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lfric_env.def
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Bootstrap: docker
From: fedora:35
%files
files/mk_arch_files_intel.sh /opt
files/oneAPI.repo /opt
files/keyword.cfg /opt
files/mosrs-cache-password /opt
files/mosrs-check /opt
files/mosrs-setup-gpg-agent /opt
files/psyclone_new.cfg /opt
#### files/container.tgz /opt
%post
# Build stack
#Intel repo
mv /opt/oneAPI.repo /etc/yum.repos.d
#Update and install pre-built software stack.
dnf -y update
dnf -y install ucx ucx-cma ucx-devel ucx-ib ucx-rdmacm libmnl numactl-libs libpsm2 librdmacm librdmacm-utils libibverbs ibutils kmod iproute libibverbs-utils time gdb libxml2-devel jansson-devel glib2-devel libtool
dnf -y install make cmake git python2 python3-devel python3 python3-pip automake wget subversion perl-URI perl-Text-Balanced perl-core perl-XML-Parser which file zlib-devel libcurl-devel vim gcc gcc-c++ hostname nano procps psmisc rsync python3-sphinx csh bzip2
dnf --nogpgcheck -y install intel-oneapi-compiler-fortran-2022.1.0
#Setup Intel
. /opt/intel/oneapi/setvars.sh
#set locale
export LC_ALL=C
#### cd /&&tar zxvf /opt/container.tgz
BUILD_DIR=/opt/build
BASE_DIR=/container
mkdir -p $BASE_DIR
mkdir -p $BUILD_DIR
NCORES=8
FCM_VERSION=2017.10.0
CYLC_VERSION=7.8.1
ROSE_VERSION=2019.01.1
MPICH=3.3.2
HDF5=1.12.0
NETCDF4=4.9.2
NETCDF_FORTRAN=4.6.0
NETCDF_CXX=4.3.1
YAXT=0.9.3
PFUNIT=3.2.9
PSYCLONE=2.3.1
#fcm
cd $BASE_DIR
wget https://github.com/metomi/fcm/archive/${FCM_VERSION}.tar.gz && \
tar xfz ${FCM_VERSION}.tar.gz && \
rm -f ${FCM_VERSION}.tar.gz fcm && \
ln -s fcm-${FCM_VERSION} fcm
cp /opt/keyword*.cfg fcm/etc/fcm
rm -f /opt/keyword*.cfg
cp /opt/mo* fcm/bin
rm -f /opt/mo*
#cylc
cd $BASE_DIR
wget https://github.com/cylc/cylc/archive/${CYLC_VERSION}.tar.gz && \
tar xfz ${CYLC_VERSION}.tar.gz && \
cd cylc-flow-${CYLC_VERSION} && \
export PATH=$PWD/bin:$PATH && \
make
cd $BASE_DIR && rm -f ${CYLC_VERSION}.tar.gz cylc && ln -s cylc-flow-${CYLC_VERSION} cylc
#rose note:Requires python2, and pip needs to be installed manually.
cd $BASE_DIR
curl https://bootstrap.pypa.io/pip/2.7/get-pip.py -o get-pip.py
python2 get-pip.py
python2 -m pip install requests
rm get-pip.py
wget https://github.com/metomi/rose/archive/${ROSE_VERSION}.tar.gz && \
tar xfz ${ROSE_VERSION}.tar.gz && \
rm -f ${ROSE_VERSION}.tar.gz rose && \
ln -s rose-${ROSE_VERSION} rose
export NETCDF_DIR=$BASE_DIR/netcdf
export MPICH_DIR=$BASE_DIR/mpich
export INSTALL_DIR=$BASE_DIR/usr
export CPPFLAGS="-I$INSTALL_DIR/include -I$NETCDF_DIR/include"
export FFLAGS="-I$INSTALL_DIR/include -I$NETCDF_DIR/include"
export LDFLAGS="-L$INSTALL_DIR/lib -L$NETCDF_DIR/lib"
export PATH=$MPICH_DIR/bin:$NETCDF_DIR/bin:$INSTALL_DIR/bin:$PATH
export LD_LIBRARY_PATH=$MPICH_DIR/lib:$NETCDF_DIR/lib:$INSTALL_DIR/lib:$LD_LIBRARY_PATH
#mpich
cd $BUILD_DIR
wget http://www.mpich.org/static/downloads/$MPICH/mpich-$MPICH.tar.gz
tar -xzf mpich-$MPICH.tar.gz
cd mpich-$MPICH
FC=ifort CC=gcc ./configure --prefix=$MPICH_DIR --enable-cxx --enable-threads=multiple --enable-shared
make -j$NCORES
make install
#Install gfortran for external dependencies. Do after MPICH build otherwise
#issues with ISO bindings for gcc/Intel
dnf -y install gcc-gfortran
#hdf5
cd $BUILD_DIR
wget http://www.hdfgroup.org/ftp/HDF5/prev-releases/hdf5-1.12/hdf5-$HDF5/src/hdf5-$HDF5.tar.gz
tar -xzf hdf5-$HDF5.tar.gz
cd $BUILD_DIR/hdf5-$HDF5
