[gmx-users] Fwd: SIMD options

Thu Sep 12 17:52:04 CEST 2019

Hi Mark,
actually running cmake in the output I can read "Did not detect build CPU
vendor - detection program did not compile".
Any suggestions about the origin of the issue and possible solutions?

Thanks
Stefano

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Il giorno gio 12 set 2019 alle ore 17:26 Mark Abraham <
mark.j.abraham at gmail.com> ha scritto:

> 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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> >
> > 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
> > --
> > 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

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