CFDEM Coupling installation in Ubuntu

Hello Everyone, I am attempting here to outline a step by step CFDEM installation procedure that worked for me. Kindly, help improve the same by suggestions and contributions.

Note: Slightly modified steps for following combination of compatibility at https://www.evernote.com/shard/s214/sh/0ec74d17-2173-4c6e-a156-6c8cbe418...
word CFDEMversion="cfdem-3.4.0";
word compatibleLIGGGHTSversion="3.4.0";
word OFversion="3.0.x-commit-ac3f6c67e02f0aac3777c27f9fb7558fc3536e37";

Note: CFDEM LIGGGHTS may not support vtk compiled LIGGGHTS, therefore, the following procedure will use non vtk compiled LIGGGHTS only. Also, CFDEM supports an speciifc version of LIGGGHTS and OpenFOAM. Therefore, if one is intended to install LIGGGHTS only for DEM use, then, it is better to have separate and very fresh installation of it. So that there is no conflict between only DEM LIGGGHTS and CFDEM LIGGGHTS. The procedure in following link can be followed to install LIGGGHTS separately:
http://www.cfdem.com/forums/liggghts-installation-guide-ubuntu-1204-lts-...

First of all check the compatibility of latest CFDEM coupling with version of LIGGGHTS and OpenFOAM.
To do so check file https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC/blob/master/src/lag...

For the present case it is like:
word CFDEMversion="cfdem-3.0.2";
word compatibleLIGGGHTSversion="3.3.1";
word OFversion="2.4.x-commit-3d8da0e960c717ff582f1517a27724144f086b83";

So, we will try installing the suggested versions only.

Reference web page https://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.4.0/Ubuntu

Reminder: Whenever you start a new terminal window or tab, you should run the alias command associated to the OpenFOAM 2.4.0 shell environment. In other words, run the following command whenever you start a new terminal:
of24x

OpenFOAM-2.4.x installation
Based on https://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.4.0/Ubuntu

1. sudo -s
2. apt-get install build-essential flex bison zlib1g-dev qt4-dev-tools libqt4-dev gnuplot libreadline-dev \
   libncurses-dev libxt-dev libopenmpi-dev openmpi-bin libboost-system-dev libboost-thread-dev libgmp-dev libmpfr-dev \
   python python-dev
3. apt-get install libglu1-mesa-dev libqt4-opengl-dev
4. exit
5. sudo apt-get install octave
6. sudo apt-get install epstool
7. git clone git://github.com/OpenFOAM/OpenFOAM-2.4.x.git
8. cd OpenFOAM-2.4.x
9. git checkout 3d8da0e960c717ff582f1517a27724144f086b83
10. see http://www.cfdem.com/forums/openfoam-installation-cfdemcoupling-publicsr... and change the export WM_MPLIB=SYSTEMOPENMPI at line number 85 (approx) [if it is not so]
11. wget "http://downloads.sourceforge.net/foam/ThirdParty-2.4.0.tgz?use_mirror=mesh" -O ThirdParty-2.4.0.tgz
12. tar -xzf ThirdParty-2.4.0.tgz
13. rm ThirdParty-2.4.0.tgz
14. mv ThirdParty-2.4.0 ThirdParty-2.4.x
15. ln -s /usr/bin/mpicc.openmpi OpenFOAM/OpenFOAM-2.4.x/bin/mpicc
16. ln -s /usr/bin/mpirun.openmpi OpenFOAM/OpenFOAM-2.4.x/bin/mpirun
17. uname -m
18. Open a new terminal
    for x86_64 enter following command
    source $HOME/OpenFOAM/OpenFOAM-2.4.x/etc/bashrc WM_NCOMPPROCS=4
19. Also, copy this line at the end of the ~/.bashrc file. And, reopen new terminal.
    echo "alias of24x='source \$HOME/OpenFOAM/OpenFOAM-2.4.x/etc/bashrc $FOAM_SETTINGS'" >> $HOME/.bashrc
    Note: This last line means that whenever you start a new terminal window or tab, you should run the alias command associated to the OpenFOAM 2.4.0 shell environment. In other words, whenever you start a new terminal, you should run:
    of24x
20. cd $WM_THIRD_PARTY_DIR
21. export QT_SELECT=qt4
22. ./Allwmake 
    (wait for the msg to come that all done, rerun the command to ensure the compilation)
23. ./Allwmake 
    (recheck it once again)
24. wmSET $FOAM_SETTINGS
    (If it says wmSET command not found then try: source OpenFOAM/OpenFOAM-2.4.x/etc/bashrc or source ../OpenFOAM-2.4.x/etc/bashrc if your are in $WM_THIRD_PARTY_DIR)
25. wmSET $FOAM_SETTINGS
    (If it says wmSET command not found then try: source OpenFOAM/OpenFOAM-2.4.x/etc/bashrc or source ../OpenFOAM-2.4.x/etc/bashrc if your are in $WM_THIRD_PARTY_DIR)
26. sed -i -e 's=version}\.3=version}.12.1=' getCmake
27. chmod +x getCmake
28. ./getCmake
29. ./makeCmake
30. wmSET $FOAM_SETTING
31. export QT_SELECT=qt4
32. sed -i -e 's=MPI_ARCH_PATH/include=MPI_ARCH_PATH/include;$MPI_INCLUDE=' etc/tools/ParaView4Functions
33. sed -i -e 's=//#define GLX_GLXEXT_LEGACY=#define GLX_GLXEXT_LEGACY=' \
    ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx/li>
34. cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0
35. wget http://www.paraview.org/pipermail/paraview/attachments/20140210/464496cc... -O Fix.patch
    patch -p1 < Fix.patch
36. cd VTK
37. wget https://github.com/gladk/VTK/commit/ef22d3d69421581b33bc0cd94b647da73b61... -O Fix2.patch
    patch -p1 < Fix2.patch
38. cd ../..
39. uname -m
40. #this will take a while... somewhere between 30 minutes to 2 hours or more
    ./makeParaView4 -python -mpi -python-lib /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0/li>
41. wmSET $FOAM_SETTINGS
42. cd $WM_PROJECT_DIR
43. find src applications -name "*.L" -type f | xargs sed -i -e 's=\ (YY\_FLEX\_SUBMINOR\_VERSION\)=YY_FLEX_MINOR_VERSION < 6 \&\& \1='
44. cd $WM_PROJECT_DIR
45. export QT_SELECT=qt4
46. ./Allwmake
47. ./Allwmake (#Run it a second time for getting a summary of the installation)
48. Test the installation
    icoFoam -help

