##########################
INSTALL PRECICE - CENTOS 7
##########################

=========================
Building: Using CMake
=========================



You could find the Roadmap in - follow the instructions on the right side of the page:: 
  
   https://github.com/precice/precice/wiki/Roadmap

And you could find the binaries in - if you have Ubuntu it is easy to install the .deb file::

   https://github.com/precice/precice/releases


Install the required dependencies and make sure you are using a recent CMake version.
For Ubuntu 18.04 or newer::

   sudo apt update && \
   sudo apt install build-essential cmake libeigen3-dev libxml2-dev petsc-dev libboost-all-dev python-dev python-numpy
   

To build precice::

   mkdir build && cd build
   cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
   make -j $(nproc)


to test precice::

   make test_base

and::

   make test

Now go to Linking to preCICE with::

   cmake CMAKE_PREFIX_PATH=~/software .

or to use preCICE from it's build directory::

  cmake -Dprecice_DIR=/precice/build/dir .

Depending on the configuration of ld it might look by default into /usr/local/lib or not. This might lead to linking problems and can be either solved by adding /usr/local/lib to the LD_LIBRARY_PATH

Now go to tutorials.


Install openFoam 5.x
======================


Install Calculix
=================





Dependencies
============


For CENTOS and other distributions


CMake versions can easily be added via the binaries here.

- C++ compiler (with support for C++11, GCC version >= 5)
- CMake (version high enough to support your boost version)
- Eigen3:
  
Download the latest epel-release::
  
     http://download-ib01.fedoraproject.org/pub/epel/7/x86_64/
     rpm -Uvh epel-release*rpm
     yum install eigen3-devel
    
Make a soft link of Eigen folder into /usr/local/bin/
   
   Test Eigen with the code::
  
        #include <iostream>
        #include <Eigen/Dense>
        using Eigen::MatrixXd;
        int main()
        {
           MatrixXd m(2,2);
           m(0,0) = 3;
           m(1,0) = 2.5;
           m(0,1) = -1;
           m(1,1) = m(1,0) + m(0,1);
           std::cout << m << std::endl;
        } 
       
Save the file into  my_program.cpp and run it by::

       g++ my_program.cpp -o my_program

   When you run the program, it produces the following output::

         3   -1
         2.5  1.5

- Boost (version >= 1.65.1)  https://pkgs.org/download/boost::

   wget https://dl.bintray.com/boostorg/release/1.67.0/source/boost_1_67_0.tar.gz
   tar -xzf boost_1_*
   cd boost_1_*
   ./bootstrap.sh 
   ./b2 install --with=all
   
This install boost in user local, if you want to install in a different place i.e /opt/boost use::

   wget https://dl.bintray.com/boostorg/release/1.67.0/source/boost_1_67_0.tar.gz
   tar -xzf boost_1_*
   cd boost_1_*
   ./bootstrap.sh --prefix=/opt/boost
   ./b2 install --prefix=/opt/boost --with=all

I had a lot of problems with precice 1.4.1 becuase it did't find the path for boost include 

To keep things simple, let's start by using a header-only library. The following 
program reads a sequence of integers from standard input, uses Boost.Lambda to 
multiply each number by three, and writes them to standard output::

   #include <boost/lambda/lambda.hpp>
   #include <iostream>
   #include <iterator>
   #include <algorithm>

   int main()
   {
       using namespace boost::lambda;
       typedef std::istream_iterator<int> in;

       std::for_each(
           in(std::cin), in(), std::cout << (_1 * 3) << " " );
   }

Copy the text of this program into a file called example.cpp.

