[gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
<stefano.guglielmo at unito.it> wrote:
>
> As an update, I have just tried a run with cpu only after compiling with
> AVX2_128 and the workstation turned off after few minutes.

That is suspicious. Perhaps a CPU cooling issue? Otherwise you may
have a BIOS/firmware issue or, less likely but possibly, a a faulty
CPU.

--
Szilárd

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> Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo <
> stefano.guglielmo at unito.it> ha scritto:
>
> > Hi Szilard,
> > thanks for your reply.
> > The compiler is gcc 4.8.5.
> > I put below the link where you can find the files coming from cmake and
> > the output for "AUTO" SIMD instruction. As for cpu only, as you had
> > suggested previously I tried a run (after compiling with AVX2_256) and it
> > worked without any problems for about 5 hours. I will try with AVX2_128 as
> > well.
> >
> > Stefano
> >
> > https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0
> >
> >
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> >
> > Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll <
> > pall.szilard at gmail.com> ha scritto:
> >
> >> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
> >> <stefano.guglielmo at unito.it> wrote:
> >> >
> >> > I apologize for the mistake, there was a typo in the object that could
> >> be
> >> > misleading, so I re-post with the correct object,
> >> > sorry.
> >> >
> >> > ---------- Forwarded message ---------
> >> > Da: Stefano Guglielmo <stefano.guglielmo at unito.it>
> >> > Date: mer 11 set 2019 alle ore 17:17
> >> > Subject: SMD options
> >> > To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> >> >
> >> >
> >> > Hi all,
> >> > following my previous post regarding anomalous crashing of the system on
> >> > running gromacs on two gpus, I have some new elements to add.
> >> > I tested the workstation with two tools for gpu and cpu I found on the
> >> web
> >> > (gpu_burn and stress); I ran the two of them at the same time for two
> >> hours
> >> > pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or
> >> > overheating have resulted, so I would say that the hardware seems to be
> >> > stable.
> >> > Despite this, I found something that perhaps could be not normal during
> >> > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD
> >> > instructions:  NONE"; in this condition I can run gromacs without any
> >> > unexpected crash, even though a little less efficiently; setting
> >> -DGMX_SIMD
> >> > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and
> >> > installation (with all the tests passed), but on running the sudden
> >> turning
> >> > off happens in the conditions I had described in the previous posts
> >> > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> >> > -gputasks 00 -pin on -pinoffset 0 -pinstride 1
> >> > plus
> >> > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
> >> > -gputasks 11 -pin on -pinoffset 28 -pinstride 1)
> >> > Do you think that there could be a relationship between SIMD options
> >> > setting and the crash of the system?
> >>
> >> Unlikely, but not impossible. I would however expect that a CPU-only
> >> GROMACS run would also lead to a crash. Can you try to do an AVX2_128
> >> CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run
> >> for a few hours?
> >>
> >> > Does anyone have any idea about the
> >> > reason why gromacs does not seem to automatically recognize any options
> >> for
> >> > my AMD threadripper? Can there be any solutions for this?
> >>
> >> That is certainly unexpected, perhaps there is an issue with your
> >> compler toolchains. What compiler are you using? Can you please share
> >> your cmake detection output and CMakeCache.txt?
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >> > Thanks again
> >> > Stefano
> >> > PS: the workstation is running with centOS 7 and aThreadripper 2990WX
> >> cpu.
> >> >
> >> > --
> >> > Stefano GUGLIELMO PhD
> >> > Assistant Professor of Medicinal Chemistry
> >> > Department of Drug Science and Technology
> >> > Via P. Giuria 9
> >> > 10125 Turin, ITALY
> >> > ph. +39 (0)11 6707178
> >> >
> >> >
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> >> >
> >> > --
> >> > Stefano GUGLIELMO PhD
> >> > Assistant Professor of Medicinal Chemistry
> >> > Department of Drug Science and Technology
> >> > Via P. Giuria 9
> >> > 10125 Turin, ITALY
> >> > ph. +39 (0)11 6707178
> >> > --
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> >
> >
> > --
> > Stefano GUGLIELMO PhD
> > Assistant Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707178
> >
> >
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
> --
> Gromacs Users mailing list
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