Installation/Linux/OpenFOAM-4.0/CentOS SL RHEL

From OpenFOAMWiki

1 Introduction

This page is dedicated to explaining how to install OpenFOAM
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in:
  • Community ENTerprise Operating System, aka CentOS.
  • Red Hat Enterprise Linux, aka RHEL.
  • Scientific Linux, aka SL.

In theory, all of the above follow the same versioning. Therefore, at the time this page was first written, RHEL, CentOS and SL were all at version 6.8.

Both SL and CentOS derive from RHEL, but CentFOAM is what inspired this (and other related instruction pages). Therefore, before even trying to follow the instructions on this page, try first CentFOAM.

Last but not least, RHEL uses Fedora as their bleeding edge Linux Distribution, where they test new features. This leads to very close similarities between them, e.g. RHEL 6.3 is very similar to Fedora 14; which means that whatever you can build on Fedora 14, you should also be able to build on RHEL 6.3!

If you do not yet feel comfortable using Linux, then perhaps you better first read the page Working with the Shell and train a bit with the shell/terminal environments, so you can have a better perception of the steps shown below.


2 Copy-Paste steps

A few notes before you start copy-pasting:

  1. Lines that start with # don't have to be copy-pasted. They are just comments to let you know what's going on.
  2. One wrong character is enough for breaking this guide, so make sure you can read the characters properly or that the installed language system does not break the copied characters!


2.1 CentOS 6.8

You can follow either one of these instructions:


Notes regarding the instructions below:

  • The instructions below were tested with CentOS 6.8, but might work with 6.6, 6.7 or newer versions.


Discussion thread where you can ask questions about these steps: No thread available. Please a create a new thread in the forum.

Steps:

  1. Switch to root mode (administrator), to install the necessary packages:
    sudo -s
    • If the 'sudo' command tells you're not in the sudoers list, then run:
      su -
  2. Install the necessary packages:
    yum groupinstall 'Development Tools' 
    yum install openmpi openmpi-devel zlib-devel texinfo gstreamer-plugins-base-devel \
    libXext-devel libGLU-devel libXt-devel libXrender-devel libXinerama-devel libpng-devel \
    libXrandr-devel libXi-devel libXft-devel libjpeg-turbo-devel libXcursor-devel \
    readline-devel ncurses-devel python python-devel
     
    #This one is useful, but not crucial
    yum upgrade
  3. Now exit from the root mode:
    exit
  4. Start a new terminal. This is because you'll need a fully refreshed shell.
  5. Download and unpack (here you can copy-paste all in single go):
    #OpenFOAM downloading and installation
    cd ~
    mkdir OpenFOAM
    cd OpenFOAM
    wget "http://download.openfoam.org/source/4-0" -O OpenFOAM-4.0.tgz
    wget "http://download.openfoam.org/third-party/4-0" -O ThirdParty-4.0.tgz
     
    tar -xzf OpenFOAM-4.0.tgz
    tar -xzf ThirdParty-4.0.tgz
     
    mv OpenFOAM-4.x-version-4.0 OpenFOAM-4.0
    mv ThirdParty-4.x-version-4.0 ThirdParty-4.0
    But we will now have to download a few more of the necessary packages for the ThirdParty-4.0 folder:
    1. First, we need to prepare for the downloads:
      cd ThirdParty-4.0
      mkdir download
    2. Now, we need to download the essential source code packages for these instructions you are following (the links are from the file README.org):
      wget -P download http://www.cmake.org/files/v3.2/cmake-3.2.1.tar.gz
      wget -P download https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-4.8/CGAL-4.8.tar.xz
      wget -P download http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.bz2
    3. Next, we need to unpack the packages we've downloaded:
      tar -xzf download/cmake-3.2.1.tar.gz
      tar -xJf download/CGAL-4.8.tar.xz
      tar -xjf download/boost_1_55_0.tar.bz2
    4. Last but not least, the final command on this sub-list is to go back to the main OpenFOAM folder:
      cd ..
  6. A few details need to be fixed, before proceeding, which will change the default Boost version:
    sed -i -e 's/\(boost_version=\)boost-system/\1boost_1_55_0/' OpenFOAM-4.0/etc/config.sh/CGAL
    sed -i -e 's/\(cgal_version=\)cgal-system/\1CGAL-4.8/' OpenFOAM-4.0/etc/config.sh/CGAL
  7. For building OpenFOAM itself, it depends on whether you have installed the i386 or x86_64 architecture of CentOS/SL/RHEL. To check this, run:
    uname -m

    Now, accordingly:

    • For i386:
      #forcefully load Open-MPI into the environment
      #the export command has been reported as needed due to the 
      #module not being available in a clean installation
      module load openmpi-i386 || export PATH=$PATH:/usr/lib/openmpi/bin
       
      #ignore any error messages given by the command above
       
      source $HOME/OpenFOAM/OpenFOAM-4.0/etc/bashrc WM_COMPILER_TYPE=ThirdParty WM_ARCH_OPTION=32 FOAMY_HEX_MESH=yes

      Also, save an alias in the personal .bashrc file, simply by running the following command:

      echo "alias of40='module load openmpi-i386; source \$HOME/OpenFOAM/OpenFOAM-4.0/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 4.0 shell environment. In other words, whenever you start a new terminal, you should run:
      of40
      
      For more information on this topic, read section Using aliases to help manage multiple OpenFOAM versions in the page Installation/Working with the Shell.
    • For x86_64, it depends on whether you need 64-bit integer support or not. But first, common to both, we will forcefully load Open-MPI into the environment (the export command has been reported as needed due to the module not being available in a clean installation):
      module load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin

      Note: Ignore any error messages given by the command above.
      Now, depending on whether you need 64-bit integer support or not:

      • For building with the normal 32-bit integer support (maximum 2.147×109 cells, faces or points):
        source $HOME/OpenFOAM/OpenFOAM-4.0/etc/bashrc WM_COMPILER_TYPE=ThirdParty FOAMY_HEX_MESH=yes
      • For building with the normal 64-bit integer support (maximum 9.22×1018 cells, faces or points):
        source $HOME/OpenFOAM/OpenFOAM-4.0/etc/bashrc WM_LABEL_SIZE=64 WM_COMPILER_TYPE=ThirdParty FOAMY_HEX_MESH=yes

      Also, save an alias in the personal .bashrc file, simply by running the following command:

      echo "alias of40='module load openmpi-x86_64; source \$HOME/OpenFOAM/OpenFOAM-4.0/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 4.0 shell environment. In other words, whenever you start a new terminal, you should run:
      of40
      
      For more information on this topic, read section Using aliases to help manage multiple OpenFOAM versions in the page Installation/Working with the Shell.

    Note: You probably will see a message similar to this one and it's meant to do so until we've built the custom Gcc version:

    Warning in /home/user/OpenFOAM/OpenFOAM-4.0/etc/config/settings.sh:
        Cannot find /home/user/OpenFOAM/ThirdParty-4.0/platforms/linux64/gcc-4.8.4 installation.
        Please install this compiler version or if you wish to use the system compiler,
        change the 'WM_COMPILER_TYPE' setting to 'system'
  8. Now we'll have to get all of the scripts we'll need to build GCC and binutils (because OpenFOAM-4.0 requires at least GCC 4.5 and CentOS only provides GCC 4.4):
    cd $WM_THIRD_PARTY_DIR
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getGcc"
    wget "https://raw.github.com/wyldckat/ThirdParty-2.0.x/binutils/makeBinutils"
    wget "https://raw.github.com/wyldckat/ThirdParty-2.0.x/binutils/getBinutils"
    chmod +x get* make*
  9. CentOS 6.8 comes with CMake 2.6.4, but ParaView 5.0.1 needs a one of the versions from the more recent CMake 3.x series and CGAL also needs CMake. Therefore, we'll need to do a custom build and we have to do it before we build the custom GCC+binutils (reason: [1]):
    cd $WM_THIRD_PARTY_DIR
    ./makeCmake > log.makeCmake 2>&1
    wmRefresh
    • Note: If you've already tried building CMake and got this error message:
      note: 'keypad' is defined in DSO /lib64/libtinfo.so.5 so try adding it to the linker command line

      Then run:

      mv $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_ARCH_OPTION/gcc-4.8.5 $WM_THIRD_PARTY_DIR/platforms/linux64/gcc-4.8.5.bak
      ./makeCmake > log.makeCmake 2>&1
      mv $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_ARCH_OPTION/gcc-4.8.5.bak $WM_THIRD_PARTY_DIR/platforms/linux64/gcc-4.8.5
      wmRefresh
  10. Now let's get and build Gcc 4.8.5 and company:
    ./getGcc gcc-4.8.5 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1
    ./makeGcc -no-multilib > log.makeGcc 2>&1
    wmRefresh

    If it still gives you the same error message from #3, then something went wrong...