Now, in the directory where you saved example.cpp, issue the following command:::

   c++ -I path/to/boost_1_65_0 example.cpp -o example

To test the result, type:::

   echo 1 2 3 | ./example

   
If you instal boost in /opt/bosst Set the PATH into .bashrc appending the line::
   
   export PATH=opt/boost/include/${PATH:+:${PATH}}
   export LD_LIBRARY_PATH=/opt/boost/lib


- libxml2
- PETSc (optional) (version >= 3.6)::

     git clone -b maint https://bitbucket.org/petsc/petsc
     cd petsc
     export PETSC_DIR=`pwd`
     export PETSC_ARCH=x86_64
     ./config/configure.py --with-shared=1 --with-x=0 --with-mpi=1 --download-hypre=1
     make PETSC_DIR=/opt/petsc PETSC_ARCH=x86_64 all
     make PETSC_DIR=/opt/petsc PETSC_ARCH=x86_64 check

  If occurs the error::
	
     	*******************Error detected during compile or link!*******************
         See http://www.mcs.anl.gov/petsc/documentation/faq.html
         /opt/petsc/src/snes/examples/tutorials ex19
        *********************************************************************************

   
       ping `hostname`

If it fails The machine has a funky network configuration and for some reason 
MPICH is unable to communicate between processes with the socket connections it 
has established. This can happen even if you are running MPICH on just one machine.
Often you will find that ping `hostname` fails with this network configuration; 
that is processes on the machine cannot even connect to the same machine. 
You can try completely disconnecting your machine from the network and see if make 
test then works or speaking with your system adminstrator. 

- Python (optional) (with NumPy)
- MPI (optional) (warning: problems with MPI_Ports using OpenMPI >= 2)
- SCons (deprecated)
- yaml-cpp 0.51 from https://github.com/jbeder/yaml-cpp/releases
- OpenFoam6


Download preCICE
================

Download and unpack the latest release of preCICE (replace x.y.z with the actual
version)::

    wget https://github.com/precice/precice/archive/vx.y.z.tar.gz
    tar -xzvf vx.y.z.tar.gz
    cd precice-x.y.z

Or from the installatoion directory (i.e. /opt)::

   git clone https://github.com/precice/precice.git

I also downloaded and tar libprecice1.4.0-bionic.tar.gz


Build preCICE
=============

Use CMake to configure and build preCICE.

See CMake Options for a list of common options to use and Troubleshooting in
case of any issues.
We strongly recommend to build preCICE as a shared library. Note that the default
prefix is /usr/local and you may want to change that.::

    mkdir build && cd build
    scl enable devtoolset-7 bash       # To run gcc 7 instead 4.8.5           
    # unset ELPA  # To avoid compiling warning
    cmake3  -DBUILD_SHARED_LIBS=ON ..  # this build libraries as dynamic
    sudo make install


test preCICE
============

run::

    make test_base

This executes the base test set.

To execute all tests, including tests known to hang or fail due to dependency
issues, run::

    make test

Also run this test::

    $PRECICE_ROOT/tools/compileAndTest.py -t --run_test="\!@MPI_Ports"
    
When I ran this test, I received the error message: 

/opt/precice-1.4.1/build/testprecice: error while loading shared libraries: libboost_timer.so.1.65.1: 
cannot open shared object file: No such file or directory

To solve this::

   echo -e "\n/usr/local/lib" | sudo tee -a /etc/ld.so.conf 
   sudo ldconfig



install preCICE to the prefix 
===============================

To install preCICE to the prefix run::

    make install

You may have to add <prefix>/lib/pkconfig
to your PKG_CONFIG_PATH in order for pkgconfig to be able to locate it.

I have to use::

   # .bashrc
   # Source global definitions
   if [ -f /etc/bashrc ]; then
   	. /etc/bashrc
   fi
   # Uncomment the following line if you don't like systemctl's auto-paging feature:
   # export SYSTEMD_PAGER=

   export PATH=/usr/local/cuda-10.1/bin:/usr/local/cuda-10.1/NsightCompute-2019.1${PATH:+:${PATH}}
   export LD_LIBRARY_PATH=/usr/local/cuda-10.1/lib64:$LD_LIBRARY_PATH

   export PATH="$PATH:/usr/lib64/openmpi-2.1.1/bin"
   export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib64/openmpi-2.1.1/lib/openmpi"

