Dependency - Geodels/eSCAPE GitHub Wiki

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Below is a step by step guide to install eSCAPE on Linux system.

Content

Default packages
MPI
PIP installation
PETSC
Additional dependencies for eSCAPE
Install eSCAPE
Notebook packages

Update your system and install default packages

Here we install python3

apt-get update -qq 
apt-get install -yq --no-install-recommends bash-completion build-essential 
apt-get install -yq --no-install-recommends python3-minimal python3-dev python3-pip
apt-get install -yq --no-install-recommends python3-tk python3-dbg cmake 
apt-get install -yq --no-install-recommends python3-setuptools wget gfortran

MPI

MPICH_VERSION="3.3"
MPICH_CONFIGURE_OPTIONS="--enable-fast=all,O3 --prefix=/opt/mpich"
MPICH_MAKE_OPTIONS="-j4"

mkdir /tmp/mpich-build
wget http://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPICH_VERSION}.tar.gz
tar xvzf mpich-${MPICH_VERSION}.tar.gz 
cd mpich-${MPICH_VERSION}              
./configure ${MPICH_CONFIGURE_OPTIONS} 
make ${MPICH_MAKE_OPTIONS}             
make install                           
ldconfig                               
cd /tmp                                
rm -fr *

export MPI_DIR=/opt/mpich
export PATH=${MPI_DIR}/bin:$PATH

PIP installation

pip3 install -U setuptools  
pip3 install -U wheel       
pip3 install --no-cache-dir numpy jupyter ipython plotly 
pip3 install --no-cache-dir matplotlib ipython scipy 
MPICC=${MPI_DIR}/mpicc MPICXX=${MPI_DIR}/mpicxx MPIFC=${MPI_DIR}/mpifort pip3 install --no-cache-dir mpi4py

PETSC

mkdir /tmp/petsc-build
export PETSC_VERSION="3.11.2"
wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${PETSC_VERSION}.tar.gz 
tar zxf petsc-lite-${PETSC_VERSION}.tar.gz && cd petsc-${PETSC_VERSION}

Configure:

./configure --with-debugging=0 --prefix=/opt/petsc                     
            --COPTFLAGS="-g -O3" --CXXOPTFLAGS="-g -O3" --FOPTFLAGS="-g -O3" 
            --with-zlib=1                   
            --download-fblaslapack=1        
            --download-ctetgen=1            
            --download-triangle=1           
            --download-hdf5=1               
            --download-mumps=1              
            --download-parmetis=1           
            --download-metis=1              
            --download-hypre=1              
            --download-scalapack=1       
            --useThreads=1               
            --with-shared-libraries      
            --with-cxx-dialect=C++11

Install:

make PETSC_DIR=/tmp/petsc-build/petsc-${PETSC_VERSION} PETSC_ARCH=arch-linux-c-opt all     
make PETSC_DIR=/tmp/petsc-build/petsc-${PETSC_VERSION} PETSC_ARCH=arch-linux-c-opt install 
make PETSC_DIR=/opt/petsc PETSC_ARCH="" test

Clean:

cd /tmp 
rm -fr *

export PETSC_DIR=/opt/petsc
export PATH=${PETSC_DIR}/bin:$PATH

Additional dependencies for eSCAPE

First HDF5 and PETSC4PY

export PYTHONPATH=$PYTHONPATH:/usr/lib
CC=h5pcc HDF5_MPI="ON" HDF5_DIR=${PETSC_DIR} python3 -m pip install --no-cache-dir --no-binary=h5py h5py python3 -m pip install --no-cache-dir petsc4py

Fillit

mkdir /workspace/lib
export F90=gfortran 
git clone -b python3 https://github.com/Geodels/fillit.git  
cd fillit  
python3 setup.py install

and using pip:

pip3 install pandas meshio rasterio meshplex ruamel.yaml

Install eSCAPE

cd /workspace/lib
git clone -b petsc3.11.2 https://github.com/Geodels/eSCAPE.git 
cd eSCAPE 
export F90=gfortran 
export PETSC_DIR=/opt/petsc 
export PETSC_ARCH=arch-linux-c-opt 
python setup.py install 
cd ..

Install eSCAPE-demo

cd examples
git clone -b petsc3.11.2 https://github.com/Geodels/eSCAPE-demo.git

Notebook packages

To run eSCAPE-demo and build the triangular meshes required by eSCAPE several packages are needed:

apt-get update -qq 
apt-get install -yq --no-install-recommends gmsh python3-gdal gdal-bin
apt-get install -yq --no-install-recommends libgeos++ libgeos-dev libgdal-dev libproj-dev

and

pip3 install setuptools wheel
pip3 install pathlib shapely descartes geopy pygeotools pygmsh stripy

GMT color scale...

git clone https://github.com/j08lue/pycpt.git 
cd pycpt 
git checkout b45f720d09da79bcd567c5cbba9a554b0a7cc1d9 
python3 setup.py install 
cd .. 
rm -rf pycpt