[gmx-users] Installing gmx 5.0.5 in mpi

[Mark Abraham]

Hi,

On Mon, Jul 13, 2015 at 4:31 AM Raju <rajiv at kaist.ac.kr> wrote:

> Dear gmx users,
>
>
> I have a 24 HPC with gtx 980ti of PC and wants to install gmx 5.0.5.
>
>
> I was able to install by configuring cuda and openmpi but when i use the
> following the commands the installation wents sucfess but they only working
> with adding mpi.
>
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> -DGMX_GPU=ON
>
>
>
>
> "which gmx" shows no gmx in but "which gmx_mpi"
> /usr/local/gromacs/bin/gmx_mpi
>
>
> I wonder is that a right way that i installed or i have reconfigured in
> other way?
>

This is normal, see
http://www.gromacs.org/Documentation/Installation_Instructions_5.0#changing-the-names-of-gromacs-binaries-and-libraries


> I am installing mpi as i wants to run 2 or 3 simulation in single PC
> contains 24 HPC processor.
>
>
> Its much appreciated if you can provide the best configuration to run gmx
> in best way, Thanks.
>

For running within a single node, you normally don't need MPI, because
GROMACS comes with its own "thread-MPI" for use within a single node. But
if you want to run several of the same kind of job within a node
like
http://manual.gromacs.org/documentation/5.1-rc1/user-guide/mdrun-features.html#running-multi-simulations
then configuring with external MPI is necessary. If you want the freedom to
run multiple mdrun on the same node independently, this is possible, but
you will have to take care of your own details of assigning a
non-overlapping subset of CPU cores to each simulation and setting the
affinity of those jobs threads to those cores. Some details at
http://manual.gromacs.org/documentation/5.1-rc1/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node

Mark

Regards
>
>
> Raju
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