CC=mpicc FC=mpif90 ./configure --prefix=$NETCDF_DIR --enable-fortran --enable-fortran2003 --enable-parallel
make -j$NCORES
make install
#netcdf
cd $BUILD_DIR
wget https://downloads.unidata.ucar.edu/netcdf-c/$NETCDF4/netcdf-c-$NETCDF4.tar.gz
tar -xzf netcdf-c-$NETCDF4.tar.gz
cd $BUILD_DIR/netcdf-c-$NETCDF4
CC=mpicc CXX=mpicxx FF=mpif90 FC=mpif90 ./configure --prefix=$NETCDF_DIR --disable-dap
make -j$NCORES
make install
export LIBS="-lnetcdf -lhdf5_hl -lhdf5 -ldl -lm -lz"
#netcdf-fortran
cd $BUILD_DIR
wget https://downloads.unidata.ucar.edu/netcdf-fortran/$NETCDF_FORTRAN/netcdf-fortran-$NETCDF_FORTRAN.tar.gz
tar -xzf netcdf-fortran-$NETCDF_FORTRAN.tar.gz
cd $BUILD_DIR/netcdf-fortran-$NETCDF_FORTRAN
CC=mpicc CXX=mpicxx FF=mpif90 FC=mpif90 ./configure --prefix=$NETCDF_DIR
make -j$NCORES
make install
#netcdf-cxx
cd $BUILD_DIR
wget https://downloads.unidata.ucar.edu/netcdf-cxx/$NETCDF_CXX/netcdf-cxx4-$NETCDF_CXX.tar.gz
tar -xzf netcdf-cxx4-$NETCDF_CXX.tar.gz
cd $BUILD_DIR/netcdf-cxx4-$NETCDF_CXX
CC=mpicc CXX=mpicxx FF=mpif90 FC=mpif90 ./configure --prefix=$NETCDF_DIR
make -j$NCORES
make install
export LIBS='-lnetcdff -lnetcdf -lhdf5_hl -lhdf5'
#yaxt
cd $BUILD_DIR
wget https://www.dkrz.de/redmine/attachments/download/520/yaxt-$YAXT.tar.gz
tar -xzf yaxt-$YAXT.tar.gz
cd $BUILD_DIR/yaxt-$YAXT
./configure --prefix=$INSTALL_DIR --with-idxtype=long CC=mpicc FC=mpif90 FPP="mpif90 -E"
make -j$NCORES
make install
#XIOS
#use mk_arch_files.sh
cd $BUILD_DIR
export HDF5_DIR=$NETCDF_DIR
svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk@2252 XIOS
cd $BUILD_DIR/XIOS
/opt/mk_arch_files_intel.sh INTEL_MPI
mv *INTEL_MPI* arch
./make_xios --full --arch INTEL_MPI --job $NCORES
cp -r lib $INSTALL_DIR
cp inc/* $INSTALL_DIR/include
mkdir -p $INSTALL_DIR/bin
cp bin/* $INSTALL_DIR/bin
rm -f /opt/mk_arch_files_intel.sh
#pFUnit
cd $BUILD_DIR
wget https://sourceforge.net/projects/pfunit/files/latest/download/pFUnit-$PFUNIT.tgz
tar -xzf pFUnit-$PFUNIT.tgz
cd pFUnit-$PFUNIT
export F90_VENDOR=Intel
export F90=ifort
export MPIF90=mpif90
#Hack for python2
ln -s /usr/bin/python2 $INSTALL_DIR/bin/python
make -j $NCORES
make install
rm $INSTALL_DIR/bin/python
#Clean up
cd $BASE_DIR
rm -fr $BUILD_DIR
#Psyclone
python3 -m pip install --no-cache-dir --upgrade pip
#python3 -m pip install --upgrade setuptools
python3 -m pip install Jinja2
python3 -m pip install PSyclone==$PSYCLONE
ln -s /usr/bin/python3 $INSTALL_DIR/bin/python
mv /opt/psyclone_new.cfg /container/psyclone_new.cfg
%environment
export LC_ALL=C
export BASE_DIR=/container
export INSTALL_DIR=$BASE_DIR/usr
export MPICH_DIR=$BASE_DIR/mpich
export PFUNIT=$INSTALL_DIR
export NETCDF_DIR=$BASE_DIR/netcdf
export CPPFLAGS="-I$INSTALL_DIR/include -I$NETCDF_DIR/include"
export FFLAGS="-I$INSTALL_DIR/include -I$INSTALL_DIR/mod -I$NETCDF_DIR/include -I$MPICH_DIR/include"
export LDFLAGS="-L$INSTALL_DIR/lib -L$NETCDF_DIR/lib"
export PATH=$MPICH_DIR/bin:$NETCDF_DIR/bin:$INSTALL_DIR/bin:/opt/intel/oneapi/compiler/latest/linux/bin/intel64:$BASE_DIR/fcm/bin:$BASE_DIR/rose/bin:$BASE_DIR/clyc/bin:$PATH
export PSYCLONE_CONFIG=/container/psyclone_new.cfg
#Library path
export LD_LIBRARY_PATH="$LOCAL_LD_LIBRARY_PATH:$MPICH_DIR/lib:$NETCDF_DIR/lib:$INSTALL_DIR/lib:/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin:$LD_LIBRARY_PATH:/usr/lib64:/usr/lib64/libibverbs:/usr/lib/host"
export FC=ifort
export FPP="cpp -traditional-cpp"
export LDMPI=mpif90
%runscript
#Unset CRAY program env
unset PE_ENV