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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  • wrkingclass_hero - Sunday, August 11, 2019 - link

    What does AMD have to do to get a Gold or Platinum recommendation?
  • oRAirwolf - Thursday, August 15, 2019 - link

    This is a good question
  • imaskar - Sunday, August 11, 2019 - link

    Single thread performance is very important for those who lives in cloud. A quick example: suppose I provision 2 core/4gig vm (this is of course hyperthreads). And on AWS I have a choice - m5 and m5a, where AMD is cheaper. What do I sacrifice? Not really throughput, because you don't run your prod workloads at 100% CPU. But there is the latency. If those cores clocked lower, I would get the same amount of responses, but slower. And since in microservice world you have a chain of calls, you get this decrease 10 times. Is it worth it?
    That was the case for 1st gen EPYC. Would 2nd gen have latency parity?
  • notashill - Sunday, August 11, 2019 - link

    It's hard to say until the cloud instances actually launch.

    The current m5a instances are using a custom SKU which is clocked at 2.5GHz max boost.

    Rome's IPC is ~15% higher and clock speeds are all around higher so single threaded performance should be quite a bit better, but ultimately the exact numbers will depend on which SKUs the cloud vendors decide to use and how high they clock.
  • duploxxx - Tuesday, August 13, 2019 - link

    did you actually ever work with hypervisors?

    there are other things than raw clock speed.... its all about scheduling and when there are more cores / socket available the scheduling is more relaxed, less ready time..... EPYC generation 1 is already awesome for hypervisor way better choice than most Intel counter parts for sure if you look at socket cost... but than again I am probably talking to a typical retard ****
  • JoeBraga - Wednesday, August 14, 2019 - link

    Can you Explain better? But the license isn't bought by the quantity of coresor Per socket?
  • imaskar - Wednesday, August 14, 2019 - link

    He probably talks about VmWare, which is licensed per socket, not per core. So with EPYC gen2 you need twice less licenses for the same cloud capacity (assuming cores are equal).
  • JoeBraga - Wednesday, August 14, 2019 - link

    Now I understood
  • imaskar - Wednesday, August 14, 2019 - link

    Rather than calling others retards, you could first dig a little deeper into an issue. No, I don't work with hypervisors directly, I'm from the other side. I write software and I want good latency (not insane one like for HFT, but still a good one). Because for throughput we could just spin one more instance. You can't buy latency horizontally.
    I'm not taking numbers out of the blue. There is a benchmark for AMD instances vs Intel instances on AWS. I'm not sure if we are allowed to post links to other resources here. Put this string into Google and you will surely find it: "A Look At The AMD EPYC Performance On The Amazon EC2 Cloud". Despite this article being very enthusiastic about those instances, you can really see that per core performance on Intel is better, meaning better latencies for web apps.
    I will probably write my own set of benchmarks, because that one seems to completely ignore web servers. I am very enthusiastic about AMD instances, but they are definitely not a no-brainer.
  • quadibloc - Tuesday, August 13, 2019 - link

    The new Ryzen chips compete well with what Intel is currently producing. But while they doubled AVX 2 support, so as to match what Intel has, Ice Lake will double that - as has been known for some time. So if this is what AMD thought would be competitive with Ice Lake, as Forrest Norrod said, AMD was not trying hard enough - and they're just lucky Ice Lake was late. AMD's position relative to Intel with its previous generations of Ryzens seems to be the limit of their ambitions. Combine that with Intel reacting to its current issues, and it looks to me that AMD will have to rethink some aspects of its strategy to avoid Intel being ahead when it comes time for next year's chips from both companies.

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