nemo

Information about nemo.

Building GPAW

We assume that the installation will be located in $HOME/source.

Setups

The setups of your choice must be installed (see also Installation of PAW datasets):

cd
GPAW_SETUP_SOURCE=$PWD/source/gpaw-setups
mkdir -p $GPAW_SETUP_SOURCE
cd $GPAW_SETUP_SOURCE
wget https://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-0.9.11271.tar.gz
tar xzf gpaw-setups-0.9.11271.tar.gz

Let gpaw know about the setups:

export GPAW_SETUP_PATH=$GPAW_SETUP_SOURCE/gpaw-setups-0.9.11271

Using the module environment

It is very handy to add our installation to the module environment:

cd
mkdir -p modulefiles/gpaw-setups
cd modulefiles/gpaw-setups
echo -e "#%Module1.0\nprepend-path       GPAW_SETUP_PATH    $GPAW_SETUP_SOURCE/gpaw-setups-0.9.11271" > 0.9.11271

We need to let the system know about our modules (add this command to ~/.profile or ~/.bashrc to execute automatically):

module use $HOME/modulefiles

such that we also see them with:

module avail

libxc

GPAW relies on libxc (see the libxc web site). To install libxc we assume that MYLIBXCDIR is set to the directory where you want to install (e.g. MYLIBXCDIR=$HOME/source/libxc):

mkdir -p $MYLIBXCDIR
cd $MYLIBXCDIR
wget https://www.tddft.org/programs/libxc/down.php?file=5.2.2/libxc-5.2.2.tar.gz -O libxc-5.2.2.tar.gz
tar xvzf libxc-5.2.2.tar.gz
cd libxc-5.2.2
mkdir install
module purge
module load compiler/gnu
./configure CFLAGS="-fPIC" --prefix=$PWD/install -enable-shared
make |tee make.log
make install

This will have installed the libs $MYLIBXCDIR/libxc-5.2.2/install/lib and the C header files to $MYLIBXCDIR/libxc-5.2.2/install/include. We create a module for libxc:

cd
mkdir modulefiles/libxc
cd modulefiles/libxc

and edit the module file 5.2.2 that should read:

#%Module1.0

#                                    change this to your path
set             source               $::env(HOME)/source
set             libxchome            $source/libxc/libxc-5.2.2/install
prepend-path    C_INCLUDE_PATH       $libxchome/include
prepend-path    LIBRARY_PATH         $libxchome/lib
prepend-path    LD_LIBRARY_PATH      $libxchome/lib

ASE release

You might want to install a stable version of ASE:

cd
ASE_SOURCE=$PWD/source/ase
mkdir -p $ASE_SOURCE
cd $ASE_SOURCE
git clone -b 3.18.1 https://gitlab.com/ase/ase.git 3.18.1

We add our installation to the module environment:

cd
mkdir -p modulefiles/ase
cd modulefiles/ase

Edit the module file 3.18.1 that should read:

#%Module1.0

devel/python/3.7.10

#           change this to your path
set source $::env(HOME)/source
set asehome $source/ase/3.18.1
prepend-path       PYTHONPATH    $asehome
prepend-path       PATH          $asehome/tools

ASE origin

We get ASE origin:

cd
ASE_SOURCE=$PWD/source/ase
mkdir -p $ASE_SOURCE
cd $ASE_SOURCE
git clone https://gitlab.com/ase/ase.git origin

which can be updated using:

cd $ASE_SOURCE/origin
git pull

We add our installation to the module environment:

cd
mkdir -p modulefiles/ase
cd modulefiles/ase

and edit the module file origin that should read:

#%Module1.0

devel/python/3.7.10

#           change this to your path
set source $::env(HOME)/source
set asehome $source/ase/origin
prepend-path       PYTHONPATH    $asehome
prepend-path       PATH          $asehome/tools

Building GPAW

We create a place for gpaw and get the origin version:

cd
GPAW_SOURCE=$PWD/source/gpaw
mkdir -p $GPAW_SOURCE
cd $GPAW_SOURCE
git clone https://gitlab.com/gpaw/gpaw.git origin

The current origin version can then be updated by:

cd $GPAW_SOURCE/origin
git pull

A specific tag can be loaded by:

cd $GPAW_SOURCE/origin
# list tags
git tag
# load version 1.2.0
git checkout 1.2.0

To build the current origin version of GPAW we need to create a file siteconfig.py that reads

# necessary MKL libs
libraries += ['mkl_intel_lp64', 'mkl_sequential', 'mkl_core', 'svml']
# Now add a EasyBuild "cover-all-bases" library_dirs
library_dirs = os.getenv('LD_LIBRARY_PATH').split(':')

Then we build the executable:

module purge
module load libxc
module load compiler/intel
module load mpi/impi
module load numlib/mkl
module load ase

cd $GPAW_SOURCE/origin
unset CC
python3 setup.py build

which builds GPAW to $GPAW_SOURCE/origin/build. We create a module that creates the necessary definitions:

cd
mkdir -p modulefiles/gpaw
cd modulefiles/gpaw

The file origin that should read:

#%Module1.0

if {![is-loaded ase]} {module load ase}
if {![is-loaded libxc]} {module load libxc}
if {![is-loaded mpi]}  {module load mpi/impi}
if {![is-loaded gpaw-setups]}  {module load gpaw-setups}

# change the following directory definition to your needs
set source $::env(HOME)/source
set gpawhome $source/gpaw/origin
 # this can stay as is
prepend-path    PATH                 $gpawhome/tools:$gpawhome/build/scripts-3.7
prepend-path    PYTHONPATH           $gpawhome:$gpawhome/build/lib.linux-x86_64-3.7

Running GPAW

A gpaw script test.py can be submitted with the help of gpaw-runscript to run on 20 cpus like this:

> module load gpaw
> gpaw-runscript test.py 20
using nemo
run.nemo written
> msub run.nemo

See options of gpaw-runscript with:

> gpaw-runscript -h