Floating Point: 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.

We used the "NAMD_2.10_Linux-x86_64-multicore" binary for our Xeons. We used the most popular benchmark load, apoa1 (Apolipoprotein A1). The results are expressed in simulated nanoseconds per wall-clock day.

NAMD molecular dynamics

To put this in perspective: our best Xeon performs slightly slower than the early Xeon Phi (7120 1.2 GHz: 4.4). A top NVIDIA GPU with CUDA based NAMD can score up to 20 and more. So it is clear that this kind of software will be run mostly on GPU accelerated servers and scales "embarrassingly well".

We found out that we can boost the NAMD performance of the Xeon E5 quite a bit by disabling hyperthreading in the BIOS. In this case, core for core, the Broadwell Xeon (Xeon E5-2695 v4) loses compared to the similar Xeon E5-2699v3. Our suspicion that Broadwell does not keep the clockspeeds as high as Haswell seems justified. 

HPC: Fluid Dynamics with OpenFOAM Closing Thoughts
Comments Locked

112 Comments

View All Comments

  • ltcommanderdata - Friday, April 1, 2016 - link

    Does anyone know the Windows support situation for Broadwell-EP for workstation use? Microsoft said Broadwell is the last fully supported processor for Windows 7/8.1 with Skylake getting transitional support and Kaby Lake will not be supported. So how does Broadwell-EP fit in? Is it lumped in with Broadwell and is fully supported or will it be treated like Skylake with temporary support until 2018 and only critical security updates after that? And following on will Skylake-EP see any Windows 7/8.1 support at all or will it not be supported since it'll presumably be released after Kaby Lake?
  • extide - Friday, April 1, 2016 - link

    When MS says they are not supporting Skylake on Windows 7 DOES NOT MEAN it won't work. It just means they are not going to add any specific support for that processor in the older OS's. They are not adding in the speed shift support, essentially.

    For some reason the press has not made this very clear, and many people are freaking out thinking that there will be a hard break here will stuff will straight up not work. That is not the case.

    Broadwell has no new OS level features over Haswell (unlike Skylake with speed shift) so there is nothing special about Broadwell to the OS. As the poster above mentions, they are all x86 cpu's and will all still work with x86 OS's.

    The difference here is between "Fully Supported" and Compatible. Skylake and even Kaby Lake will be compatible with WIndows 7/8/8.1.
  • aryonoco - Friday, April 1, 2016 - link

    Johan, this is yet again by far the best Enterprise CPU benchmark that's available anywhere on the net.

    Thank you for your detailed, scientific and well documented work. Works like this are not easy, I can only imagine how many man hours (weeks?) compiling this article must have taken. I just want you to know that it's hugely appreciated.
  • JohanAnandtech - Friday, April 1, 2016 - link

    Great to read this after weeks of hard work! :-D
  • fsdjmellisse - Friday, April 1, 2016 - link

    hello, i want to buy E5-2630L v4
    any one can give me website for buy it ?

    Best regards
  • HrD - Friday, April 1, 2016 - link

    I'm confused by the following:

    "The following compiler switches were used on icc:

    -fast -openmp -parallel

    The results are expressed in GB per second. The following compiler switches were used on icc:

    -O3 –fopenmp –static"

    Shouldn't one of these refer to icc and the other to gcc?
  • JohanAnandtech - Friday, April 1, 2016 - link

    Pretty sure I did not mix them up. "-fast" does not work on gcc neither does -fopenmp work on icc.
  • patrickjp93 - Friday, April 1, 2016 - link

    Um, wrong and wrong. -Ofast works with GCC 4.9 and later for sure. And -fopenmp is a valid ICC flag post-ICC 13.
  • JohanAnandtech - Saturday, April 2, 2016 - link

    "-fast" is a typical icc flag. (I did not write -"Ofast" that works on gcc 4.8 too)
  • extide - Friday, April 1, 2016 - link

    Johan, if you read the comment, you can see that you mention icc for BOTH.

Log in

Don't have an account? Sign up now