[gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

I cannot say about BIOS/firmware yet, I made a quite "standard"
installation of centOS 7, but I'll try to check; as for cpu, for what it
means, I made the stress test which brought up temperature for two hours
together with gpu_burn, so I would exclude cooling failure.

A further update: I yum-installed devtoolset-8-toolchain, so now cmake
finds gcc 8.3.1, but again SIMD instructions detection failed.
Sorry for bothering but I must say that I am getting a bit confused.

Stefano

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Il giorno gio 12 set 2019 alle ore 16:35 Szilárd Páll <
pall.szilard at gmail.com> ha scritto:

> 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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-- 
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