Floating Point: NAMD

After quite a bit of trouble, we managed to port a real floating point application to our POWER8 system: 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 parallellization 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. Since there was no LE Linux version for POWER8, we built our own. We got it working with the g++ compiler and used these settings:

-O3 -mcpu=power8 -ftree-vectorize -mpopcntd

These setting should push GCC to generate as much VSX (Vector Scalar eXtenstion) code as possible. 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: an early Xeon Phi (7120 1.2 GHz) scores about 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.

But it is nonetheless a real world HPC benchmark. The IBM POWER8 is once again on par with the Xeon E5-2695v3. The NAMD binary does not seem to leverage AVX2, as the Xeon E5-2667 (16 cores) does not outperform the Xeon E5-2690 (AVX) with a large margin.

Floating Point & Compilers Database Performance: MySQL
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  • extide - Friday, November 6, 2015 - link

    No he meant that in a lot of the european countries they use the dot as a comma, so it would be 50.000 to mean 50 thousand.
  • Murloc - Sunday, November 8, 2015 - link

    the international system dictates that , and . are the same thing, and as a separator you should use a space.
    In many countries in Europe, ' is also used. That's fine too as there is no ambiguity.
    Using . and , for anything that is not the decimal separator in international websites just creates confusion imho.
    I guess AT doesn't have a style book though.
  • duploxxx - Friday, November 6, 2015 - link

    nice review.
    but Xeon is not 95% of the market. AMD is still just a bit above 5% on its own. so it deserves a bit salt :) not to mention the fact that competition is good for all of us. if reviewers continue like this all narrowed readers will think there is no competition.
  • silverblue - Friday, November 6, 2015 - link

    I'm left wondering what a Steamroller-based 16+ core CPU would do here, considering multithreading is better than with previous models. Yes, the Xeons have a large single-threading lead, but more cores = good in the server world, not to mention that such a CPU would severely undercut the price of the competition.

    Shame it isn't ever going to happen!
  • lmcd - Friday, November 6, 2015 - link

    Or even an Excavator! It's a shame AMD didn't just keep Bulldozer developing internally until at least Piledriver, and iterate on Thuban.
  • Kevin G - Saturday, November 7, 2015 - link

    AMD killed off both Streamroller and Excavator chips early on as the Bulldozer and Piledriver chips weren't as competitive. More importantly, OEMs simply were not interested even if those parts were upgrades based upon existing designs. Thus the great AMD server drought began as they effectively have left that market and are hoping for a return with Zen.

    Also I should point out that Seattle, AMD's first ARM based Opteron has yet to arrive. This was supposed to be out a year ago and keep AMD's server business going throughout 2015 during the wait for Zen and K12 in 2016. Well K12 has already been delayed into 2017 and Seattle is no where to be found in commercial systems (there are a handle of Seattle developer boards).
  • JoeMonco - Saturday, November 7, 2015 - link

    When you account for only 5% of the market while the other side commands 95%, you aren't really much of a credible competitor.
  • xype - Sunday, November 8, 2015 - link

    That’s not always correct, though. You can have 5% of the market and 20% of the profits, for example, which would put you in a way better position than your competitors (because only a small increase in market share would pay big time).
  • Murloc - Sunday, November 8, 2015 - link

    that applies more to consumer products, e.g. apple.
  • dgingeri - Friday, November 6, 2015 - link

    I've been dealing with IBM Power based machines for 5 years now. Such experience has only given me a major disdain for AIX.

    I do NOT advise it for anyone. It sucks to work on. There is a certain consistent, spartan logic to it, but it is difficult to learn, and learning materials are EXTREMELY expensive. I never liked the idea of paying $12,000 for a one week class that taught me barely a tenth of what I needed to know to run an AIX network. (My company paid for the class, but I could not get them to pay for the rest of them, for some reason.) This makes people who can support AIX extremely expensive to employ. Figure on paying twice the rate of a Windows admin in order to employ an AIX admin. Then there is the massive expense of maintenance agreements. Even the software only maintenance agreement, just to get patches for AIX, is $4000 per year per system. They may be competitive in cost up front, but they drain money like vampires to maintain.

    Even the most modern IBM Power based machine takes 20-30 minutes to reboot or power up due to POST diagnostics. That alone is annoying enough to make me avoid AIX as much as I can.

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