[gmx-users] Problems with TI on GPUs

[Yannic Alber]

Hi,

In short, this works for every combination. But with the big disadvantage
of being very slow and not using our precious little gpu´s.

Thanks for your fast reply Mark.

> Hi,
>
> What happens in your failing cases (or even all of them) when adding -nb
> cpu, to force the run off the GPU?
>
> Mark
>
> On Tue, 12 Jul 2016 19:02 Yannic Alber <yannic.alber at tu-dortmund.de>
> wrote:
>
>> Dear all,
>>
>> we struggle to get a TI on our computer running. The specifications are
>> listed below. As you can see, its a two socket, two graphics cards
>> machine. Therefore, the plan is to run two simulations in parallel. But
>> we
>> can't get a single one to run.
>>
>> Running on 1 node with total 20 cores, 20 logical cores, 2 compatible
>> GPUs
>> Hardware detected:
>>   CPU info:
>>     Vendor: GenuineIntel
>>     Brand:  Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
>>     SIMD instructions most likely to fit this hardware: AVX2_256
>>     SIMD instructions selected at GROMACS compile time: AVX2_256
>>   GPU info:
>>     Number of GPUs detected: 2
>>     #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat:
>> compatible
>>     #1: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat:
>> compatible
>>
>> The simulation system in question is a protein-ligand-complex in
>> TIP3P-water and amber ff99SB as force field.
>>
>> Now lets get into the messy details. We tried different mdrun
>> commandline
>> argument rotations, for example:
>>
>> gmx mdrun -s md.tpr -pin on -ntomp 2 -ntmpi 5 -gpu_id 00000 -deffnm md
>> (does not work)
>> gmx mdrun -s md.tpr -pin on -ntomp 5 -ntmpi 2 -gpu_id 00 -deffnm md
>> (does not work)
>> gmx mdrun -s md.tpr -pin on -ntomp 10 -ntmpi 1 -gpu_id 0 -deffnm md
>> (does not work)
>> gmx mdrun -s md.tpr -deffnm md
>> (does work, uses the complete compute node including the both gpu´s)
>>
>> The error which gromacs gives us, is rather irritating (explanation
>> follows further down). Here a little excerpt:
>>
>> Step 191, time 0.382 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000002, max 0.000010 (between atoms 3421 and 3424)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>    3702   3703   31.0    0.1090   0.1090      0.1090
>> Wrote pdb files with previous and current coordinates
>>
>> These errors vary, but refer all to a misplacement or unusual rotations.
>> Gromacs states, that this is because of our "unstable" system. However,
>> this explanation can be excluded, because the starting configuration of
>> the
>> simulations in question already ran 20 ns in gromacs on a CPU-Cluster.
>>
>> We also tested different commands for cmake. A example is shown here:
>>
>> cmake .. -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DGMX_GPU=on
>> -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=ON
>> -DREGRESSIONTEST_DOWNLOAD=ON
>>
>> Compilerwise we tried gcc (v.4.8.5) and intel (v.15.0.1).
>>
>> I would really appreciate your help and thank you very much in advance.
>>
>>
>> Sincerely,
>> Yannic
>>
>>
>>
>>
>>
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>