254 lines
7.2 KiB
Modula-2
254 lines
7.2 KiB
Modula-2
###########################################################################
|
|
###########################################################################
|
|
##
|
|
## Apptainer Build File: Skyply
|
|
## Function: Fully-integrated Simulation stack for WRF, CMAQ, & SCICHEM
|
|
##
|
|
## Documentation:
|
|
##
|
|
###########################################################################
|
|
###########################################################################
|
|
|
|
Bootstrap: localimage
|
|
From: base.sif
|
|
|
|
%labels
|
|
Author HPCStack
|
|
Version 1.0
|
|
Description "Rocky 9 base with development tools for WRF/CMAQ"
|
|
|
|
%files
|
|
/mnt/src/* /opt/src
|
|
|
|
%post
|
|
# ---------------------- Define Relevant Paths and Settings ------------------
|
|
export HPC_PATH=/opt/hpc
|
|
export MODEL_PATH=/opt/models
|
|
export SOURCE_PATH=/opt/src
|
|
|
|
export MPI_HOME=$HPC_PATH/mpi
|
|
export HDF5=$HPC_PATH/hdf5
|
|
export NETCDF=$HPC_PATH/netcdf
|
|
export IOAPI=$HPC_PATH/ioapi
|
|
|
|
export PATH=$MPI_HOME/bin:$NETCDF/bin:$PATH
|
|
export LD_LIBRARY_PATH=$MPI_HOME/lib:$HDF5/lib:$NETCDF/lib:$LD_LIBRARY_PATH
|
|
|
|
# ---------------------- Build OpenMPI ------------------
|
|
cd ${SOURCE_PATH}/openmpi
|
|
TAR_FILE=$(ls -1t *.tar.gz *.tgz 2>/dev/null | head -n1 || true)
|
|
if [ -n "$TAR_FILE" ]; then
|
|
tar -xzf "$TAR_FILE"
|
|
TOP_DIR=$(tar -tf "$TAR_FILE" | sed -n '1p' | cut -f1 -d"/")
|
|
cd "$TOP_DIR"
|
|
else
|
|
echo "No tarball found in ${SOURCE_PATH}/openmpi"
|
|
exit 1
|
|
fi
|
|
|
|
./configure --prefix=$MPI_HOME
|
|
make -j$(nproc)
|
|
make install
|
|
|
|
# Compiler wrappers for MPI-enabled builds (used by all packages below)
|
|
# Set these once so each package build uses the same compilers
|
|
export CC=$MPI_HOME/bin/mpicc
|
|
export CXX=$MPI_HOME/bin/mpicxx
|
|
export FC=$MPI_HOME/bin/mpif90
|
|
|
|
export CPPFLAGS="-I${HDF5}/include"
|
|
export LDFLAGS="-L${HDF5}/lib"
|
|
export LD_LIBRARY_PATH=${HDF5}/lib:$LD_LIBRARY_PATH
|
|
|
|
# ---------------------- Build Parallel HDF5 ------------------
|
|
|
|
cd ${SOURCE_PATH}/hdf5
|
|
|
|
# get the latest tarball
|
|
TAR_FILE=$(ls -1t *.tar.gz *.tgz 2>/dev/null | head -n1 || true)
|
|
[ -n "$TAR_FILE" ] || { echo "No tarball found"; exit 1; }
|
|
|
|
# extract tarball
|
|
tar -xzf "$TAR_FILE"
|
|
|
|
# cd into the only directory created (ignore files)
|
|
cd */ || { echo "No directory found after extraction"; exit 1; }
|
|
|
|
# configure and install
|
|
./configure --prefix=$HDF5 --enable-parallel --enable-fortran
|
|
make -j$(nproc)
|
|
make install
|
|
|
|
# ---------------------- Build NetCDF-C ------------------
|
|
|
|
cd ${SOURCE_PATH}/netcdf-c
|
|
TAR_FILE=$(ls -1t *.tar.gz *.tgz 2>/dev/null | head -n1 || true)
|
|
if [ -n "$TAR_FILE" ]; then
|
|
tar -xzf "$TAR_FILE"
|
|
TOP_DIR=$(tar -tf "$TAR_FILE" | sed -n '1p' | cut -f1 -d"/")
|
|
cd "$TOP_DIR"
|
|
else
|
|
echo "No tarball found in ${SOURCE_PATH}/netcdf-c"
|
|
exit 1
|
|
fi
|
|
|
|
./configure --prefix=$NETCDF --enable-parallel-tests
|
|
make -j$(nproc)
|
|
make install
|
|
|
|
# ---------------------- Build NetCDF-Fortran ------------------
|
|
cd ${SOURCE_PATH}/netcdf-fortran
|
|
TAR_FILE=$(ls -1t *.tar.gz *.tgz 2>/dev/null | head -n1 || true)
|
|
if [ -n "$TAR_FILE" ]; then
|
|
tar -xzf "$TAR_FILE"
|
|
TOP_DIR=$(tar -tf "$TAR_FILE" | sed -n '1p' | cut -f1 -d"/")
|
|
cd "$TOP_DIR"
|
|
else
|
|
echo "No tarball found in ${SOURCE_PATH}/netcdf-fortran"
|
|
exit 1
|
|
fi
|
|
|
|
CPPFLAGS="-I$NETCDF/include" \
|
|
LDFLAGS="-L$NETCDF/lib" \
|
|
./configure --prefix=$NETCDF --enable-large-files
|
|
|
|
make -j$(nproc)
|
|
make install
|
|
|
|
# ---------------------- Install WRF ------------------
|
|
cd ${SOURCE_PATH}/wrf
|
|
TAR_FILE=$(ls -1t *.tar.gz *.tgz 2>/dev/null | head -n1 || true)
|
|
if [ -n "$TAR_FILE" ]; then
|
|
tar -xzf "$TAR_FILE"
