> I have two GTX1080s (EVGA ACX3.0) running amber and the key is to ensure
you apply update 6, which came out last week.
> Without update 6, you will get the error : "cudaMemcpyToSymbol: SetSim
copy to cSim failed invalid device symbol"
Thanks! This worked for me.
In terms of my performance I benchmark with a custom ~13,000 atom system
with 2 fs steps and 8 A cutoff. The GTX980Ti would give ~256 ns/day while
the GTX1080 gives ~330 ns/day.
On Thu, Jun 23, 2016 at 4:49 PM, Beavil, Andrew <andrew.beavil.kcl.ac.uk>
wrote:
>
> I have two GTX1080s (EVGA ACX3.0) running amber and the key is to ensure
> you apply update 6, which came out last week.
>
> Without update 6, you will get the error : "cudaMemcpyToSymbol: SetSim
> copy to cSim failed invalid device symbol"
>
>
>
> I’m using : Amber16/Cuda8.0RC/Nvidia driver 367.27 on Centos 7
>
>
>
> it’s probably best to use ‘make distclean’ before running configure as
> that cleans out old half compiled junk and forces the updates to be applied.
>
>
>
> The one remaining issue I’m having is that the 367.27 driver (which is
> needed for the GTX1080s) doesn’t seem to support ‘exclusive process’ mode
> i.e., 'nvidia-smi -c 3’ - they two cards work fine if I use ‘export
> CUDA_VISIBLE_DEVICES=...'
>
>
>
> In terms of performance, for a system similar in size to the DHFR
> benchmark, running NTP MD with 2fs steps & 10A cutoff I get
>
> ~110 ns/day on a GTX980
>
> ~135ns/day on GTX980ti
>
> ~170ns/day on GTX1080
>
>
>
> performance drops slightly if both cards are running at the same time
> because the physically lower card heats the higher one somewhat.
>
> Although the performance boost is welcome, the thing I like most is that
> you can control the power usage of these cards and if I set the GTX1080 to
> 120watts, I get ~150ns/day (similar but better than the GTX980ti) for only
> half the power consumption of the GTX980ti.
>
> [it makes for a cooler and quieter office!]
>
> [the cards run at 1900MHz flat out ~165watts or 1500MHz 90watts - 120watts
> seems a sensible compromise and leads to ~1800Mhz]
>
>
>
> Does anyone have experience of the founders edition cards and are they
> better at pushing heat out of the back of the system ?
>
> ie less heating of neighbouring cards ?
>
>
>
> Best wishes,
>
>
>
> Andrew Beavil
>
>
>
>
>
> -------------------------------------------------------------------------
>
> Dr. Andrew J. Beavil, Phone: (+44) (0)20 78488064
>
> Senior Lecturer in Molecular Biophysics Fax : (+44) (0)20 78486410
>
>
>
>
>
>
>
> MRC & Asthma UK Centre in Allergic Mechanisms of Asthma
>
> King's College London,
>
> The Randall Division,
>
> New Hunt's House, Email: andrew.beavil.kcl.ac.uk
> <mailto:andrew.beavil.kcl.ac.uk>
>
> Guy's Campus,
>
> London Bridge,
>
> London. SE1 1UL
>
> -------------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Date: Thu, 23 Jun 2016 10:35:33 -0400
>
> From: Zack Scholl <zns.duke.edu<mailto:zns.duke.edu>>
>
> Subject: Re: [AMBER] AMBER support for gtx1080
>
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
>
> Message-ID:
>
> <CAH7kaX=e+C684h47UJh-99x624rs7pO-NVvhdW_Kd-9qEbG-Zg.mail.gmail.com
> <mailto:CAH7kaX=e+C684h47UJh-99x624rs7pO-NVvhdW_Kd-9qEbG-Zg.mail.gmail.com
> >>
>
> Content-Type: text/plain; charset=UTF-8
>
>
>
> In our lab we upgraded to GTX1080 from GTX980Ti and we are indeed seeing
>
> about 30% improvement. Make sure you have Amber16 and CUDA-8.0 (the
>
> developer version). Also be aware you might have to get new drivers (we're
>
> using RHEL 7 and the card wouldn't load on the system until we updated
>
> them). You can download CUDA8.0 and get the new drivers here:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__developer.nvidia.com_cuda-2Dtoolkit&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=FP2fpv7m5EE7ig51Epdhkg&m=BHsb8Cu33zV49trr__ffTkVWGdKW-awaTBPJyZc88lQ&s=W5V0WcHHC_CtHQdaHDzNCiuQx82pFPWem22LmrnI3k0&e=
> .
>
>
>
> Currently I'm a little worried something is wrong with the GTX1080 with
>
> AMBER16. Though it initially worked for me, it has since failed every
>
> simulation saying simply "cudaMemcpyToSymbol: SetSim copy to cSim failed
>
> invalid device symbol". Reinstalling Amber16 has not succeeded in fixing
>
> this error. I'd be curious if you or anyone else has run into this. I will
>
> try to reinstall CUDA8.0 to see if that is a possible fix, but I can't
>
> think of a way to reset the system beyond that (except reinstalling the OS
>
> I suppose!). If I keep running into this I'd probably suggest getting a
>
> GTX980Ti until the GTX1080 system is more stable.
>
> --
>
>
>
>
>
> _______________________________________________
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>
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>
--
---------------------------------------------
Zackary N. Scholl, Ph.D.
Duke University
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Received on Wed Jun 29 2016 - 12:30:05 PDT
