[gmx-users] About gpu

[Mark Abraham]

On Thu, Apr 11, 2013 at 8:14 AM, 陈照云 <chenzhaoyun06 at gmail.com> wrote:

> I have tested gromacs-4.6.1 with k20. But when I run the mdrun, I met some
> problems.
>
> 1.Configure options are -DGMX_MPI=ON ,-DGMX_DOUBLE=ON -DGMX_GPU=OFF .
>
> But if I run parallely with mpirun, it would get wrong.
>
> "Note: file tpx version 58, software tpx version 83
>

You've prepared your input file with some ancient version of grompp and run
into problems with a modern version of mdrun trying to run on hardware that
didn't exist when the code for your version of grompp was compiled. That's
expected. Use a matching version of grompp.


>
> Fatal error in PMPI_Bcast: Invalid buffer pointer, error stack:
>
> PMPI_Bcast(2011): MPI_Bcast(buf=(nil), count=56, MPI_BYTE, root=0,
> MPI_COMM_WORLD) failed
>
> PMPI_Bcast(1919): Null buffer pointer
>
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
>
> "
>
> 2. Configure options are -DGMX_MPI=ON ,-DGMX_GPU=ON -DGMX_DOUBLE=OFF . But
> if I run with gpu, the program would get wrong.
>
> run one process with gpu:
>
> "Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single
> precision)
>
> Note: file tpx version 73, software tpx version 83
>

Same. And this beta version of GROMACS 4.5.1 should have been deleted in
October 2010. There is no excuse for using it now with 4.6.1!

Mark

NOTE: GPU(s) found, but the current simulation can not use GPUs
>
> To use a GPU, set the mdp option: cutoff-scheme = Verlet
>
> (for quick performance testing you can use the -testverlet option)
>
> Using 1 MPI process
>
> 1 GPU detected on host node11:
>
> #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible
>
> Back Off! I just backed up ener.edr to ./#ener.edr.4#
>
> starting mdrun 'Protein'
>
> -1 steps, infinite ps.
>
> Segmentation Fault (core dumped)
>
> run eight processes with gpu:
>
> Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
>
> Note: file tpx version 73, software tpx version 83
>
> NOTE: GPU(s) found, but the current simulation can not use GPUs
>
> To use a GPU, set the mdp option: cutoff-scheme = Verlet
>
> (for quick performance testing you can use the -testverlet option)
>
> Non-default thread affinity set, disabling internal thread affinity
>
> Using 8 MPI processes
>
> 1 GPU detected on host node11:
>
> #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible
>
> Back Off! I just backed up ener.edr to ./#ener.edr.6#
>
> starting mdrun 'Protein'
>
> -1 steps, infinite ps.
>
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)"
>
> Thanks for your help!
> --
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