[gmx-developers] std::vector<Rvec> slowness

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 23 10:42:34 CET 2016


On Wed, Mar 23, 2016 at 9:44 AM Berk Hess <hess at kth.se> wrote:

> Hi,
> Luckily Szilard does thorough testing and noticed a performance
> degradation in change set 25 of https://gerrit.gromacs.org/#/c/5232/ The
> only signifcant change with respect to previous sets is replacing C
> pointers by std::vector. I traced the performance difference back to a
> single loop, which must have become several factors slower to explain
> the time difference. I get the performance back when replacing the
> vector by a pointer extracted with .data(), see below. I looked at the
> assembly code from gcc 5.3.1 and the vector case generated 200 extra
> instructions, which makes it difficult to see what the actual difference
> is. The pointer case uses a lot of vmovss and vaddss, which the vector
> one does much less, but this is only serial SIMD instruction. I thought
> that [] in vector might does bounds checking,

Definitely not in release builds.

> but it seems it does not.
> Can anyone explain why the vector case can be so slow?

If this is a general issue (with RVec or more?), we need to always extra
> a pointer with .data() for use in all inner-loops. This is pretty
> annoying and difficult to enforce.
> Cheers,
> Berk
>                         const std::vector<RVec> f_foreign =
> idt_foreign->force

This does a copy of the vector, and doesn't seem to be in any version of
this patch in gerrit. Is this what you meant to write?


>                         const RVec               *f_foreign   =
> idt_foreign->force.data();
>                          int natom = atomList->atom.size();
>                          for (int i = 0; i < natom; i++)
>                          {
>                              int ind = atomList->atom[i];
>                              rvec_inc(f[ind], f_foreign[ind]);
>                          }
> --
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