[gmx-users] (cross-)compiling mdrun independently from the rest of gromacs tools

Vedat Durmaz vedat.durmaz at gmx.net
Mon Mar 25 14:28:04 CET 2019

hi guys,

according to the gromacs installation instructions (i think a saw it
it could make sense to compile gromacs mdrun independently from the
other gromacs tools in order to have a cross-compiled installation
working with compiler optimization flags.

i am compiling gromacs inside a singularity container on a local machine
and running it on a cluster. it works fine, but since i want to use high
level compiler flags for simulation optimization (e.g. AVX_256) which is
not available on the login nodes where i want to (need to) run commands
such as editconf, solvate, etc., but available on the cluster nodes
where mdrun is executed, i indeed need to compile mdrun independently
from the rest. i just don't know how exactly to achieve that. currently,
i'm compiling in two stages (non-mpi and mpi version) inside the container:

GMXVSN="gromacs-2018.1" #"gromacs-5.1.2"

## first round (without MPI)
tar xzf ${GMXVSN}.tar.gz
mv ${GMXVSN} ${GMXVSN}_src
mkdir ${GMXVSN}
cd ${GMXVSN}_src
mkdir build && cd build
make install
rm -r ${GMXVSN}_src
mv ${GMXVSN} ${GMXVSN}_BAK    # backup install dir

## second round (with MPI)
tar xzf ${GMXVSN}.tar.gz
mv ${GMXVSN} ${GMXVSN}_src
mv ${GMXVSN}_BAK ${GMXVSN}    # restore install dir to put in mdrun_mpi
cd ${GMXVSN}_src
mkdir build && cd build
make install

would some expert please give me an as concrete as possible hint, where
to put which modification in order to have mdrun compiled separately
(with AVX_256) from the other tools?

many thanks in advance & best wishes


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