Installation/Linux/OpenFOAM-v1712/CentOS SL RHEL

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< Installation‎ | Linux‎ | OpenFOAM-v1712
Revision as of 16:49, 27 October 2018 by Wyldckat (Talk | contribs)

1 Introduction

This page is dedicated to explaining how to install OpenFOAM+ OF Version 1712plus.png 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 6.9.

Both SL and CentOS derive from RHEL, but CentFOAM is what inspired this (and other related instruction pages).

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 6.9

Here you have the following choices:

  • You can install from source, by either:


Notes regarding the instructions below:

  • The instructions below were tested with CentOS 6.9, but might work with older or newer 6.x versions. Try it out and let us know on the forum.


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 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
     
    #This one is useful, but not crucial
    yum upgrade
  3. Optional: Python 2.6 that is provided in CentOS 6.x is not enough to use ParaView 5.4.0 with Python support. Therefore, either Python 2.7, 3.3 or newer has to be installed from another repository or it has to be built from source code. In these instructions we will rely on the Software Collections ( SCL ) Repository, which can be used to install software in a non-intrusive way... which will require its own environment loading mechanism. The steps to install it are as follows:
    1. Still as root, install the aforementioned SCL repository:
      yum install centos-release-SCL
    2. Then install the Python 2.7 package:
      yum install python27
    3. To check if it's installed, run:
      scl --list
    4. For future reference, the easiest way to activate the environment on the current command line is to run, but do not do this right now:
      source /opt/rh/python27/enable

      This command will be indicated to be executed at the right point in the instructions below.

  4. Now exit from the root mode:
    exit
  5. Start a new terminal. This is because you'll need a fully refreshed shell.
  6. Download and unpack (here you can copy-paste all in single go):
    #OpenFOAM+ downloading and installation
    cd ~
    mkdir OpenFOAM
    cd OpenFOAM
    wget "http://downloads.sourceforge.net/openfoamplus/files/OpenFOAM-v1712.tgz?use_mirror=mesh" -O OpenFOAM-v1712.tgz
    wget "http://downloads.sourceforge.net/openfoamplus/files/ThirdParty-v1712.tgz?use_mirror=mesh" -O ThirdParty-v1712.tgz
     
    tar -xzf OpenFOAM-v1712.tgz
    tar -xzf ThirdParty-v1712.tgz
  7. A few details need to be fixed, before proceeding:
    sed -i -e 's=gmp-system=gmp-5.1.2=' -e 's=mpfr-system=mpfr-3.1.2='  -e 's=mpc-system=mpc-1.0.1=' OpenFOAM-v1712/etc/config.sh/compiler
    sed -i -e 's/\(boost_version=\)boost-system/\1boost_1_55_0/' OpenFOAM-v1712/etc/config.sh/CGAL
    sed -i -e 's/\(cgal_version=\)cgal-system/\1CGAL-4.10/' OpenFOAM-v1712/etc/config.sh/CGAL
    sed -i -e 's/\(cmake_version=\)cmake-system/\1cmake-3.9.0/' OpenFOAM-v1712/etc/config.sh/paraview
  8. 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:
      source $HOME/OpenFOAM/OpenFOAM-v1712/etc/bashrc WM_COMPILER_TYPE=ThirdParty WM_COMPILER=Gcc48 WM_ARCH_OPTION=32 WM_MPLIB=OPENMPI

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

      echo "alias of1712='source \$HOME/OpenFOAM/OpenFOAM-v1712/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-v1712 shell environment. In other words, whenever you start a new terminal, you should run:
      of1712
      
      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:
      • For building with the normal 32-bit integer support (maximum 2.147×109 cells, faces or points):
        source $HOME/OpenFOAM/OpenFOAM-v1712/etc/bashrc WM_COMPILER_TYPE=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=OPENMPI
      • For building with the normal 64-bit integer support (maximum 9.22×1018 cells, faces or points):
        source $HOME/OpenFOAM/OpenFOAM-v1712/etc/bashrc  WM_LABEL_SIZE=64 WM_COMPILER_TYPE=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=OPENMPI

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

      echo "alias of1712='source \$HOME/OpenFOAM/OpenFOAM-v1712/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-v1712 shell environment. In other words, whenever you start a new terminal, you should run:
      of1712
      