  11. Now let's get and build a custom GNU Binutils:
    ./getBinutils
    ./makeBinutils gcc-4.8.5 > log.makeBinutils 2>&1
  12. Now let's build CGAL, because we need to use custom options and we need the shell environment to be updated afterwards, for CGAL to be properly picked up for building OpenFOAM:
    # This next command will take a little while...
    ./makeCGAL gmp-5.1.2 mpfr-3.1.2 > log.makeCGAL 2>&1
     
    #update the shell environment
    wmRefresh
  13. CentOS 6.8 comes with Qt 4.6.2, but ParaView 5.0.1 needs at least 4.7. Therefore, we'll need to do a custom build of Qt 4.8.6:
    cd $WM_THIRD_PARTY_DIR
     
    #Get the scripts we need
    wget https://github.com/wyldckat/scripts4OpenFOAM3rdParty/raw/master/getQt
    wget https://github.com/OpenFOAM/ThirdParty-2.4.x/raw/master/makeQt
    wget -P etc/tools/ https://github.com/OpenFOAM/ThirdParty-2.4.x/raw/master/etc/tools/QtFunctions
     
    #make them executable
    chmod +x getQt makeQt
     
    #define correct download version and download it
    sed -i -e 's=4\.6=4.8=' -e 's=4\.8\.4=4.8.6=' -e 's=/\$major/\$tarFile=/$major/$version/$tarFile=' getQt
    ./getQt
     
    ./makeQt qt-4.8.6 > log.makeQt 2>&1
  14. Now, in order to build ParaView 5.0.1 that comes with OpenFOAM:
    1. For building ParaView 5.0.1 with Python and MPI, run:
      cd $WM_THIRD_PARTY_DIR
       
      #this will take a while... somewhere between 30 minutes to 2 hours or more
      ./makeParaView -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.6/bin/qmake -mpi -python > log.makePV 2>&1
    2. Once the makeParaView script is finished running, make sure to check the contents of the file log.makePV and check if there are any errors. If you have any problems building or using ParaView, please check the ParaView installation FAQ page.
    3. Finally, update the shell environment:
      wmRefresh
  15. Now let's build OpenFOAM:
    1. Go into OpenFOAM's main source folder:
      cd $WM_PROJECT_DIR
    2. This next command will take a while... somewhere between 30 minutes to 3-6 hours:
      ./Allwmake -j 4 > log.make 2>&1

      Note: The "4" refers to the number of cores to be used for building in parallel. In addition, the amount of RAM needed for building scales with the number of cores used, something like 1GB of RAM per core; a minimum of 1.5GB is needed for linking the libraries, which is not done in parallel.

    3. Run it a second time for getting a summary of the installation:
      ./Allwmake -j 4 > log.make 2>&1

      Note: Technically, the build will stop as soon as the first error is found. Running a second time only makes it easier to sort through between what's already been built and where the crash occurred.

  16. To check if everything went well:
    1. Check if icoFoam is working, by running this command:
      icoFoam -help

      which should tell you something like this:

      Usage: icoFoam [OPTIONS]
      options:
        -case <dir>       specify alternate case directory, default is the cwd
        -noFunctionObjects
                          do not execute functionObjects
        -parallel         run in parallel
        -roots <(dir1 .. dirN)>
                          slave root directories for distributed running
        -srcDoc           display source code in browser
        -doc              display application documentation in browser
        -help             print the usage

      Note: And keep in mind that you need to be careful with the letter case of the command. It's icoFoam, not icoFOAM.

    2. If the previous command failed to work properly, then edit the file log.make and check if there are any error messages. A few examples on how you can edit this file:
      • By using kwrite:
        kwrite log.make
      • By using gedit:
        gedit log.make
      • By using nano:
        nano log.make

        You can then exit by using the key combination Ctrl+X and following any instructions it gives you.

      Note: It's the first error message that matters.

    3. If you don't understand the output, then please compress the log-file log.make and attach the compressed file to a post in the designated thread.
      If you do not know how to create a compressed file, then try one of the following examples:
      • You can compress the file with gzip by running this command:
        gzip < log.make > log.make.gz

        Then attach the resulting package file named log.make.gz to a post in the designated thread.

      • Or you can compress one or more log-files into a tarball package file, by running this command:
        tar -czf logs.tar.gz log.*

        Then attach the resulting package file named logs.tar.gz to a post in the designated thread.

    4. Instructions on how to further diagnose the issue yourself, have a look at the section Common errors when building OpenFOAM from source code in the page FAQ/Installation and Running.
  17. Now you can go read the User Guide: official OpenFOAM User Guide


Reminder: Whenever you start a new terminal window or tab, you should run the alias command associated to the OpenFOAM 4.0 shell environment. In other words, run the following command whenever you start a new terminal:
of40
For more information on this topic, read section Using aliases to help manage multiple OpenFOAM versions in the page Installation/Working with the Shell.


Discussion thread where you can ask questions about these steps: No thread available. Please a create a new thread in the forum.