Installation/Linux/OpenFOAM-2.4.0/CentOS SL RHEL

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< Installation‎ | Linux‎ | OpenFOAM-2.4.0
Revision as of 15:18, 27 October 2018 by Wyldckat (Talk | contribs)

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1 Introduction

This page is dedicated to explaining how to install OpenFOAM OF Version 240.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 6.6.

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 5.11

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 5.11, but might work with 5.10 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 readline-devel ncurses-devel \
    texinfo gstreamer-plugins-base-devel libXext-devel libGLU-devel libXt-devel \
    libXrender-devel libXinerama-devel libpng-devel libXrandr-devel libXi-devel \
    libXft-devel libXcursor-devel
     
    #This one is useful, but not crucial
    yum upgrade
  3. In addition to this, we need the EPEL repository, so that we can install the package qtwebkit-devel needed for building ParaView 4.1.0 with Python 2.6. The latest RPM link is usually available here: EPEL FAQ: How can I install the packages from the EPEL software repository? The commands we'll use for this are as follows (the first one you might have to get the latest RPM link from the FAQ indicated above):
    wget http://download.fedoraproject.org/pub/epel/5/i386/epel-release-5-4.noarch.rpm
    rpm -Uvh epel-release-5-4.noarch.rpm
     
    #disable the EPEL repository from being turned on by default
    sed -i -e 's/enabled=1/enabled=0/' /etc/yum.repos.d/epel.repo
     
    #now install the packages we need from EPEL
    yum install --enablerepo=epel python26 python26-devel
  4. For building OpenFOAM itself and using the dedicated Open-MPI version, 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
      mpi-selector --system --set openmpi-1.4-gcc-i386
    • For x86_64:
      #forcefully load Open-MPI into the environment
      mpi-selector --system --set openmpi-1.4-gcc-x86_64
  5. Now exit from the root mode:
    exit
  6. Start a new terminal. This is because you'll need a fully refreshed shell.
  7. 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/foam/OpenFOAM-2.4.0.tgz?use_mirror=mesh" -O OpenFOAM-2.4.0.tgz
    wget "http://downloads.sourceforge.net/foam/ThirdParty-2.4.0.tgz?use_mirror=mesh" -O ThirdParty-2.4.0.tgz
     
    tar -xzf OpenFOAM-2.4.0.tgz 
    tar -xzf ThirdParty-2.4.0.tgz
  8. A few details need to be fixed, before proceeding, which will change the default GCC version 4.8.2 to 4.8.4, as well as switching to a custom built Boost version:
    sed -i -e 's=gcc\-4\.8\.2=gcc-4.8.4=' OpenFOAM-2.4.0/etc/config/settings.sh
    sed -i -e 's=boost-system=boost_1_54_0=' OpenFOAM-2.4.0/etc/config/CGAL.sh
  9. 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:
      #make sure you start a new terminal window!!
       
      #here you can change 4 to the number of cores you've got
      source $HOME/OpenFOAM/OpenFOAM-2.4.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty \
      WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI WM_ARCH_OPTION=32

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

      echo "alias of240='source \$HOME/OpenFOAM/OpenFOAM-2.4.0/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 2.4.0 shell environment. In other words, whenever you start a new terminal, you should run:
      of240
      
      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:
      #make sure you start a new terminal window!!
       
      #here you can change 4 to the number of cores you've got
      source $HOME/OpenFOAM/OpenFOAM-2.4.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty \
      WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI

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

      echo "alias of240='source \$HOME/OpenFOAM/OpenFOAM-2.4.0/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 2.4.0 shell environment. In other words, whenever you start a new terminal, you should run:
      of240
      
      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-2.4.0/etc/config/settings.sh:
        Cannot find /home/user/OpenFOAM/ThirdParty-2.4.0/platforms/linux64/gcc-4.8.4 installation.
        Please install this compiler version or if you wish to use the system compiler,
        change the 'foamCompiler' setting to 'system'
  10. Now we'll have to get all of the scripts we'll need to build GCC and binutils (because OpenFOAM 2.3 requires at least GCC 4.5 and CentOS only provides GCC 4.4):
    cd $WM_THIRD_PARTY_DIR
     
    # see Note below about wget
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getGcc"
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getBoost"
    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*
     
    #we need to disable the ''multilib'' functionality, since we won't need to build both 32 and 64bit architectures.
    sed -i -e 's=\(--with-system-zlib \)=\1--disable-multilib =' makeGcc

    Note: You can use an alias for wget command, because older systems can't handle very well HTTPS accesses, for example to raw.github.com. Therefore, before you run the first wget command, please run the following command:

    alias wget="wget --no-check-certificate"
  11. CentOS 5.11 comes with CMake 2.6.4, but ParaView 4.1.0 needs a one of the versions from the more recent CMake 2.8.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
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getCmake"
    sed -i -e 's=version}\.3=version}.12.1=' getCmake
    chmod +x getCmake
    ./getCmake
    ./makeCmake > log.mkcmake 2>&1
    wmSET $FOAM_SETTINGS

