Installation guide for DAFoam v2.2.0 and before

Edit me

Note: This section assumes you want to compile the DAFoam optimization package (v2.0) from the source on a Linux system. If you use the Docker image, there is no need to compile anything and you can skip this section.

The DAFoam package can be compiled with various dependency versions. Here we elaborate on how to compile it on Ubuntu 18.04 using the dependencies shown in the following table.

Ubuntu	Compiler	OpenMPI	mpi4py	PETSc	petsc4py	CGNS	Python	Numpy	Scipy	Cython
18.04	gcc/7.5	1.10.7	3.0.2	3.11.4	3.11.0	3.3.0	3.6.5	1.14.3	1.1.0	0.29.21

To compile, you can just copy the code blocks in the following steps and run them on the terminal.

Note: If a code block contains multiple lines, copy all the lines and run them on the terminal. Make sure each step run successfully before going to the next one. The entire compilation may take a few hours, the most time-consuming part is to compile OpenFOAM.

Prerequisites

Run this on terminal to install prerequisites:

sudo apt-get update && \
sudo apt-get install -y build-essential flex bison cmake zlib1g-dev libboost-system-dev libboost-thread-dev libreadline-dev libncurses-dev libxt-dev qt5-default libqt5x11extras5-dev libqt5help5 qtdeclarative5-dev qttools5-dev libqtwebkit-dev freeglut3-dev libqt5opengl5-dev texinfo  libscotch-dev libcgal-dev gfortran swig wget git vim cmake-curses-gui libfl-dev apt-utils libibverbs-dev --no-install-recommends

After this, create a “packages” in your home directory:

mkdir -p $HOME/packages

Python

Install Anaconda3-5.2.0 by running this command:

cd $HOME/packages && \
wget https://repo.anaconda.com/archive/Anaconda3-5.2.0-Linux-x86_64.sh && \
chmod 755 Anaconda3-5.2.0-Linux-x86_64.sh && \
./Anaconda3-5.2.0-Linux-x86_64.sh -b -p $HOME/packages/anaconda3 && \
echo '# Anaconda3' >> $HOME/.bashrc && \
echo 'export PATH=$HOME/packages/anaconda3/bin:$PATH' >> $HOME/.bashrc && \
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/packages/anaconda3/lib' >> $HOME/.bashrc && \
. $HOME/.bashrc

Then upgrade the pip utility:

pip install --upgrade pip

OpenMPI

First append relevant environmental variables by running:

echo '# OpenMPI-1.10.7' >> $HOME/.bashrc && \
echo 'export MPI_INSTALL_DIR=$HOME/packages/openmpi-1.10.7/opt-gfortran' >> $HOME/.bashrc && \
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPI_INSTALL_DIR/lib' >> $HOME/.bashrc && \
echo 'export PATH=$MPI_INSTALL_DIR/bin:$PATH' >> $HOME/.bashrc && \
. $HOME/.bashrc

Then, configure and build OpenMPI:

cd $HOME/packages && \
wget https://download.open-mpi.org/release/open-mpi/v1.10/openmpi-1.10.7.tar.gz  && \
tar -xvf openmpi-1.10.7.tar.gz && \
cd openmpi-1.10.7 && \
./configure --prefix=$MPI_INSTALL_DIR && \
make all install

To verify the installation, run:

mpicc -v

You should see the version of the compiled OpenMPI.

Finally, install mpi4py-3.0.2:

pip install mpi4py==3.0.2

Petsc

First append relevant environmental variables by running:

   
echo '# Petsc-3.11.4' >> $HOME/.bashrc && \
echo 'export PETSC_DIR=$HOME/packages/petsc-3.11.4' >> $HOME/.bashrc && \
echo 'export PETSC_ARCH=real-opt' >> $HOME/.bashrc && \
echo 'export PATH=$PETSC_DIR/$PETSC_ARCH/bin:$PATH' >> $HOME/.bashrc && \
echo 'export PATH=$PETSC_DIR/$PETSC_ARCH/include:$PATH' >> $HOME/.bashrc && \
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PETSC_DIR/$PETSC_ARCH/lib' >> $HOME/.bashrc && \
echo 'export PETSC_LIB=$PETSC_DIR/$PETSC_ARCH/lib' >> $HOME/.bashrc
. $HOME/.bashrc