CFDEM-3.0.2 and LIGGGHTS-3.3.1 installation preparation:

1. cd
2. sudo apt-get install octave
3. sudo apt-get install epstool
4. sudo apt-get install python-numpy
5. gedit ~/.bashrc
6. add at the bottom alias lpp="python $HOME/LPP/src/lpp.py"
7. cd
8. mkdir CFDEM
9. cd CFDEM
10. git clone git://github.com/CFDEMproject/CFDEMcoupling-PUBLIC.git CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION
11. [Optional]
    To get the latest version, open a terminal, go to the location of your local installation and type: Warning: git stash will remove your changes in $HOME/CFDEM/CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION!
    cd $HOME/CFDEM/CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION
    git stash
    git pull
12. cd
13. git clone git://github.com/CFDEMproject/LIGGGHTS-PUBLIC.git LIGGGHTS-PUBLIC
14. Download Pizza.py Toolkit from http://www.sandia.gov/~sjplimp/download.html and put the extracted dir as $HOME/
15. cd
16. Preparing liggghts
    LIGGGHTS has to be compiled with -fPIC CCFLAG switch thus, it is suggested to compile with Makefile.fedora_fpic, and ensure the following lines in it:
    CCFLAGS = -O2 \
    -funroll-loops -fstrict-aliasing -Wall -Wno-unused-result -fPIC
    SHFLAGS = -fPIC

LIGGGHTS-3.3.1 installation (see http://www.cfdem.com/forums/liggghts-installation-guide-ubuntu-1204-lts-... for any troubleshooting):

1. sudo apt-get install libvtk5-dev libeigen2-dev libopenmpi-dev g++ git-core
2. sudo apt-get install build-essential git
3. sudo apt-get install openmpi-common openmpi-bin libopenmpi-dev
4. sudo apt-get install cmake
5. sudo apt-get install cmake-curses-gui
6. ##Checking installations
   which mpirun
   /usr/bin/mpirun comes up?
   which mpic++
   /usr/bin/mpic++ comes up?
   mpic++ -v
   gcc-Version 4.7.3 (Ubuntu/Linaro 4.7.3-1ubuntu1) comes up at the last line?
7. sudo add-apt-repository ppa:jon-severinsson/ffmpeg
8. sudo apt-get update
9. sudo apt-get install ffmpeg
10. sudo apt-get install frei0r-plugins
11. cd
12. wget https://sites.google.com/site/rahuliitdhn/files-1/language-specs.tar.gz?...
13. tar -zxvf language-specs.tar.gz?...1
14. sudo mv $HOME/language-specs/liggghts.lang /usr/share/gtksourceview-3.0/language-specs
15. cd $HOME/LIGGGHTS-PUBLIC/src/
16. sudo make clean-all
17. sudo make fedora_fpic
18. sudo ln -s /$HOME/LIGGGHTS-PUBLIC/src/lmp_fedora_fpic /usr/bin/liggghts_fedora
19. sudo gedit ~/.bashrc
20. alias "liggghts_fedora=$HOME/LIGGGHTS-PUBLIC/src/lmp_fedora_fpic"

