday, August 8, 2019 - link

    and what would u do if i dont?
  • Oliseo - Thursday, August 8, 2019 - link

    Tell your mum you're up late again and she will force you to go outside, and we all know how much your dislike having to do that.
  • prophet001 - Monday, August 12, 2019 - link

    I don't get the hate for windows server? How you gonna run a domain and active directory in linux?
  • CaedenV - Wednesday, August 21, 2019 - link

    I use to work in schools, and a few that could not afford Windows Server would run AD through some Linux application. It was not exactly full-featured, but it worked well enough for 'free' solution.
  • deltaFx2 - Wednesday, August 7, 2019 - link

    @Pancakes: Are you kidding? 1T perf is at par with Skylake. Windows licenses per core. Why would anyone buy a SKU with more cores than they need? And if they did do that, why would they not run them on a VM? Do these people also buy more racks than they need and run windows just for the fun of it?

Log in

Don't have an account? Sign up now