   #export BOOST_ROOT=/usr/local/boost/
   export LD_LIBRARY_PATH="usr/local/lib:$LD_LIBRARY_PATH"

   export PATH=/usr/local/bin/eigen3/${PATH:+:${PATH}}

   export PETSC_DIR=/opt/petsc/
   export PETSC_ARCH=x86_64

   export LD_LIBRARY_PATH=/opt/libprecice1.4.1-bionic/bin:$LD_LIBRARY_PATH
   export LD_LIBRARY_PATH=/opt/libprecice1.4.1/build:${LD_LIBRARY_PATH}
   export PRECICE_ROOT=/opt/precice-1.4.1

   # User specific aliases and functions

   alias rapid='source /opt/RapidCFD/RapidCFD-dev/etc/bashrc WM_COMPILER_TYPE=system WM_COMPILER=Gcc48 WM_LABEL_SIZE=64 WM_MPLIB=OPENMPI FOAMY_HEX_MESH=yes'
   alias rapid='source /opt/RapidCFD/RapidCFD-dev/etc/bashrc WM_LABEL_SIZE=64 WM_MPLIB=OPENMPI FOAMY_HEX_MESH=yes'

   alias of5x='source \/opt/OpenFOAM/OpenFOAM-5.x/etc/bashrc $FOAM_SETTINGS'





Pages for installation help
===========================

- `Building the precice openfoam adapter <https://github.com/precice/openfoam-adapter/wiki/Building>`_
- `libprecice-cannot-be-found-at-runtime <https://github.com/precice/precice/wiki/Linking-to-preCICE#libprecice-cannot-be-found-at-runtime>`_
- `static-libraries-vs-dynamic-libraries <https://medium.com/@StueyGK/static-libraries-vs-dynamic-libraries-af78f0b5f1e4>`_
- `gitter, Good help from Gerasimos <https://gitter.im/precice/Lobby>`_
- `yaml-cpp <https://github.com/jbeder/yaml-cpp/releases>`_
- `petsc <https://www.dealii.org/current/external-libs/petsc.html>`_
- `Fedora packages <https://download-ib01.fedoraproject.org/pub/epel/7/x86_64/Packages/>`_
- `Boost <https://pkgs.org/download/boost>`_
- `pkgs yaml-cpp <https://pkgs.org/download/yaml-cpp>`_


yaml-cpp install
=================

Download yaml-cpp 0.6.2::
 
   yaml-cpp-yaml-cpp-0.6.2.tar.gz
   tar xf yaml-cpp-yaml-cpp-0.6.2.tar.gz
   scl enable devtoolset-7 bashrc
   cd yamy-cpp-yaml-cpp-0.6.2
   mkdir build
   cd build
   sudo chown -R hgasca:users .
   cmake3 -DBOOST_ROOT=$BOOST_ROOT -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
   sudo make install
   
   




Plate duct openfoam-openfoam
=============================

Clone and `download The adapter <https://github.com/precice/openfoam-adapter/tree/OpenFOAM5.x>`_:
then go to openfoam-adapter-OpenFOAM5.x folder and run::

    scl enable devtoolset-7 bash
    of5x
    ./Allclean
    ./Allwmake

    
    
If errors review the .log file and use `Precice Lobby <https://gitter.im/precice/Lobby>`_
for the fastest solution.

Run tutorial case
------------------

go to the folder and run::

    cd tutorials/CHT/flow-over-plate/buoyantPimpleFoam-laplacianFoam
    of6
    ./Allclean
    ./Allrun

To understand::
    
    https://github.com/precice/openfoam-adapter/wiki/OpenFOAM-setup-(fluid)
    
    
- Review Fluid.log in order to see if the adapter is running.
- Open paraview
- Open /CHT/flow-over-plate/buoyantPimpleFoam-laplacianFoam/Fluid/Fluid.foam and
- /CHT/flow-over-plate/buoyantPimpleFoam-laplacianFoam/Solid/Solid.foam to postprocess


.. The below lines are copied from the precice page for future review.

   To use preCICE in your project, Linking to preCICE.
   =====================================================


   Note: here it is assumed that you installed a binary package for your linux distribution or built preCICE with CMake
   and installed it.

   Depending on what build system your adapter/solver uses, linking to preCICE can differ, but it is very easy in everycase. In any case, please include e.g. the SolverInterface.hpp file as precice/SolverInterface.hpp

   You have now installed preCICE somewhere on your system, either with e.g. a Debian package or with running make install.

