[gmx-users] Gromacs-4.6 on two Titans GPUs

[Richard Broadbent]

Dear James,

On 05/11/13 11:16, James Starlight wrote:
> My suggestions:
>
> 1) During compilstion using -march=corei7-avx-i I have obtained error that
> somethng now found ( sorry I didnt save log) so I compile gromacs without
> this flag
>
> 2) I have twice as better performance using just 1 gpu by means of
>
> mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test
>
> than using of both gpus
>
> mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test
>
> in the last case I have obtained warning
>
> WARNING: Oversubscribing the available 12 logical CPU cores with 24 threads.
>           This will cause considerable performance loss!
>
here you are requesting 2 thread mpi processes each with 12 openmp 
threads, hence a total of 24 threads however even with hyper threading 
enabled there are only 12 threads on your machine. Therefore, only 
allocate 12. Try

mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test

or even

mdrun -v  -deffnm md_CaM_test

I believe it should autodetect the GPUs and run accordingly for details 
of how to use gromacs with mpi/thread mpi openmp and GPUs see

http://www.gromacs.org/Documentation/Acceleration_and_parallelization

Which describes how to use these systems

Richard

> How it could be fixed?
> All gpu are recognized correctly
>
>
> 2 GPUs detected:
>    #0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
> compatible
>    #1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
> compatible
>
>
> James
>
>
> 2013/11/4 Szilárd Páll <pall.szilard at gmail.com>
>
>> You can use the "-march=native" flag with gcc to optimize for the CPU
>> your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
>> CPUs.
>> --
>> Szilárd Páll
>>
>>
>> On Mon, Nov 4, 2013 at 12:37 PM, James Starlight <jmsstarlight at gmail.com>
>> wrote:
>>> Szilárd, thanks for suggestion!
>>>
>>> What kind of CPU optimisation should I take into account assumint that
>> I'm
>>> using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12
>>> nodes in Debian).
>>>
>>> James
>>>
>>>
>>> 2013/11/4 Szilárd Páll <pall.szilard at gmail.com>
>>>
>>>> That should be enough. You may want to use the -march (or equivalent)
>>>> compiler flag for CPU optimization.
>>>>
>>>> Cheers,
>>>> --
>>>> Szilárd Páll
>>>>
>>>>
>>>> On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <
>> jmsstarlight at gmail.com>
>>>> wrote:
>>>>> Dear Gromacs Users!
>>>>>
>>>>> I'd like to compile lattest 4.6 Gromacs with native GPU supporting on
>> my
>>>> i7
>>>>> cpu with dual GeForces Titans gpu mounted. With this config I'd like
>> to
>>>>> perform simulations using cpu as well as both gpus simultaneously.
>>>>>
>>>>> What flags besides
>>>>>
>>>>> cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5
>>>>>
>>>>>
>>>>> should I define to CMAKE for compiling optimized gromacs on such
>>>> workstation?
>>>>>
>>>>>
>>>>> Thanks for help
>>>>>
>>>>> James
>>>>> --
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