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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  • negusp - Wednesday, August 7, 2019 - link

    hard F in the chat for intel
  • pancakes - Wednesday, August 7, 2019 - link

    F in chat for wallets of people running Windows server
  • azfacea - Wednesday, August 7, 2019 - link

    windows server in 2019 LUL
  • diehardmacfan - Wednesday, August 7, 2019 - link

    on-prem Windows Server is probably at an all time high in 2019?
  • azfacea - Thursday, August 8, 2019 - link

    desperate for a comeback huh? cool hold your 10% tight and gloat about upcoming bfloat16
  • diehardmacfan - Thursday, August 8, 2019 - link

    Sorry, who is desperate for a comeback? Bring up a floating point format when called out on the ridiculous notion that Windows Server isn't still a large part of the marketplace? say wha
  • mkaibear - Thursday, August 8, 2019 - link

    Just hopping in to say that I am an IT manager for a major employer in the UK and of our 1800 servers more than 80% of them are Windows... this is not a trend which I see changing any time soon.
  • Deshi! - Thursday, August 8, 2019 - link

    I work as an application engineer for a major global finance company that develops and hosts banking and e-commerce software used by banks and major shopping outlets. 90% of all our servers are either Linux or AIX mainly running websphere or standalone Java instances. We only have a handful of Windows servers, mainly for stuff like active directory and Outlook/ SharePoint. So yeah allot of it depends on the use case, but allot of the big boys do use Linux or AIX. It's cheaper and performs better for these use cases.
  • cyberguyz - Thursday, August 8, 2019 - link

    I guess we all have to ask ourselves, who are the customers that would benefit most from a 64-core, 128 gen 4 PCIe processors? SMB or huge customers that would shell out many millions of $$$ for their middleware & backend systems? @Deshi! I or one of my L3 colleagues an L3 engineer contacted by your global finance company to fix Websphere problems some years back ;)
  • FreckledTrout - Thursday, August 8, 2019 - link

    @cyberguz, Who would benefit from these high core servers? Any company running VM's so pretty much every large company. This goes doubly for cloud providers.

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