Then, configure and compile:

cd $HOME/packages && \
wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.11.4.tar.gz  && \
tar -xvf petsc-3.11.4.tar.gz && \
cd petsc-3.11.4 && \
./configure --PETSC_ARCH=real-opt --with-scalar-type=real --with-debugging=0 --with-mpi-dir=$MPI_INSTALL_DIR --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --download-fblaslapack=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11 && \
make PETSC_DIR=$HOME/packages/petsc-3.11.4 PETSC_ARCH=real-opt all

Finally, install petsc4py-3.11.0:

pip install petsc4py==3.11.0

CGNS

First append relevant environmental variables by running:

  
echo '# CGNS-3.3.0' >> $HOME/.bashrc && \
echo 'export CGNS_HOME=$HOME/packages/CGNS-3.3.0/opt-gfortran' >> $HOME/.bashrc && \
echo 'export PATH=$PATH:$CGNS_HOME/bin' >> $HOME/.bashrc && \
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CGNS_HOME/lib' >> $HOME/.bashrc && \
. $HOME/.bashrc

Then, configure and compile:

cd $HOME/packages && \
wget https://github.com/CGNS/CGNS/archive/v3.3.0.tar.gz  && \
tar -xvaf v3.3.0.tar.gz && \
cd CGNS-3.3.0 && \
mkdir -p build && \
cd build && \
cmake .. -DCGNS_ENABLE_FORTRAN=1 -DCMAKE_INSTALL_PREFIX=$CGNS_HOME -DCGNS_BUILD_CGNSTOOLS=0 && \
make all install

MACH-Aero framework

The supported repo versions in the MACH-Aero framework for DAFoam-v3.1.2 is as follows

baseclasses	pySpline	pyGeo	multipoint	pyHyp	cgnsUtilities	IDWarp	pyOptSparse	pyOFM	DAFoam
v1.2.0	v1.2.0	v1.2.0	v1.2.0	v2.2.0	v2.2.0	v2.2.1	v2.1.3	v1.2.0	v3.1.2

To install all the repos in MACH-Aero, first create a “repos” folder in the $HOME directory:

mkdir -p $HOME/repos

Now run this command to install all the repos for MACH-Aero:

cd $HOME/repos && \
wget https://github.com/mdolab/baseclasses/archive/v1.2.0.tar.gz -O baseclasses.tar.gz && \
tar -xvf baseclasses.tar.gz && cd baseclasses-1.2.0 && pip install . && \
cd $HOME/repos && \
wget https://github.com/mdolab/pyspline/archive/v1.2.0.tar.gz -O pyspline.tar.gz && \
tar -xvf pyspline.tar.gz && cd pyspline-1.2.0 && \
cp config/defaults/config.LINUX_GFORTRAN.mk config/config.mk && \
make && pip install . && \
cd $HOME/repos && \
wget https://github.com/mdolab/pygeo/archive/v1.2.0.tar.gz -O pygeo.tar.gz && \
tar -xvf pygeo.tar.gz && cd pygeo-1.2.0 && pip install . && \
cd $HOME/repos && \
wget https://github.com/mdolab/multipoint/archive/v1.2.0.tar.gz -O multipoint.tar.gz && \
tar -xvf multipoint.tar.gz && cd multipoint-1.2.0 && pip install . && \
cd $HOME/repos && \
wget https://github.com/mdolab/pyhyp/archive/v2.2.0.tar.gz -O pyhyp.tar.gz && \
tar -xvf pyhyp.tar.gz && cd pyhyp-2.2.0 && \
cp -r config/defaults/config.LINUX_GFORTRAN_OPENMPI.mk config/config.mk && \
make && pip install . && \
cd $HOME/repos && \
wget https://github.com/mdolab/cgnsutilities/archive/v2.2.0.tar.gz -O cgnsutilities.tar.gz && \
tar -xvf cgnsutilities.tar.gz && cd cgnsutilities-2.2.0 && \
cp config.mk.info config.mk && \
make && pip install . && \
cd $HOME/repos && \
wget https://github.com/mdolab/idwarp/archive/v2.2.1.tar.gz -O idwarp.tar.gz && \
tar -xvf idwarp.tar.gz && cd idwarp-2.2.1 && \
cp -r config/defaults/config.LINUX_GFORTRAN_OPENMPI.mk config/config.mk && \
make && pip install . && \
cd $HOME/repos && \
wget https://github.com/mdolab/pyoptsparse/archive/v2.1.3.tar.gz -O pyoptsparse.tar.gz && \
tar -xvf pyoptsparse.tar.gz && cd pyoptsparse-2.1.3 && \
pip install .

