[gmx-users] SSE4 → AVX2

Wed Aug 27 15:40:30 CEST 2014

Thank you Mark ;)


2014-08-27 15:08 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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 If you are compiling on that machine, I suspect you have an outdated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
> > > >> > --
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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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> >
> >
> >
> > --
> > 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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-- 
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