Artemis uw-full-stack setup script

artemis.pbs

#!/bin/bash
#PBS -P BGH
#PBS -N UW_Run
#PBS -l select=1:ncpus=4:mem=3GB
#PBS -l walltime=00:20:00
#PBS -q defaultQ

source /project/RDS-FSC-BGH-RW/codes/UWGeodynamics_2.10.1.sh

cd $PBS_O_WORKDIR


OUTPUTPATH=`pwd`
MODELNAME="foobar"

SCRIPT="Tutorial_11_Coupling_with_Badlands.py"

export OPENBLAS_NUM_THREADS=1
# execution
mpiexec python3 ./$SCRIPT 1> $OUTPUTPATH/$MODELNAME.$PBS_JOBID.log 2> $OUTPUTPATH/$MODELNAME.$PBS_JOBID.err

setup.sh

#!/bin/bash

module purge
module load gcc/4.9.3 python/3.6.5 hdf5-gcc-mpich-3.2/1.10.1

# this is missing in the module
export HDF_DIR=/usr/local/hdf5-gcc-mpich-3.2/1.10.1
export PATH=$HDF_DIR/bin:$PATH

export GROUP=m18
export USER=
export INSTALL_NAME=UWGeodynamics_2.10

export CODES_PATH=/project/RDS-FSC-BGH-RW/codes
export UW_OPT_DIR=$CODES_PATH/opt
export INSTALL_PATH=$CODES_PATH/$INSTALL_NAME

export SWIG_VERSION=3.0.12
export SWIG_PATH=$UW_OPT_DIR/swig-$SWIG_VERSION
export PATH=$SWIG_PATH/bin:$PATH

export OMPI_MCA_io=ompio

export CDIR=$PWD

install_swig() {
	tmp_dir=$(mktemp -d -t ci-XXXXXXXXXX)
	cd $tmp_dir
	wget http://prdownloads.sourceforge.net/swig/swig-$SWIG_VERSION.tar.gz
	tar -xvzf swig-$SWIG_VERSION.tar.gz
	cd swig-$SWIG_VERSION
	./configure --prefix=$SWIG_PATH
	make
	make install
	rm $tmp_dir
	cd $CDIR
}


install_petsc(){
	source $INSTALL_PATH/bin/activate
	module load cmake

	export PETSC_CONFIGURE_OPTIONS="
		--with-debugging=no  \
                --useThreads=0 \
                --with-shared-libraries \
		--download-ctetgen  \
		--download-fblaslapack=yes  \
		--download-metis=yes  \
		--download-mumps=yes  \
		--download-parmetis=yes  \
		--download-scalapack  \
		--download-triangle  \
		--prefix=$UW_OPT_DIR/petsc-3.12.5  \
		--with-hdf5-dir=/usr/local/hdf5-gcc-mpich-3.2/1.10.1  \
		--with-fortran-interfaces=1  \
		-I/usr/local/gcc/4.9.3/include  \
		-I/usr/local/gmp/5.1.3/include  \
		-I/usr/local/mpc/1.0.3/include  \
		-I/usr/local/mpfr/3.1.4/include  \
		-I/usr/local/mpich/3.2/include  \
		-I/usr/local/openssl/1.0.1s/include  \
		-I/usr/local/python/3.6.5/include  \
		-I/usr/local/zlib/1.2.8/include  \
		-L/usr/local/gcc/4.9.3/lib64  \
		-L/usr/local/gmp/5.1.3/lib  \
		-L/usr/local/mpc/1.0.3/lib  \
		-L/usr/local/mpfr/3.1.4/lib  \
		-L/usr/local/mpich/3.2/lib  \
		-L/usr/local/openssl/1.0.1s/lib  \
		-L/usr/local/zlib/1.2.8/lib  \
		CFLAGS=-I/usr/local/python/3.6.5/include/python3.6m  \
		CPPFLAGS=-I/usr/local/python/3.6.5/include/python3.6m  \
		CXXFLAGS=-I/usr/local/openssl/1.0.1s/include  \
		LDFLAGS=-L/usr/local/python/3.6.5/lib"

        CC=mpicc CXX=mpicxx FC=mpif90 pip install petsc==3.12.5 -vvv

}

install_python_dependencies(){
	source $INSTALL_PATH/bin/activate
	pip3 install --upgrade pip
	pip3 install Cython numpy==1.18.4
	pip3 install scons==3.1.1
	pip3 install cmake lavavu==1.4.14
	pip3 install mpi4py
	CC="mpicc" HDF5_MPI="ON" pip3 install --no-binary=h5py h5py

}

install_underworld(){
	source $INSTALL_PATH/bin/activate
        export PYTHON_DIR=/usr/local/python/3.6.5/

	# Artemis specific
	export PETSC_DIR=$UW_OPT_DIR/petsc-3.12.5

	tmp_dir=$(mktemp -d -t ci-XXXXXXXXXX)
	cd $tmp_dir
        # git clone https://github.com/underworldcode/underworld2.git $tmp_dir
        pip3 install underworld==2.10.0b
}

install_uwgeodynamics(){
	source $INSTALL_PATH/bin/activate
	tmp_dir=$(mktemp -d -t ci-XXXXXXXXXX)
	cd $tmp_dir
        # git clone https://github.com/underworldcode/uwgeodynamics.git $tmp_dir
        pip3 install UWGEOdynamics==2.10.1 
        rm -rf $tmp_dir	
	cd $CDIR
}

check_underworld_exists(){
	source $INSTALL_PATH/bin/activate
	return $(python3 -c "import underworld") 
}

check_uwgeodynamics_exists(){
	source $INSTALL_PATH/bin/activate
	return $(python3 -c "import UWGeodynamics") 
}

check_badlands_exists(){
	source $INSTALL_PATH/bin/activate
	return $(python3 -c "import badlands") 
}

install_badlands(){
       source $INSTALL_PATH/bin/activate
       pip3 install badlands
}

install_full_stack(){
    if ! command -v swig 2>/dev/null; then
           install_swig  
    else
           echo "Found swig"
    fi
    
    install_python_dependencies
    
    if ! check_underworld_exists; then
          install_underworld
    fi
    
    if ! check_uwgeodynamics_exists; then
          install_uwgeodynamics
    fi
    
    if ! check_badlands_exists; then
          install_badlands
    fi
}


if [ ! -d "$INSTALL_PATH" ]
then
    echo "Environment not found, creating a new one"
    mkdir -p $INSTALL_PATH
    python3 --version
    python3 -m venv $INSTALL_PATH
else
    echo "Found Environment"
    source $INSTALL_PATH/bin/activate
fi