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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  • Mondozai - Friday, November 6, 2015 - link

    That's too bad. Over 90% of the world population exists outside of it and even if you look at the HPC market, the vast majority of that is, too.

    The world doesn't revolve around you. Get out of your bubble.
  • bji - Friday, November 6, 2015 - link

    He never claimed the world revolved around him, he just made a true statement that may be worth consideration. Your response is unnecessarily hostile and annoying.

    I would expand Jtaylor1986's statement: I believe that most if not all native English speaking populations use commas for thousands grouping in numbers. Since this site is written in English, it might be worthwhile to stick to conventions of native English speakers.

    It's possible that there are many more non-native English speakers reading this site who would prefer dots instead of commas, but I doubt it. Only the site maintainers would know though.
  • Jtaylor1986 - Friday, November 6, 2015 - link

    You read my mind :)
  • mapesdhs - Tuesday, November 10, 2015 - link

    Talking to numerous people around Europe about tech stuff, I can't think of any nation from which someone used the decimal point in their emails instead of a comma in this context. I'd assumed the comma was standard for thousands groupings. So which non-US countries do use the point instead? Anyone know?
  • lmcd - Friday, November 6, 2015 - link

    Cool on the rest of the world part, but the period vs comma as delimiters in the world numeric system ARE backward. In language (universal, or nearly), a comma is used to denote a pause or minor break, and a period is used to denote the end of a complete thought or section. Applied to numerics, and you end up with the American way of doing it.

    ^my take
  • JohanAnandtech - Saturday, November 7, 2015 - link

    Just for the record, this was not an attempt to nag the US people. Just the mighty force of habit.
  • ZeDestructor - Saturday, November 7, 2015 - link

    For future use: just use a space for thousands seperation (that's how I do it on anything that isn't limited to a 7seg-style display), and confuse readers by mixing commas and periods for decimals :P
  • tygrus - Sunday, November 8, 2015 - link

    I like to use a fullstop for the decimal point, an apostrophe for the thousands separator, a comma for separating items in the list, don't start a sentance with a digit.
    One list of numbers may be : 3'500'000, 45.08, 12'500.8, 9'500. Second list : 45'000, 15'000, 25'000. We use apostrophes when we contract words like don't so why not use it for contracting numbers where we would otherwise have the words thousand, millions, billions etc ?
  • mapesdhs - Tuesday, November 10, 2015 - link

    I have a headache in my eyeballs! :D
  • ws3 - Friday, November 6, 2015 - link

    North America is on the majority side on this issue. Asia, in particular, is almost completely on the side of using a dot as the decimal separator and a comma to put breaks in long numbers.

    Get with the program Europe. The world doesn't revolve around you!

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