[gmx-users] Gromacs 2018 and GPU

[paul buscemi]

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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