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

[Mark Abraham]

Hi,

If so, then we might want a helper function like as_rvec_array, but
as_real_array instead.

Mark

On Wed, Mar 23, 2016 at 10:51 AM Berk Hess <hess at kth.se> wrote:

> On 2016-03-23 10:50, Erik Lindahl wrote:
>
> Hi,
>
> I haven’t followed the discussion in detail, but a long time ago I
> remember having simliar issues in the kernels when using a list[] of rvec[]
> (in plain-old-c, no c++) instead of extracting the pointer and handling the
> multiply-by-3 manually. Could it be something similar here, e.g. that the
> compiler things it does not know enough about RVec rather than something
> going from with the outer list?
>
> That would be my guess. The index used in the same loop comes from a
> vector as well and doesn't seem to affect performance.
>
>
> Berk
>
>
> Cheers,
>
> Erik
>
> On 23 Mar 2016, at 10:44, Berk Hess <hess at kth.se> wrote:
>
> On 2016-03-23 10:42, Mark Abraham wrote:
>
> Hi,
>
> 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?
>
> I tried this. But my original "vectorized" patch set took a pointer from
> idt_foreign and did not copy the vector, that gives the same, slow,
> performance.
>
> Berk
>
>
> Mark
>
> or
>>                         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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>
>
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