   As you want to use preCICE in your solver, your project/adapter should know where preCICE is installed. This mainly means:

     where are the header files that I need? (namely precice/SolverInterface.hpp or precice/SolverInterfaceC.h etc).
       where is the library binary (namely libprecice.so or libprecice.a).
       in case I am using preCICE as a static library (not recommended if you don't know why you need it), which other
       dependencies do I need to link against?

   Since preCICE is a CMake project, other CMake projects can easily use it, if they know where it is installed. For Autotools
   or any other build system, you can get all the information you need through pkg-config, a simple and widely used tool for
   this purpose.

   When installing preCICE, you also get a file named libprecice.pc, which mainly provides two important variables: the CFLAGS
   (where to find the headers) and the LIBS (where to find the library and dependencies). Running pkg-config --cflags --libs
   libprecice should give you this information, if pkg-config can find libprecice.pc. In case you installed preCICE in a directory
   different than /usr/lib/, you need to set your PKG_CONFIG_PATH variable to point to the path where libprecice.pc is located.

   If, at runtime, the shared library cannot be found, have a look into the troubleshooting.

   Please note that, as of preCICE v1.4.0, we don't yet provide the dependency information there yet, so linking to a static
   libprecice.a may require some tinkering.

   Linking from CMake
   ---------------------

   Linking to preCICE from a CMake project is simple. Use find_package(precice) and link precice::precice to your target:

   .. code-block:: bash

     find_package(precice REQUIRED CONFIG)
     add_executable(myTarget main.cpp)
     target_link_libraries(myTarget PRIVATE precice::precice)

   This works out-of-the-box if you installed preCICE using the debian package.

   If you built preCICE and installed it into a custom prefix e.g. ~/software/, you can set the following cmake option:

   .. code-block:: bash

       $ cmake CMAKE_PREFIX_PATH=~/software .

   To use preCICE directly from its build directory, set the following cmake option:

   .. code-block:: bash

       $ cmake -Dprecice_DIR=/prefice/build/bir .


   ==========================
   PRECICE-OPENFOAM ADAPTER
   ==========================

   Building
   =========

   To build the adapter, you need to install a few dependencies and then execute the Allwmake script.

   1. Download the adapter or (better) install git and clone this repository: git clone https://github.com/precice/openfoam-adapter.git

    For openFoam6 openfoam-adapter-OpenFOAM6.zip

   2. Install the latest yaml-cpp headers and shared library, preferably from your Linux distribution's repository. (at least yaml-cpp 0.5.x)

       - If you use Boost >= 1.67, you also need yaml-cpp >= 0.6 (read more here). Similarly, if you use Boost < 1.67, you also need yaml-cpp < 0.6.
       - If you are using Ubuntu (and Boost < 1.67), you are looking for the package libyaml-cpp-dev. For example, run sudo apt install libyaml-cpp-dev.
       - If you want to build yaml-cpp from source, you need to build it as a shared library (cmake -DBUILD_SHARED_LIBS=ON).
         You also need to set it in your CPLUS_INCLUDE_PATH and LD_LIBRARY_PATH:
         export CPLUS_INCLUDE_PATH="path/to/yaml-cpp/include:${CPLUS_INCLUDE_PATH}"
         export LD_LIBRARY_PATH="path/to/yaml-cpp/build:${LD_LIBRARY_PATH}"

   In my case for centos 7 and Boost 1.65 I used

   .. code-block:: bash

       https://centos.pkgs.org/7/epel-x86_64/yaml-cpp-devel-0.5.1-1.el7.2.x86_64.rpm.html


   a. Download latest epel-release rpm from

   .. code-block:: bash

       http://download-ib01.fedoraproject.org/pub/epel/7/x86_64/

   b. Install epel-release rpm:

   .. code-block:: bash

       # rpm -Uvh epel-release*rpm

   c. Install yaml-cpp-devel rpm package:

   .. code-block:: bash

       # yum install yaml-cpp-devel


   NOTE: I have any doubts about it, because when i run the last install it installed also Boost 1.53.


