[gmx-developers] Small hack regarding dihedrals
murozturk at ku.edu.tr
Thu Sep 26 09:25:36 CEST 2013
Are you referring to the pdihs_noener_simd() function?
It seems that there is a "#define SIMD_BONDEDS" instruction that is just
for this job? If I delete that line, does the SIMD functionality go away?
If not, where exactly does the code decide whether to use SIMD functions?
Can I disable SIMD selectively for dihedrals only?
Also, would it be preferable to use 4.6 and disable SIMD, or go back to 4.5
and do the hack over there, performance wise? I understand 4.5 has many
native assembly loops, whereas 4.6 takes advantage of the compiler, so if I
am going to disable SIMD, is it better to use the 4.5 version with native
I am probably going to be locked into 1 or 2 cores with this system, so I
need to squeeze the maximum out of them.
On Thu, Sep 26, 2013 at 10:02 AM, Berk Hess <hess at kth.se> wrote:
> But note that in 4.6 with SIMD (SSE/AVX) enablebd, dihedrals mostly
> (when only forces, no energies are needed) get calculated by a special SIMD
> dihedral function. You will need modifiy the conditional such that the
> plain C function always gets called.
> On 09/26/2013 08:04 AM, MURAT OZTURK wrote:
> Thank you very much. I need to build a toy system to test it, but sounds
> just about right. I might even hard-code the square of threshold to save
> another flop, following your philosophy. A flop is a flop :)
> Again, thank you.
> On Thu, Sep 26, 2013 at 12:10 AM, Bogdan Costescu <bcostescu at gmail.com>wrote:
>> On Wed, Sep 25, 2013 at 5:29 PM, MURAT OZTURK <murozturk at ku.edu.tr>
>> > Is it OK to intorduce the conditional into pdihs(), and bypass even
>> > dopdihs() if r_kj ( as reported by calling dih_angle() ) is less then
>> > threshold?
>> Yes. It makes sense to abort calculating as soon as you have enough
>> information to make the decision. You can place your test immediately
>> after calling dih_angle(), as it gives you r_jk. The code could look
>> like (based on your own proposal):
>> /* outside of the loop */
>> threshold2 = threshold * threshold;
>> for (i = 0; (i < nbonds); )
>> phi = dih_angle(...)
>> midDist2 = iprod(r_jk, r_jk);
>> if (midDist2 > threshold2)
>> Please note the comparison done on the squares of distances instead of
>> distances, saving some CPU cycles.
>> Good luck!
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