[gmx-users] gromacs on GPU

[Szilárd Páll]

On Wed, Jan 9, 2013 at 10:27 AM, James Starlight <jmsstarlight at gmail.com>wrote:

> 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)
>

Have you set the CPU acceleration manually to "None"? If you did *don't* do
that, let the build system pick what's best for you. However, if you did
not do that, there is some issue with our auto-detection; a log file as a
start would possibly help in identifying the issue.


>
> 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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