    Note: You can use an alias for wget command, because older systems can't handle very well HTTPS accesses, for example to raw.github.com. Therefore, before you run the first wget command, please run the following command:

    alias wget="wget --no-check-certificate"

    In addition to the previous note about wget:

    • 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-4.8.4 $WM_THIRD_PARTY_DIR/platforms/linux64/gcc-4.8.4.bak
      ./makeCmake > log.mkcmake 2>&1
      mv $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_ARCH_OPTION/gcc-4.8.4.bak $WM_THIRD_PARTY_DIR/platforms/linux64/gcc-4.8.4
      wmSET $FOAM_SETTINGS
  12. Now let's get and build Gcc 4.8.4 and company:
    ./getGcc gcc-4.8.4 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1
    ./makeGcc gcc-4.8.4 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1 > log.mkgcc 2>&1
    wmSET $FOAM_SETTINGS

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

  13. Now let's get and build a custom GNU Binutils:
    ./getBinutils
    ./makeBinutils gcc-4.8.4 > log.mkbinutils 2>&1
  14. Now let's get and unpack Boost and fix the version in makeCGAL:
    ./getBoost
    sed -i -e 's=boost-system=boost_1_54_0=' makeCGAL
  15. 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.mkcgal 2>&1
     
    #update the shell environment
    wmSET $FOAM_SETTINGS
  16. Now let's make a quick hack and then build OpenFOAM:
    #Go into OpenFOAM's main source folder
    cd $WM_PROJECT_DIR
     
    #little hack for using libncurses for setSet
    sed -i -e 's/LINK_FLAGS="\-lreadline"/LINK_FLAGS="-lreadline -lncurses"/' \
      $FOAM_UTILITIES/mesh/manipulation/setSet/Allwmake
     
    # This next command will take a while... somewhere between 30 minutes to 3-6 hours.
    ./Allwmake > log.make 2>&1
     
    #Run it a second time for getting a summary of the installation
    ./Allwmake > log.make 2>&1
  17. 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.
  18. CentOS 5.11 comes with Qt 4.2.1, but ParaView 4.1.0 needs at least 4.7. Therefore, we'll need to do a custom build of Qt 4.8.6:
    cd $WM_THIRD_PARTY_DIR
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getQt"
    chmod +x getQt
    sed -i -e 's=4\.6=4.8=' -e 's=4\.8\.4=4.8.6=' -e 's=/\$major/\$tarFile=/$major/$version/$tarFile=' getQt
    ./getQt
     
    ./makeQt qt-4.8.6 > log.mkqt 2>&1

    Note: You can use an alias for wget command, because older systems can't handle very well HTTPS accesses, for example to raw.github.com. Therefore, before you run the first wget command, please run the following command:

    alias wget="wget --no-check-certificate"
  19. Now, in order to build ParaView 4.1.0 that comes with OpenFOAM:
    1. We need to first apply a fix and then we can build with both MPI and Python support:
      cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0
      wget http://www.paraview.org/pipermail/paraview/attachments/20140210/464496cc/attachment.bin -O Fix.patch
      patch -p1 < Fix.patch
      cd ..
       
      sed -i -e 's=which python=which python26=' etc/tools/ParaView4Functions
    2. Now let's build ParaView:
      ./makeParaView4 -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.6/bin/qmake \
      PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python26 -mpi -python > log.makePV 2>&1

      While ParaView is being built, you might want to check the file log.makePV to check how it's coming along with the build and to check if there were any major errors; there could be some error messages, but some of them will not stop the build from concluding with success.

    3. Now let's build the official OpenFOAM reader for ParaView:
      cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers 
      wmSET $FOAM_SETTINGS
      ./Allwclean 
      ./Allwmake
  20. 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 the OpenFOAM environment is possibly not properly activated.
    2. You can also find the more recent OpenFOAM Foundation User Guides online at the following page: official OpenFOAM User Guide - but be careful if you use the version that is too much ahead of the version you are currently using, given that some features have changed overtime.


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:
of240
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.


2.2 CentOS 6.6

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 6.6, but might work with 6.5 or newer versions.


Discussion thread where you can ask questions about these steps: Installing OpenFOAM 2.4.0 on CentOS 6.6

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://downloads.sourceforge.net/foam/OpenFOAM-2.4.0.tgz?use_mirror=mesh" -O OpenFOAM-2.4.0.tgz
    wget "http://downloads.sourceforge.net/foam/ThirdParty-2.4.0.tgz?use_mirror=mesh" -O ThirdParty-2.4.0.tgz
     
    tar -xzf OpenFOAM-2.4.0.tgz 
    tar -xzf ThirdParty-2.4.0.tgz
  6. A few details need to be fixed, before proceeding, which will change the default GCC version 4.8.2 to 4.8.4, as well as switching to a custom built Boost version:
    sed -i -e 's=gcc\-4\.8\.2=gcc-4.8.4=' OpenFOAM-2.4.0/etc/config/settings.sh
    sed -i -e 's=boost-system=boost_1_54_0=' OpenFOAM-2.4.0/etc/config/CGAL.sh
  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
       
