[gmx-users] gromacs installation

[Wes Barnett]

On Thu, Sep 7, 2017 at 3:25 PM, vijayakumar gosu <vijayakumargosu at gmail.com>
wrote:

> Hi,
>
> I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus.
> I am allotted to use only 2 nodes with 80 cpus. after installation when i
> did sample md run only 20 cpus are being utilized. How can I fully utilize
> the all 80 CPUs for mdrun.
>
> I have used below cmake command for the installation
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
> -DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> -DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs
>
> I have not seen any errors during installation.
>

You should go ahead and just install 2016.3 instead of 5.1.

What is your exact command when you run mdrun?

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu
http://wbarnett.us