[gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

 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