[gmx-users] Fwd: SIMD options

Thu Sep 12 17:25:32 CEST 2019

Hi,

There will have been reports by cmake about whether the detection program
compiled and/or ran successfully, which would be useful diagnostic
information. Please run cmake in a fresh build directory and look for that.
It is possible to run that program individually, if the issue is that it
compiles and fails to run somehow (e.g. that linking is broken)

Mark

On Thu, 12 Sep 2019 at 17:06, Stefano Guglielmo <stefano.guglielmo at unito.it>
wrote:

> 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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> priva di virus. www.avast.com
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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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> > >
> > > Mail
> > > priva di virus. www.avast.com
> > > <
> >
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> > >
> > > <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > >
> > > 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
> > > >
> > > >
> > > > <
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> > Mail
> > > > priva di virus. www.avast.com
> > > > <
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> > >
> > > >
> >
> <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > >
> > > > 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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> > > >> >
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> > > >> > <
> > > >>
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> > > >> >
> > > >> > <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > >> >
> > > >> >
> > > >> > --
> > > >> > 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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