[gmx-users] Force GROMACS 5.0 to use GPU
nizar.fkub08 at gmail.com
Fri Jul 18 15:52:38 CEST 2014
On Jul 17, 2014, at 15:10, Nizar <nizar.fkub08 at gmail.com> wrote:
> On Jul 14, 2014, at 15:57, Mirco Wahab <mirco.wahab at chemie.tu-freiberg.de> wrote:
>> On 14.07.2014 10:21, Nizar wrote:
>>> Can I force GROMACS 5.0 to use both CPU and GPU?
>>>> Afaik unfortunately not.
>>>>>> I thought it could be forced as GROMACS 4.5.x did
>>> I simulate a protein using GROMACS 5.0 installed on old Macbook Pro Mid-2009 having 2,26 Core2Duo Proc and NVIDIA GeForce 9400M supporting CUDA technology. My GPU, however has computing ability of 1.1, where GROMACS 5.0 requires CUDA-capable GPU with computing ability of 2.0.
>>> I tried to use GPU by using verlet cut-off scheme. GOMACS exactly recognised my GPU. However, GROMACS said that my GPU was incompatible as it has only computing ability of 1.1.
>>> I need to use all my macbook resources optimally. Using 1 core was painfully slow as i spent 3 weeks to completely simulate a protein having 40.000 atoms. I wish i could take 4-5 days if GROMACS use 2 cores of CPU and CUDA-capable GPU.
>>>> Gromacs can't be expected to run reasonably fast on low-performance
>>>> components. I think you could make very good use of your laptop if
>>>> you use it for input-file creation, short test runs and data
>>>> presentation. For long runs, I'd generally would not recommend
>>>> laptops because they aren't built for this (heat generation,
>>>> component lifetime).
>>>> I tried to look up some cheap components but it looks like
>>>> in your country modern (haswell) i5 processors and corresponding
>>>> socket 1150 mainboards aren't readily available so far.
>>>> If that's the case, you could try to get parts for a older
>>>> socket 1155-system (e.g. ASRock B75M mainboard, i5-3570
>>>> processor, 2 x 2GB DDR3 RAM) combined with a more modern
>>>> graphics card (Geforce GTX 760 2GB). Build this box,
>>>> install Linux on it (small, cheap harddisk will suffice)
>>>> and use it for simulations.
>>>> But these are wild guesses only, I don't really know how affordable
>>>> hardware is in your country - I tried to give you some idea of what
>>>> possibly to do next.
>>>>>> Haswell has already been available Indonesia. I actually want to build a computer after this project is done, but I thought It can’t wait. My Configuration is the following: quad core intel i7-4770K, GTX 650 Ti, 2x4 GB ddr3 on ASRock Z87E-miniITX, PSU seasonic gold 360W.
>>>>>> My question: 1) Can I use over clocking on GROMACS? If not I’d rather to downgrade my spec to i7-4930k on a cheaper ASRock H87M and save money for a better GPU
>>>>>> 2) which GPU that GROMACS prefer? One having more CUDA cores or one having higher computing ability. If CUDA core is more important, then i’d rather prefer choosing GTX 650 Ti as it has more cuds cores than GTX 750. If computing ability is more important, then i’d rather prefer buying GTX 750 as it has higher computing ability than GTX 650Ti
>> M. Wahab
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> My best regards, Nizar
> Medical Faculty of Brawijaya University, Indonesia
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