   3. Install the preCICE headers and library, following its building instructions.

       If you want to use preCICE as a static library, check and adjust its dependencies in Allwmake (ADAPTER_PRECICE_DEP).

   4. Install a compatible OpenFOAM distribution.

       We are looking for a nice way to support multiple versions at the same time. In the meantime, the following OpenFOAM versions work but are seen as special cases:

       OpenFOAM 6 - openfoam.org: A compatible variant of the adapter is provided in the OpenFOAM6 branch (see this pull request).
       OpenFOAM-dev - openfoam.org (at least version 20190204): A compatible variant of the adapter is provided in the OpenFOAMdev branch. (see this pull request).

   Compatible OpenFOAM solvers

   The following OpenFOAM solvers (in the respective OpenFOAM versions) are known to work with the adapter. However, more solvers may be compatible.
   See also the section "Solver requirements".


   Conjugate heat transfer
   Compressible

       buoyantPimpleFoam
       buoyantSimpleFoam

   Incompressible

       buoyantBoussinesqPimpleFoam

   Basic

       laplacianFoam

   Fluid-structure interaction
   Incompressible

       pimpleFoam / pimpleDyMFoam

   .. note::

      the \*DyMFoam dynamic mesh solvers were deprecated and merged into the
      respective standard solvers in OpenFOAM 6 and OpenFOAM v1806.
      The adapter-specific configuration is not affected, but you need to choose
      the correct one for your OpenFOAM version.


   Solver requirements

   The adapter can be loaded by any official OpenFOAM solver, but there are some requirements to use a
   solver for conjugate heat transfer simulations. See also Configuration.

   First of all, the solver needs to be able to simulate heat transfer. This means that the solver should
   create a Temperature field (named T) and provide thermal conductivity or diffusivity fields.

   Three categories of solvers are assumed: compressible, incompressible and basic solvers.
   Compressible turbulent flow solvers

   For example buoyantPimpleFoam or buoyantSimpleFoam. These solvers simulate heat transfer and compute
   the effective thermal conductivity automatically. They include the file turbulentFluidThermoModel.H and
   instantiate a compressible::turbulenceModel. This is needed in the adapter as a part of the effective
   conductivity is affected by the turbulence.

   Assumptions:

       Temperature is a registered IOObject named T.
       The dictionaries turbulenceProperties and thermophysicalProperties are provided.

   Incompressible turbulent flow solvers
   Conjugate heat transfer

   For example buoyantBoussinesqPimpleFoam or buoyantBoussinesqSimpleFoam. These solvers simulate heat
   transfer but do not compute the effective thermal conductivity, as they don't know the density of the
   fluid or the heat capacity. Therefore, values for these need to be provided. The adapter looks for them
   in the transportProperties dictionary.

   For example, the following lines need to be added in the constant/transportProperties file:

   rho              rho [ 1 -3  0  0 0 0 0 ] 50;
   Cp               Cp  [ 0  2 -2 -1 0 0 0 ] 5;

   The solver itself does not need to read these values.

   Assumptions:

       Temperature is a registered IOObject named T.
       The dictionaries turbulenceProperties and transportProperties are provided.
       transportProperties contains density rho and heat capacity Cp.
       The turbulent thermal diffusivity is a registered IOObject named alphat. If it is not found, then only the
       laminar part of the thermal diffusivity is used (a warning is triggered in this case).

       Fluid-structure interaction

       For incompressible solvers (e.g. pimpleFoam), the adapter tries expects the kinematic viscosity nu and
       the density rho in the constant/transportProperties file. See also Configuration.
       Basic solvers

   For example laplacianFoam can simulate heat transfer, using a thermal diffusion parameter DT. The adapter
   additionally expects a value for the conductivity k in the transportProperties dictionary.

   For example, the following lines need to be present in the constant/transportProperties file for the laplacianFoam:

   DT               DT  [ 0  2 -1  0 0 0 0 ] 1;
   k                k   [ 1  1 -3 -1 0 0 0 ] 100;

   Do not delete the, already provided in the pure solver, DT, as laplacianFoam expects it. The value of k is connected
   to the one of DT and depends on the density (rho [ 1 -3 0 0 0 0 0 ]) and heat capacity (Cp [ 0 2 -2 -1 0 0 0 ]).
   It needs to hold DT = k / rho / Cp. The solver itself does not need to read the additional parameter.

