Installation on Snellius

Snellius

2022 toolchain

module load 2022
module load foss/2022a
module load netCDF-Fortran/4.6.0-gompi-2022a
module load CMake/3.23.1-GCCcore-11.3.0
# module load Hypre/2.25.0-foss-2022a # optional

mkdir build
cd build
export SYST=gnu-fast
cmake .. -DUSE_FFTW=True
# or, for single precision:
# cmake .. -DUSE_FFTW=True -DFIELD_PRECISION=32 -DPOIS_PRECISION=32

make -j 8

2021 toolchain

Tested Nov 2021, 48h RICO test successful. Further tuning for the AMD architecture also see this compiler options document

module load 2021
module load foss/2021a
# module load FFTW/3.3.9-gompi-2021a # included in foss
module load netCDF-Fortran/4.5.3-gompi-2021a
module load CMake/3.20.1-GCCcore-10.3.0
# module load Hypre/2.21.0-foss-2021a # optional

mkdir build
cd build
export SYST=gnu-fast
cmake .. -DUSE_FFTW=True
make -j 8

job script:

#!/bin/bash
# uses 1/4 of a node
#SBATCH --nodes=1
#SBATCH --ntasks=32
#SBATCH --partition=thin
#SBATCH --time=01:00:00

# Other useful SBATCH options
# #SBATCH --ntasks-per-node=16

module load 2021
module load foss/2021a
module load netCDF-Fortran/4.5.3-gompi-2021a
module load CMake/3.20.1-GCCcore-10.3.0
# module load Hypre/2.21.0-foss-2021a # optional

NAMOPTIONS=namoptions-144.001
DALES=/home/janssonf/snellius/build/src/dales4.3
CASE=`pwd`
WORK=run-1

mkdir -p $WORK
cd $WORK
cp $CASE/{lscale.inp.001,$NAMOPTIONS,prof.inp.001,scalar.inp.001} ./

echo DALES $DALES
echo CASE $CASE
echo WORK $WORK
echo hostname `hostname`

srun $DALES $NAMOPTIONS | tee output.txt

Intel toolchain (WIP, compiles, not tested)

Locally install missing netCDF modules (instructions from https://github.com/microhh/microhh/issues/73):

module load 2021
module load eb/4.4.2

# eb -S netcdf  # search for packages

eblocalinstall netCDF-4.8.0-iimpi-2021a.eb
eblocalinstall netCDF-Fortran-4.5.3-iimpi-2021a.eb

module load 2021
module load intel/2021a
module load FFTW/3.3.9-intel-2021a # optional
module load CMake/3.20.1-GCCcore-10.3.0
module load netCDF-Fortran/4.5.3-iimpi-2021a  # locally installed above
# no Hypre-intel module available in easybuild for 2021a

# Compiler must me invoked as mpiifort because mpif90 is gfortran
# choosing SYST=lisa-intel which invokes mpiifort and has the optimization option -xHost

mkdir build-intel
cd build-intel/
export SYST=lisa-intel
cmake .. -DUSE_FFTW=True
make -j 8