[gmx-users] Fwd: SIMD options

[Szilárd Páll]

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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