[gmx-users] gromacs on GPU

[James Starlight]

I've solved previous problem but havent been able to launch
mdrun-openmm. Below you can find mdrun's output

Back Off! I just backed up md_test.log to ./#md_test.log.3#
Reading file md_test.tpr, VERSION 4.6-beta3 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.146

Compiled acceleration: None (Gromacs could use AVX_256 on this
machine, which is better)

1 GPU detected:
  #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC:  no, stat: compatible

1 GPU auto-selected to be used for this run: #0

Program mdrun-openmm, VERSION 4.6-beta3
Source code file:
/home/own/gromacs-4.6-beta3/src/kernel/openmm_wrapper.cpp, line: 1367

Fatal error:
OpenMM exception caught while initializating: Error setting device
flags cannot set while device is active in this process
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I'm still using cuda-5-toolkit with the 304.54 driver. Also my
question about openCL is still valid. I've browesed manual but didnt
found how I can compile gromacs with openCL instead of Cuda. On openMM
group developers told me that openCL would give much performance for
gpu-accelerated simulation in comparison to the CUDA.

James

2013/1/9 James Starlight <jmsstarlight at gmail.com>:
> As I understood that gromacs version already has included openMM so
> the installation of the external openMM sources is not needed, isnt it
> ?
>
> also I wounder to know what exactly CUDA version is needed ? For
> example I've tried lattest cuda-5.0 but with that version i've obtain
> error from mdrun-openmm that platform cuda was not detected (gromacs
> was compilated without any errors). I've seen that erorr in other
> posts in the mailing list but could not found any possible sollutions.
>
> by the way is it possible to compilate gromacs-4.6 agains other
> platgorm ( e.g openCL) ? I have no problems with the compatibility of
> the openCL and openMM.
>
> James
>
> 2013/1/9 Szilárd Páll <szilard.pall at cbr.su.se>:
>> On Tue, Jan 8, 2013 at 3:22 PM, James Starlight <jmsstarlight at gmail.com>wrote:
>>
>>> So could someone provide me more about gpu-accelerated MD implemented
>>> in the 4.6 gromacs ? Does it require openMM (what version is supported
>>>
>>
>> FYI, if nobody can, trust G:
>> http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
>> http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
>>
>> The wiki and mailing list contains quite extensive information (indexed by
>> G).
>>
>> Otherwise, release notes (not final):
>> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
>>
>> Install guide is at the expected location:
>> http://www.gromacs.org/Documentation/Installation_Instructions
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>> for that gromacs release ?) installed? By the way at present time I
>>> force with the problem of compilation 4.1.1 openMM (i need to compile
>>> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
>>> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
>>>
>>>
>>> James
>>>
>>> 2013/1/7 James Starlight <jmsstarlight at gmail.com>:
>>> > Hi Szilárd!
>>> >
>>> > As I understood you correctly gromacs-4.6 have specific algorithm
>>> > (independent on openMM?) for gpu-based calculations havent ? If it
>>> > true how I should compilate such new gpu-based gromacs? In the
>>> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
>>> > installation via cmake
>>> >
>>> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>>> >
>>> >
>>> > James
>>> >
>>> > 2013/1/7 Szilárd Páll <szilard.pall at cbr.su.se>:
>>> >> Szilárd
>>> --
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