[gmx-users] SSE4 → AVX2

[Mark Abraham]

Naturally. It depends how much of your time is worth GROMACS running faster
on this machine, of course :-) If you're going to run a simulation for a
month, then an hour working out how to get the latest gcc for your ubuntu
version gets you your result several days sooner. Using AVX_256 probably
gets you a week earlier. YMMV. If you're just doing a tutorial, forget it
:-)

Mark


On Wed, Aug 27, 2014 at 2:53 PM, nicola staffolani <n.staffolani at unitus.it>
wrote:

> @ Szilárd: g++ (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
>
> But I have only one machine...
>
> I know that Google knows more, the problem is that I have a finite amount
> of time to solve my problems and I have to make a decision on how to spend
> it ;) (which is, however, in conflict with the fact that, having already
> come all this way, then I am a priori curios to know what comes next ;)
>
>
>
> 2014-08-27 14:04 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:
>
> > --
> > Szilárd
> >
> >
> > On Wed, Aug 27, 2014 at 12:32 PM, nicola staffolani
> > <n.staffolani at unitus.it> wrote:
> > > Thanx Szilárd!
> > >
> > > The concept of cross compilation is not perfectly 100% clear to me :s
> >
> > Briefly: given machine A and B (with different architectures), compile
> > binary for B on machine A (e.g. compiling for cluster nodes).
> >
> > Google knows even more.
> >
> > > software: GROMACS 4.6.5
> > > hardware: Intel® Core™ i7-4790 CPU @ 3.60GHz × 8
> > > message: Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on
> this
> > > machine, which is better)
> > >
> > > Have I given you the info you had requested?
> >
> > If you are compiling on that machine, I suspect you have an outdated
> > compiler. What compiler are you using?
> >
> > >
> > >
> > >
> > >
> > > 2014-08-27 12:00 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:
> > >
> > >> Normally the highest supported SIMD instructions set, which is in your
> > >> case AVX2, is detected during configuration phase. The fact that you
> > >> are getting that message means that:
> > >> - you are cross-compiling on an SSE4.1 node (e.g. cluster head node)
> > >> for AVX2 machines;
> > >> - your compiler does not support AVX/AVX2 and SSE4.1 was chosen as
> > >> fallback; cmake should have warned about this during configuration.
> > >>
> > >> What is your hardware/software setup? Using -DGMX_SIMD=AVX2 should
> > >> work in the former case.
> > >>
> > >> Cheers,
> > >>
> > >> --
> > >> Szilárd
> > >>
> > >>
> > >> On Wed, Aug 27, 2014 at 10:44 AM, nicola staffolani
> > >> <n.staffolani at unitus.it> wrote:
> > >> > Dear Gromacs users & developers,
> > >> >
> > >> > my computer tells me that, if I'd use AVX_256 instead of SSE4, then
> my
> > >> > simulations would be done much faster. Which changes in which files
> > do I
> > >> > have to do in order to achieve this? I have serched the mailing list
> > but
> > >> > couldn't find the explicit answer: I warn you that I am not so much
> > of a
> > >> > geek, therefore suggesting me, for example, to change the path,
> > without
> > >> > telling me which precise actions I have to carry on (for example, as
> > >> > already said, which lines I have to change/add in which file) in
> > order to
> > >> > achieve this, will only generate the next email from my side and
> then,
> > >> > since by then you will have already started answering me, you will
> > lose
> > >> > more time answering me back than if you would have precisely
> > described in
> > >> > the first reply the order of precise actions needed to be done in
> > order
> > >> to
> > >> > achieve the goal ;)
> > >> >
> > >> > Thank you for helping and have a nice day/night,
> > >> >
> > >> > Nicola
> > >> > --
> > >> > Nicola Staffolani PhD
> > >> > Biophysics & Nanoscience Centre CNISM <
> > http://www.unitus.it/biophysics>
> > >> > Università della Tuscia
> > >> > Largo dell'Università s.n.c., I-01100 Viterbo
> > >> > email: n.staffolani at unitus.it
> > >> > tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
> > >> > * Please search the archive at
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> > >> posting!
> > >> >
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> > >> --
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> > >
> > >
> > >
> > > --
> > > Nicola Staffolani PhD
> > > Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics
> >
> > > Università della Tuscia
> > > Largo dell'Università s.n.c., I-01100 Viterbo
> > > email: n.staffolani at unitus.it
> > > tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36
> > > --
> > > Gromacs Users mailing list
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> > posting!
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>
>
> --
> Nicola Staffolani PhD
> Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
> Università della Tuscia
> Largo dell'Università s.n.c., I-01100 Viterbo
> email: n.staffolani at unitus.it
> tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36
> --
> Gromacs Users mailing list
>
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