[gmx-users] Gromacs 2018 and GPU

[Justin Lemkul]

On 5/5/18 8:51 PM, paul buscemi wrote:
> Mark, Justin
>
> I was able to access the GPU  using simply :
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON \
>           -DREGRESSIONTEST_DOWNLOAD=ON \
>           -DGMX_MPI=on \
>           -DGMX_GPU=on
>
> the result for the lysozyme MD run ( with the appropriate quote ) was:
>
>
>                       Core t (s)   Wall t (s)        (%)
>         Time:      281.756       35.220      800.0
>                             (ns/day)    (hour/ns)
> Performance:      245.323        0.098
>
> GROMACS reminds you: "You still have to climb to the shoulders of the giants" (Vedran Miletic)
>
>
> You were correct, the problem was that the tutorial was accessing an earlier install  of gromacs 5.1
> and I had to access gmx-2018 MD by adding the path to the mdrun command
>
> /home/rgb/Desktop/gromacs-gpu-2018/build/bin/gmx mdrun -deffnm md_0_1
>
> which is not ideal. This is more of a linux question, but can you suggest a way to clean up older installations, or is it sufficient to
> ensure the PATH points to the correct version ?

Either:

1. Remove the old installation and replace with the version you want
2. Adjust your PATH
3. source the appropriate GMXRC when starting your work

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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