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 Reply
  • pancakes - Wednesday, August 7, 2019 - link

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

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

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

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

    Many smaller IT depts in smaller companies use Windows because of familiarity for desktop support such as Active Directory for domains, but none of major critical data center centric, HPC, military, infrastructure are running Windows. Most especially not with EPYC since the Windows scheduler is broken. Reply
  • Manch - Thursday, August 8, 2019 - link

    NPZ, You may be speaking for your bubble, but not for the rest. Reply
  • blaktron - Thursday, August 8, 2019 - link

    this is 100% false. I do infrastructure consulting for 9 figure companies and they are all primarily windows in their corporate infrastructure. all of them. the only linux you will find in the Fortune 50 is legacy applications and web presentation layer. There are exceptions, but that's true enough to form a rule. Reply

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