LinuxInstall

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How to compile Kratos: Linux

In this section we are going to go through the process of compiling a basic version of Kratos Multiphysics under linux environments. Specifically, we explain how to compile in Ubuntu 14.04 LTS, with the latest checked libraries. A basic knowledge of Linux is assumed ( execute commands, create directories, etc...)

Git

  • Objectives:
    • Install git
    • Get Kratos Multiphysics source code

The first thing you will need is the Kratos Multiphysics source code. To download the code you will have to use a git. You can install the default git by using this command:

   sudo apt-get install git

Once git is installed you can fetch the code by using these commands:

   git clone https://github.com/KratosMultiphysics/Kratos Kratos

Dev Packages

  • Objectives:
    • Get Python3-dev
    • Get G++
    • Get Fortran compiler
    • Get LIBBLAS and LIBLAPACK

You will need python dev files in order to compile kratos and some of its dependent libraries. Whether you wish to use python 3 ( recommended ) or python 2, you will need to install its dev files. This guide will show the process to install python 3.4 dev files, as is its recommended version. Additionally you will need a G++ and fortran compiler, which are not present in ubuntu 14.04 by default. Finally it will be also need an implementation of blas and lapack. You can obtain all these dependencies by running this command:

   sudo apt-get install python-dev python3-dev gcc g++ gfortran libblas-dev liblapack-dev

Boost

  • Objectives:
    • Compile boost libraries

Important: Version 1.60, 1.63 and 1.64 are not compatible with Kratos

The next step will consist in compile Boost. Kratos Multiphysics needs Boost libraries to support some of its functions. You can use any version from version 1.54 onward, except version 1.60, which is not supported due to a bug with python wrappers. This bug has been fixed in version 1.61.

It's very important to add the correct path to the boost library in the configure.sh, see more below. You can download boost from its official website:

   http://www.boost.org/users/download/

Navigate to the directory where you have extracted boost and execute this command:

   sh bootstrap.sh

Some additional files will be generated.

By default, boost will try to link with python 2.7. It is important to manually specify that we want to use python 3 by adding “using python : 3.4 : /usr ;” to the file project-config.jam. It will look like this:

   # Boost.Build Configuration
   # Automatically generated by bootstrap.sh
   
   import option ;
   import feature ;
   
   # Compiler configuration. This definition will be used unless
   # you already have defined some toolsets in your user-config.jam
   # file.
   if ! gcc in [ feature.values <toolset> ]
   {
       using gcc ; 
   }
   
   project : default-build <toolset>gcc ;
   
   # Python configuration
   using python : 3.4 : /usr ;
   
   # List of --with-<library> and --without-<library>
   # options. If left empty, all libraries will be built.
   # Options specified on the command line completely
   # override this variable.
   libraries =  ;
   
   # These settings are equivalent to corresponding command-line
   # options.
   option.set prefix : /usr/local ;
   option.set exec-prefix : /usr/local ;
   option.set libdir : /usr/local/lib ;
   option.set includedir : /usr/local/include ;
   
   # Stop on first error
   option.set keep-going : false ;

After modifying it you will have to compile the required boost libraries using this command. Notice that this will only compile “serialization” and “python” libraries. If you need further libraries, you will need to explicitly tell boost to compile them.

   ./b2 stage --with-python --with-serialization cxxflags="-std=c++11" link=shared,static

If you don't intend to debug your code you may want to compile with the 'variant=release' option which will reduce approximately 20% the compilation time:

   ./b2 stage --with-python --with-serialization cxxflags="-std=c++11" variant=release link=shared,static

CMake

  • Objectives:
    • Install CMake

Cmake is the tool used to compile kratos. To install it, the first option is to execute the following command (but check the version that will be installed, not all versions work, so see the warnings after these lines):

   sudo apt-get install cmake

Warn_icon.gif Warning. Please, note that:

Configure

  • Objectives:
    • Configure Kratos for the first time compilation

In order to compile kratos for the first time you will need to configure the project. First, navigate to your kratos/cmake_build folder and make a copy of the template file:

   cp example_configure.sh.do_not_touch configure.sh

Then, open configure.sh with any text editor and modify the lines that tell cmake where some components are located. You will need to provide at least BOOST_ROOT, PYTHON_LIBRARY and PYTHON_INCLUDE_DIR.

Option:

  • BOOST_ROOT: Directory where you have compiled boost
  • PYTHON_LIBRARY: Location of the python librarie used to compile boost
  • PYTHON_INCLUDE_DIR: Location of the python headers

Kratos has moved to C++11 recently, Please mind to add the "-std=c++11" to your compiler of choice. If you follow the example below, it is already present ( notice the flag in CMAKE_CXX_FLAGS, highlighted in bold)

For example, in ubuntu it will look something like:

   cmake ..                                                                            \
   -DCMAKE_C_COMPILER=/usr/bin/gcc                                                     \
   -DCMAKE_INSTALL_RPATH="/home/example/kratos/libs"                                   \
   -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE                                            \
   -DCMAKE_CXX_COMPILER=/usr/bin/g++                                                   \
   -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} -msse3" 		                               \
   -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -msse3 -std=c++11" 		               \
   -DBOOST_ROOT="~/compiled_libraries/boost_1_57_0"                                    \
   -DPYTHON_LIBRARY="/usr/lib/python3.4/config-3.4m-x86_64-linux-gnu/libpython3.4m.so" \
   -DPYTHON_INCLUDE_DIR="/usr/include/python3.4"                                       \
   -DMESHING_APPLICATION=ON                                                            \
   -DEXTERNAL_SOLVERS_APPLICATION=ON                                                   \
   
   // More options ( do not include this line )

Note that the "\" must be the last character in the line. Even an space will cause an error! (and the returned message is completely misleading, so be careful with this!!)