OpenFOAM

Compile OpenFOAM-v1812 by running:

mkdir -p $HOME/OpenFOAM && \
cd $HOME/OpenFOAM && \
wget https://sourceforge.net/projects/openfoamplus/files/v1812/OpenFOAM-v1812.tgz/download -O OpenFOAM-v1812.tgz && \
wget https://sourceforge.net/projects/openfoamplus/files/v1812/ThirdParty-v1812.tgz/download -O ThirdParty-v1812.tgz && \
tar -xvf OpenFOAM-v1812.tgz && \
tar -xvf ThirdParty-v1812.tgz && \
cd $HOME/OpenFOAM/OpenFOAM-v1812 && \
wget https://github.com/DAFoam/files/releases/download/v1.0.0/UPstream.C && \
mv UPstream.C src/Pstream/mpi/UPstream.C && \
. etc/bashrc && \
export WM_NCOMPPROCS=4 && \
./Allwmake

Note: In the above command, we replaced the OpenFOAM-v1812’s built-in UPstream.C file with a customized one because we need to prevent OpenFOAM from calling the MPI_Finialize function when wrapping OpenFOAM functions using Cython.

Note: NOTE: The above command will compile OpenFOAM using 4 CPU cores. If you want to compile OpenFOAM using more cores, change the WM_NCOMPPROCS parameter before running ./Allwmake

Finally, verify the installation by running:

simpleFoam -help

It should see some basic information of OpenFOAM

pyOFM

First install Cython:

pip install cython==0.29.21

Then, compile pyOFM by running:

cd $HOME/repos && \
wget https://github.com/mdolab/pyofm/archive/v1.2.0.tar.gz -O pyofm.tar.gz && \
tar -xvf pyofm.tar.gz && cd pyofm-1.2.0 && \
. $HOME/OpenFOAM/OpenFOAM-v1812/etc/bashrc && \
make && pip install .

DAFoam

Compile DAFoam by running:

cd $HOME/repos && \
wget https://github.com/mdolab/dafoam/archive/v3.1.2.tar.gz -O dafoam.tar.gz && \
tar -xvf dafoam.tar.gz && cd dafoam-* && \
. $HOME/OpenFOAM/OpenFOAM-v1812/etc/bashrc && \
./Allmake && pip install .

Once DAFoam is compiled, run the regression test:

cd $HOME/repos/dafoam/tests && ./Allrun

The regression tests should take less than 30 minutes. The test progress will be printed to screen. Make sure you see this at the end:

   
************************************************************
**************** All DAFoam tests passed! ******************
************************************************************

Note: Load the OpenFOAM environments: source $HOME/OpenFOAM/OpenFOAM-v1812/etc/bashrc before running any jobs!

In summary, here is the folder structures for all the installed packages:

   
$HOME
  - OpenFOAM
    - OpenFOAM-v1812
    - ThirdParty-v1812
  - packages
    - anaconda3
    - CGNS-3.3.0
    - mpi4py-3.0.2
    - petsc-3.11.4
    - petsc4py-3.11.0
  - repos
    - baseclasses
    - cgnsutilities
    - dafoam
    - idwarp
    - multipoint
    - pygeo
    - pyhyp
    - pyofm
    - pyoptsparse
    - pyspline

Here is the DAFoam related environmental variable setup that should appear in your bashrc file:

# OpenMPI-1.10.7
export MPI_INSTALL_DIR=$HOME/packages/openmpi-1.10.7/opt-gfortran
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPI_INSTALL_DIR/lib
export PATH=$MPI_INSTALL_DIR/bin:$PATH
# PETSC
export PETSC_DIR=$HOME/packages/petsc-3.11.4
export PETSC_ARCH=real-opt
export PATH=$PETSC_DIR/$PETSC_ARCH/bin:$PATH
export PATH=$PETSC_DIR/$PETSC_ARCH/include:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PETSC_DIR/$PETSC_ARCH/lib
export PETSC_LIB=$PETSC_DIR/$PETSC_ARCH/lib
# CGNS-3.3.0
export CGNS_HOME=$HOME/packages/CGNS-3.3.0/opt-gfortran
export PATH=$PATH:$CGNS_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CGNS_HOME/lib