[gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

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.

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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