Notice that you can also turn ON/OFF parts of the code according to your necessities:

   -DSTRUCTURAL_APPLICATION=ON/OFF                                 

Warn_icon.gif Warning. Please, note that:

  • Cmake requires all definitions in a single line! The line concatenation character '\' therefore MUST NOT be followed by any whitespace in the same line as this would prevent the cmake from running the lines below

Compile

  • Objectives:
    • Compile kratos.

If you followed all the steps correctly, compile kratos should be as easy as executing the configure script:

   sh configure.sh

Please, notice that kratos is big and the compilation process can easily take 1 or 2 hours, depending on which applications are being compiled. A typical compilation process with the default configuration takes approximately 45 minutes with a i7 / 8GB Ram computer.

Setting up your enviroment

  • Objectives:
    • Tell Linux how to execute kratos

Once Kratos is compiled, you will have to tell the OS where to find the libraries. You can do that by executing these commands. Notice that you have to put the same path as in the section "Configure"

  echo "export PYTHONPATH=$PYTHONPATH:/path/to/my/kratos/installation" >> $HOME/.bashrc
  echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/my/kratos/installation/libs" >> $HOME/.bashrc

If you have enabled the embedded python option -DINSTALL_EMBEDDED_PYTHON=ON, you can also add

  echo "export PATH=$PATH:/path/to/my/kratos/installation" >> $HOME/.bashrc

In order to have the "runkratos" available as a regular command.

Now each time you open a terminal these commands will be executed and the paths set automatically. If you don't want to reset your terminal the first time, just execute:

   source ~/.bashrc

Test

  • Objectives:
    • Tests kratos

To to tests the compilation, you can execute a simple python script containing this line:

   from KratosMultiphysics import *

We strongly recommend you to run kratos scripts with the "runkratos" binary that will be generated inside your Kratos installation folder. You can also run them by using python (if you have compiled with python version 2.x.x), or python3 (if you have compiled with python version 3.x.x)

    runkratos test.py
    python test.py
    python3 test.py

If everething was ok you will see this message:

    |  /           |             
    ' /   __| _` | __|  _ \   __|
    . \  |   (   | |   (   |\__ \ 
   _|\_\_|  \__,_|\__|\___/ ____/
              Multi-Physics 3.3.11016

Troubleshooting

In this section we provide will try to provide solutions to the most common problems and issues that may appear during the compilation process

Cannot find KratosMultiphysics

Usually this happens when some environment variables are set wrong, or Kratos was not compiled. Make sure you compiled Kratos with no errors and you followed all the steps in the section Setting up your environment. To make sure that the variables are set correctly, you can always print their value from the terminal by typing:

echo $LD_LIBRARY_PATH

or

echo $PYTHONPATH

or

echo $PATH

Some shell interpreters have issues with the separator token. If environment variables above listed are correctly set, try to remove the ":" if kratos is the only path there.

# This may cause problem
echo $PYTHONPATH
:path/to/kratos
# Should be
export PYTHONPATH=path/to/kratos
echo $PYTHONPATH
path/to/kratos

I am getting Python link errors

This errors appear if the version of python used to compile boost is not the same as the one used by Kratos.

There are several causes that may be causing this. Pleas try the following:

Python version mismatch

The most provable reason for this error to happend is a missmatch between the python versions used by Kratos and Boost. Please, double check you have the same version of python in the projet-config.jam (boost) and configure.sh (Kratos) files.

Old version of CMake

If the error remains, please check that CMake version is 3.0.2 or newer. If it is not, it will be unable to load python 3.4. To solve the error please upgrade to CMake 3.0.2.

It has been observed that compiling with IDE's ( QTCreator, Netbeans, ...) sometimes causes this error as well. If you are experiencing this problem, try to modify the configure.sh script and replace cmake by the absolute path of CMake 3.0.2:

   /path/to/correct/cmake ..                                               \
   -DCMAKE_C_COMPILER=/usr/bin/gcc					   \
   ...


If for some reason you have to use an older version of CMake you can manually add support for python 3.4 by adding the version to these files:

   /usr/share/cmake-2.8/Modules/FindPythonLibs.cmake (line 41)
   /usr/share/cmake-2.8/Modules/FindPythonInterp.cmake (line 36)

Please add the version at the begining of the list:

   SET(_PYTHON1_VERSIONS 1.6 1.5)
   SET(_PYTHON2_VERSIONS 2.7 2.6 2.5 2.4 2.3 2.2 2.1 2.0)
   SET(_PYTHON3_VERSIONS 3.4 3.3 3.2 3.1 3.0)

I am getting lots of warnings when I compile Kratos

It is known that in some cases warnings appear while including boost files due to the fact that the flag "-Wunused-local-typedefs" is set by default in gcc.

This does not have any impact on the final code, but if you want a cleaner output you can add the flag "-Wno-unused-local-typedefs" to the configuration files:

   -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -msse3 -Wno-unused-local-typedefs" 		\
   -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} -msse3 -Wno-unused-local-typedefs" 		\
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