|
|
TOP_DIR=$(tar -tf "$TAR_FILE" | sed -n '1p' | cut -f1 -d"/")
|
|
# move whatever was extracted to the models path (wrf)
|
|
mv "$TOP_DIR" ${MODEL_PATH}/wrf
|
|
else
|
|
echo "No tarball found in ${SOURCE_PATH}/wrf"
|
|
exit 1
|
|
fi
|
|
|
|
cd ${MODEL_PATH}/wrf
|
|
|
|
printf "34\n1\n" | ./configure
|
|
|
|
ulimit -s unlimited
|
|
|
|
./compile em_real -j $(nproc) 2>&1 | tee compile.log || true
|
|
|
|
ls -lh main || true
|
|
ls -lh run || true
|
|
|
|
# ---------------------- Install WPS ------------------
|
|
cd ${SOURCE_PATH}/wps
|
|
|
|
# Extract WPS source and move to models path
|
|
TAR_FILE=$(ls -1t *.tar.gz *.tgz 2>/dev/null | head -n1 || true)
|
|
if [ -n "$TAR_FILE" ]; then
|
|
tar -xzf "$TAR_FILE"
|
|
TOP_DIR=$(tar -tf "$TAR_FILE" | sed -n '1p' | cut -f1 -d"/")
|
|
mv "$TOP_DIR" ${MODEL_PATH}/wps
|
|
else
|
|
echo "No tarball found in ${SOURCE_PATH}/wps"
|
|
exit 1
|
|
fi
|
|
|
|
cd ${MODEL_PATH}/wps
|
|
|
|
# Tell WPS where WRF is installed
|
|
export WRF_DIR=${MODEL_PATH}/wrf
|
|
|
|
# Configure automatically (choose Linux + gfortran)
|
|
printf "1\n" | ./configure
|
|
|
|
# Compile WPS
|
|
./compile 2>&1 | tee compile.log || true
|
|
|
|
# Verify binaries
|
|
ls -lh geogrid/src/geogrid.exe || true
|
|
ls -lh ungrib/src/ungrib.exe || true
|
|
ls -lh metgrid/src/metgrid.exe || true
|
|
|
|
%environment
|
|
############################################################
|
|
## Compiler Settings
|
|
############################################################
|
|
|
|
# Intel Compiler
|
|
export CC=icc
|
|
export CXX=icpc
|
|
export FC=ifort
|
|
export F77=ifort
|
|
|
|
# GNU Compiler
|
|
#export CC=gcc
|
|
#export CXX=g++
|
|
#export FC=gfortran
|
|
#export F77=gfortran
|
|
|
|
############################################################
|
|
## General
|
|
############################################################
|
|
export HPC_PATH=/opt/hpc
|
|
export MODEL_PATH=/opt/models
|
|
export SOURCE_PATH=/opt/src
|
|
|
|
|
|
############################################################
|
|
## OpenMPI Settings
|
|
############################################################
|
|
export MPI=/opt/hpc/mpi
|
|
|
|
|
|
############################################################
|
|
## OpenMP Settings
|
|
############################################################
|
|
export OMP_NUM_THREADS=1
|
|
export OMP_PROC_BIND=spread
|
|
export OMP_PLACES=cores
|
|
|
|
|
|
############################################################
|
|
## HDF5 Settings
|
|
############################################################
|
|
export HDF5=$HPC_PATH/hdf5
|
|
export PHDF5=$HDF5
|
|
|
|
|
|
############################################################
|
|
## NetCDF Settings
|
|
############################################################
|
|
export NETCDF_INCDIR
|
|
export NETCDF_LIBDIR
|
|
export NETCDF=$HPC_PATH/netcdf
|
|
export NETCDF=$NETCDF
|
|
|
|
|
|
############################################################
|
|
## IO/API Settings
|
|
############################################################
|
|
export MPI_HOME=$HPC_PATH/mpi
|
|
export IOAPI=$HPC_PATH/ioapi
|
|
|
|
|
|
############################################################
|
|
## WRF Settings
|
|
############################################################
|
|
export WRF_DIR=$MODEL_PATH/wrf
|
|
export PATH=$MPI_HOME/bin:$NETCDF/bin:$PATH
|
|
export LD_LIBRARY_PATH=$MPI_HOME/lib:$HDF5/lib:$NETCDF/lib:$IOAPI/lib:$LD_LIBRARY_PATH
|
|
|
|
|
|
############################################################
|
|
## WPS Settings
|
|
############################################################
|
|
export WPS_DIR=$MODEL_PATH/wps
|
|
|
|
|
|
############################################################
|
|
## CMAQ Settings
|
|
############################################################
|
|
export CMAQ_DIR=$MODEL_PATH/cmaq
|
|
export JASPERLIB=/usr/lib64
|
|
export JASPERINC=/usr/include
|