[gmx-users] Gromacs 2018 and GPU

[paul buscemi]

Mark

Yes, it was your suggestions that finally set me on the right $PATH.  The examples and analyses work as intended.  
Thanks
Paul

> On May 6, 2018, at 2:24 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> I already referred you to the install guide for ideas on how to access the
> version of GROMACS that you want. Did you look there?
> 
> Mark
> 
> On Sun, May 6, 2018, 02:52 paul buscemi <pbuscemi at q.com> 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 ?
>> 
>> thanks for your help
>> Paul
>> 
>> 
>>> On May 5, 2018, at 12:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>> 
>>> Hi,
>>> 
>>> It's also GROMACS 5.1.2 not the 2018 you reported trying to install. You
>>> need to make sure your terminal has been given access to the GROMACS that
>>> you want to use (see that part of the install guode.).
>>> 
>>> Also, your CMake line tried to use OpenCL which is not what you want for
>>> running on an Nvidia GPU (even though you can get it to work).
>>> 
>>> Mark
>>> 
>>> On Sat, May 5, 2018, 00:55 Justin Lemkul <jalemkul at vt.edu> wrote:
>>> 
>>>> 
>>>> 
>>>> On 5/4/18 6:53 PM, paul buscemi wrote:
>>>>> Justin,
>>>>> 
>>>>> Here is the install script  and a snippit from the log file .
>>>>> 
>>>>> Gromacs runs normally with this ( fresh ) install but without GPU use
>>>>> 
>>>>> Paul
>>>>> 
>>>>> cmake .. -DGMX_BUILD_OWN_FFTW=ON \
>>>>>             -DGMX_GPU=on   \
>>>>>             -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit \
>>>>>            -DGMX_USE_OPENCL=on
>>>>> 
>>>>> Command line:
>>>>>  gmx mdrun -deffnm md_0_1
>>>>> 
>>>>> GROMACS version:    VERSION 5.1.2
>>>>> Precision:          single
>>>>> Memory model:       64 bit
>>>>> MPI library:        thread_mpi
>>>>> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
>>>>> GPU support:        disabled
>>>> 
>>>> Well, here's what you need to know. Something failed in trying to enable
>>>> GPU acceleration. Take a look at the cmake output.
>>>> 
>>>> -Justin
>>>> 
>>>> --
>>>> ==================================================
>>>> 
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>> 
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>> 
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>> 
>>>> ==================================================
>>>> 
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