[gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 3:25 PM Stefano Guglielmo
<stefano.guglielmo at unito.it> wrote:
>
>  Hi Szilard,
> thanks for your reply.
> The compiler is gcc 4.8.5.

That is ancient. From your cmake.out:

-- Detection for best SIMD instructions failed, using SIMD - None
-- SIMD instructions disabled

Update your compiler toolchain to a modern compiler (e.g. gcc 8),
you'll also get much better performance.

Cheers,
--
Szilárd

> 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
> --
> Gromacs Users mailing list
>
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