   Assumptions:

       Temperature is a registered IOObject named T.
       The dictionary transportProperties is provided.
       transportProperties contains the conductivity k.

   Other solvers

   If a solver uses different variable names, or if its type is not determined automatically, you may define these in
   the adapter's configuration file.

   Notes on OpenFOAM features
   End of the simulation

   The adapter (by default) ignores the endTime set in the controlDict and stops the simulation when preCICE says so.

   Let's see this with more details. During the simulation, both the solver and preCICE try to control when the simulation
   should end. While in an explicit coupling scenario this is clearly defined, in an implicit coupling scenario the solver
   may schedule its exit (and therefore the last call to the adapter) before the coupling is complete. See how function
   objects are called for more details on this.

   In order to prevent early exits from the solver, the solver's endTime is set to infinity and it is later set to the
   current time when the simulation needs to end. This has the side effect of not calling any function object's end()
   method normally, so these are triggered explicitly at the end of the simulation.

   In order to disable this behavior, you may define the option preventEarlyExit: No in the adapter's configuration file.
   Still, if the solver exits before the coupling completes, a warning will be reported.
   Function Objects

   In principle, using other function objects alongside the preCICE adapter is possible. They should be defined before
   the adapter in the system/controlDict, as (by default and opt-out) the adapter controls when the simulation should
   end and explicitly triggers (only) the end() methods of any other function objects at the end of the simulation.
   If the end() of a function object depends on its execute(), then the latter should have been called before the preCICE
   adapter's execute().

   If you want to test this behavior, you may also include e.g. the ``systemCall``
   function object in your system/controlDict::

     functions
     {

         systemCall1
         {
           type        systemCall;
           libs        ("libutilityFunctionObjects.so");

           executeCalls
           (
               "echo \*\*\* systemCall execute \*\*\*"
           );

           writeCalls
           (
               "echo \*\*\* systemCall write \*\*\*"
           );

           endCalls
           (
               "echo \*\*\* systemCall end \*\*\*"
           );
         }

       preCICE_Adapter
       {
           type preciceAdapterFunctionObject;
           libs ("libpreciceAdapterFunctionObject.so");
       }

     }

   Writing results

   As soon as OpenFOAM writes the results, it will not try to write again if the time takes the same value again. Therefore, during an implicit coupling, we write again when the coupling timestep is complete. See also a relevant issue.
   Adjustable timestep and modifiable runTime

   In the system/controlDict, you may optionally specify the following:

   adjustTimeStep  yes;
   maxCo           0.5;

   runTimeModifiable yes;

   The adapter works both with fixed and adjustable timestep and it supports the runTimeModifiable feature. However, if you set a fixed timestep and runTimeModifiable, changing the configured timestep during the simulation will not affect the timestep used. A warning will be shown in this case.
   Disclaimer

   This offering is not approved or endorsed by OpenCFD Limited, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM® and OpenCFD® trade marks.

   5. Execute the build script: ./Allwmake.

           See and adjust the configuration in the beginning of the script first, if needed.
           If everything goes well, you will receive a success message.
           If you receive a message that there were undefined symbols, this probably means that you used preCICE as a static library,
           but you didn't specify its dependencies correctly.
           In any case, make sure that your OpenFOAM environment is loaded correctly (e.g. see the WM_PROJECT_VERSION value in the
           beginning of the Allwmake output).

        Note: If any dependencies are not installed in the standard system paths, the locations of their headers need to be specified
        in the CPLUS_INCLUDE_PATH and of their libraries in the LIBRARY_PATH or LD_LIBRARY_PATH.

   Configuration
   ===============

   In order to run a coupled simulation, you need to:

   - prepare a preCICE configuration file (described in the preCICE configuration),
   - prepare an adapter's configuration file,
   - set the coupling boundaries in the OpenFOAM case,
   - load the adapter, and
   - start all the solvers normally, from the same directory, e.g. in two different terminals.