      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/bmss/OpenFOAM/OpenFOAM-v1712/etc/config.sh/settings:
    Cannot find 'Gcc48' compiler installation
        /home/bmss/OpenFOAM/ThirdParty-v1712/platforms/linux64/gcc-4.8.5
     
        Either install this compiler version, or use the system compiler by setting
        WM_COMPILER_TYPE to 'system' in $WM_PROJECT_DIR/etc/bashrc.
    ===============================================================================
    </li>
     
    <li>Now we'll have to get all of the scripts we'll need to build GCC and binutils (because OpenFOAM-1712 requires at least GCC 4.8 and CentOS only provides GCC 4.4):
    <bash>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 6.9 comes with CMake 2.6.4, but ParaView 5.4.0 needs a one of the versions from the more recent CMake 3.0 or newer 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
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getCmake"
    chmod +x getCmake
    sed -i -e 's=2\.8=3.9=' -e 's=version}\.3=version}.0=' getCmake
    ./getCmake
    ./makeCmake cmake-3.9.0 > log.makeCM 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 cmake-3.9.0 > log.mkcmake 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 > log.mkgcc 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.mkbinutils 2>&1
  12. CentOS 6.9 comes with Qt 4.6.2, but ParaView 5.4.0 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
     
    #make it executable
    chmod +x getQt
     
    #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
     
    #need to remove the c++11 standard from the build options, since this Qt version doesn't properly support this standard
    export WM_CXXFLAGS=$(echo $WM_CXXFLAGS | sed -e 's/-std=c++11 //')
     
    ./makeQt qt-4.8.6 > log.mkqt 2>&1
  13. For building ParaView 5.4.0 with Python and MPI, it depends on whether you have installed the i686 or x86_64 architecture of CentOS 6.:
    1. To check this, run:
      uname -m

      Now, accordingly:

      • For i686:
        cd $WM_THIRD_PARTY_DIR
         
        # Load the Python 2.7 that came with the SCL repository
        source /opt/rh/python27/enable
         
        #this will take a while... somewhere between 30 minutes to 2 hours or more
        ./makeParaView -qt-4.8.6 -mpi -python -python-lib /opt/rh/python27/root/usr/lib/libpython2.7.so -python-include /opt/rh/python27/root/usr/include/python2.7 > log.makePV 2>&1

        Note: If the SCL repository is not being used when following these instructions, then run the last line like this:

        ./makeParaView -qt-4.8.6 -mpi > log.makePV 2>&1
      • For x86_64:
        cd $WM_THIRD_PARTY_DIR
         
        # Load the Python 2.7 that came with the SCL repository
        source /opt/rh/python27/enable
         
        #this will take a while... somewhere between 30 minutes to 2 hours or more
        ./makeParaView -qt-4.8.6 -mpi -python -python-lib /opt/rh/python27/root/usr/lib64/libpython2.7.so -python-include /opt/rh/python27/root/usr/include/python2.7 > log.makePV 2>&1

        Note: If the SCL repository is not being used when following these instructions, then run the last line like this:

        ./makeParaView -qt-4.8.6 -mpi > 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
  14. Now let's build OpenFOAM:
    1. Go into OpenFOAM's main source folder:
      cd $WM_PROJECT_DIR
    2. We need to temporarily populate CMAKE_PREFIX_PATH with the path to the custom Qt build, so that qmake is properly found when building OpenFOAM's plug-in libraries for ParaView:
      export CMAKE_PREFIX_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.6/
    3. 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.

    4. 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.

  15. 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.
  16. Now you can go read the User Guide, where you may have more than one choice:
    1. Which you can find a local copy of the User Guide by running the following command:
      ls -A1 $WM_PROJECT_DIR/doc/Guides*/*UserGuide*.pdf
      • You should see two available formats: A4 and US-Letter.
      • But if it instead tells you that there is No such file or directory, then either the OpenFOAM environment is possibly not properly activated, or the version no longer provides PDF documentation with the installation.
    2. You can find the more recent OpenFOAM Documentation online that is provided by ESI-OpenCFD at the following page: OpenFOAM® Documentation - but be careful that if your version is older than the current release, then the instructions on the documentation may not work, because the documentation is updated with each new release.
      That said, if you need to upgrade custom code that was built with the older versions, they do provide instructions on what changed in the source code, that you will need to adapt to.


Reminder: Whenever you start a new terminal window or tab, you should run the alias command associated to the OpenFOAM-v1712 shell environment. In other words, run the following command whenever you start a new terminal:
of1712
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.