CFDEM-3.0.2 installation:

1. Setting up Environment Variables:
2. Add following lines at bottom
   ##================================================#
   ##- source cfdem env vars
   export CFDEM_VERSION=PUBLIC
   export CFDEM_PROJECT_DIR=$HOME/CFDEM/CFDEMcoupling-$CFDEM_VERSION-$WM_PROJECT_VERSION
   export CFDEM_SRC_DIR=$CFDEM_PROJECT_DIR/src
   export CFDEM_SOLVER_DIR=$CFDEM_PROJECT_DIR/applications/solvers
   export CFDEM_DOC_DIR=$CFDEM_PROJECT_DIR/doc
   export CFDEM_UT_DIR=$CFDEM_PROJECT_DIR/applications/utilities
   export CFDEM_TUT_DIR=$CFDEM_PROJECT_DIR/tutorials
   export CFDEM_PROJECT_USER_DIR=$HOME/CFDEM/$LOGNAME-$CFDEM_VERSION-$WM_PROJECT_VERSION
   export CFDEM_bashrc=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/bashrc
   export CFDEM_LIGGGHTS_SRC_DIR=$HOME/LIGGGHTS-PUBLIC/src
   export CFDEM_LIGGGHTS_MAKEFILE_NAME=fedora_fpic
   export CFDEM_LPP_DIR=$HOME/LPP/src
   export CFDEM_PIZZA_DIR=$HOME/PIZZA/pizza-9Oct15/src
   . $CFDEM_bashrc
   #================================================#
3. Reopen new terminal

or

4. bash
5. It will prompt to add user-public dir then say yes
6. check to see if any other errors are there
7. Save the ~/.bashrc, open a new terminal and test the settings. The commands:
   $CFDEM_PROJECT_DIR
   $CFDEM_SRC_DIR
   $CFDEM_LIGGGHTS_SRC_DIR
   should give "...: is a directory" otherwise something went wrong and the environment variables in ~/bashrc are not set correctly.
8. To specify the paths of pizza, please check the settings in
   $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/bashrc
   (Note that the lines similar to what we have added in the $HOME/.bashrc is available here but all are commented by default so no need to touch them)
9. If $CFDEM_SRC_DIR is set correctly, you can type
   cfdemSysTest
   to get some information if the paths are set correctly.

Compile LIGGGHTS(R) and CFDEM(R)coupling:

1. Go to your LIGGGHTS src directory and perform
   sudo make clean-all
2. Now compile:
   cfedmCompLIG
3. If previous compilation was successful, then compile CFDEM:
   Try things in following sequence (although cfdemCompCFDEM should be sufficient but we can try to compile one by one so that we can see where is error being logged):
   cfdemCompCFDEMsrc
   cfdemCompCFDEMsol
   cfdemCompCFDEMuti
   cfdemCompCFDEMall
   cfdemCompCFDEM
4. If you see the file $HOME/CFDEM/CFDEMcoupling-PUBLIC-2.4.x/src/lagrangian/cfdemParticle/etc/compileCFDEMcoupling.sh then it already compiles src, solver and utilities in the sequence and we have already compiled LIGGGHTS so only cfdemCompCFDEM is required.
5. Run cfdemTestTut to test the tutorials if the compilation was done properly.
6. Important commands related to CFDEM compilation defined in $HOME/CFDEM/CFDEMcoupling-PUBLIC-2.3.x/src/lagrangian/cfdemParticle/etc/bashrc
   cfdemCleanCFDEM cleans the cfdem built
   cfdemPullLIG pull the LIGGGHTS from web
   cfdemPullCFDEMcoupling pull cfdem coupling
   cfdemCompCFDEMall compiling cfdem coupling with LIGGGHTS
   cfdemCompCFDEM compiling cfdem (src+solvers)
   cfdemCompCFDEMsrc compiling cfdem src
   cfdemCompCFDEMsol compiling solvers
   cfdemCompCFDEMuti compiling utilities
   See full list of command in $HOME/CFDEM/CFDEMcoupling-PUBLIC-2.3.x/src/lagrangian/cfdemParticle/etc/bashrc