      #here you can change 4 to the number of cores you've got
      source $HOME/OpenFOAM/OpenFOAM-2.4.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty \
      WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI WM_ARCH_OPTION=32

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

      echo "alias of240='module load openmpi-i386; source \$HOME/OpenFOAM/OpenFOAM-2.4.0/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 2.4.0 shell environment. In other words, whenever you start a new terminal, you should run:
      of240
      
      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:
      #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 
       
      #ignore any error messages given by the command above
       
      #here you can change 4 to the number of cores you've got
      source $HOME/OpenFOAM/OpenFOAM-2.4.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty \
      WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI

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

      echo "alias of240='module load openmpi-x86_64; source \$HOME/OpenFOAM/OpenFOAM-2.4.0/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 2.4.0 shell environment. In other words, whenever you start a new terminal, you should run:
      of240
      
      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-2.4.0/etc/config/settings.sh:
        Cannot find /home/user/OpenFOAM/ThirdParty-2.4.0/platforms/linux64/gcc-4.8.4 installation.
        Please install this compiler version or if you wish to use the system compiler,
        change the 'foamCompiler' setting to 'system'
  8. Now we'll have to get all of the scripts we'll need to build GCC and binutils (because OpenFOAM 2.3 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/scripts4OpenFOAM3rdParty/master/getBoost"
    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*
     
    #we need to disable the ''multilib'' functionality, since we won't need to build both 32 and 64bit architectures.
    sed -i -e 's=\(--with-system-zlib \)=\1--disable-multilib =' makeGcc
  9. CentOS 6.6 comes with CMake 2.6.4, but ParaView 4.1.0 needs a one of the versions from the more recent CMake 2.8.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: [2]):
    cd $WM_THIRD_PARTY_DIR
    ./makeCmake > log.mkcmake 2>&1
    wmSET $FOAM_SETTINGS
    • 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-4.8.4 $WM_THIRD_PARTY_DIR/platforms/linux64/gcc-4.8.4.bak
      ./makeCmake > log.mkcmake 2>&1
      mv $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_ARCH_OPTION/gcc-4.8.4.bak $WM_THIRD_PARTY_DIR/platforms/linux64/gcc-4.8.4
      wmSET $FOAM_SETTINGS
  10. Now let's get and build Gcc 4.8.4 and company:
    ./getGcc gcc-4.8.4 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1
    ./makeGcc gcc-4.8.4 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1 > log.mkgcc 2>&1
    wmSET $FOAM_SETTINGS

    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-4.8.4 > log.mkbinutils 2>&1
  12. Now let's get and unpack Boost and fix the version in makeCGAL:
    ./getBoost
    sed -i -e 's=boost-system=boost_1_54_0=' makeCGAL
  13. 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.mkcgal 2>&1
     
    #update the shell environment
    wmSET $FOAM_SETTINGS
  14. Now let's build OpenFOAM:
    #Go into OpenFOAM's main source folder
    cd $WM_PROJECT_DIR
     
    # This next command will take a while... somewhere between 30 minutes to 3-6 hours.
    ./Allwmake > log.make 2>&1
     
    #Run it a second time for getting a summary of the installation
    ./Allwmake > log.make 2>&1
  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. CentOS 6.6 comes with Qt 4.6.2, but ParaView 4.1.0 needs at least 4.7. Therefore, we'll need to do a custom build of Qt 4.8.6:
    cd $WM_THIRD_PARTY_DIR
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getQt"
    chmod +x getQt
    sed -i -e 's=4\.6=4.8=' -e 's=4\.8\.4=4.8.6=' -e 's=/\$major/\$tarFile=/$major/$version/$tarFile=' getQt
    ./getQt
     
    ./makeQt qt-4.8.6 > log.mkqt 2>&1
  17. Now, in order to build ParaView 4.1.0 that comes with OpenFOAM:
    1. We need to first apply a fix and then we can build with both MPI and Python support:
      cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0
      wget http://www.paraview.org/pipermail/paraview/attachments/20140210/464496cc/attachment.bin -O Fix.patch
      patch -p1 < Fix.patch
      cd ..
    2. Now let's build ParaView:
      ./makeParaView4 -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.6/bin/qmake \
      -mpi -python > log.makePV 2>&1

      While ParaView is being built, you might want to check the file log.makePV to check how it's coming along with the build and to check if there were any major errors; there could be some error messages, but some of them will not stop the build from concluding with success.

    3. Now let's build the official OpenFOAM reader for ParaView:
      cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers 
      wmSET $FOAM_SETTINGS
      ./Allwclean 
      ./Allwmake
  18. 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 the OpenFOAM environment is possibly not properly activated.
    2. You can also find the more recent OpenFOAM Foundation User Guides online at the following page: official OpenFOAM User Guide - but be careful if you use the version that is too much ahead of the version you are currently using, given that some features have changed overtime.


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:
of240
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: Installing OpenFOAM 2.4.0 on CentOS 6.6


2.3 CentOS 7.1

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 7.1, but might work with 7.0 or newer versions.
  • There is no support for the 32-bit architectures in CentOS 7, therefore these instructions only address the x86_64 architecture.


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 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 cmake qt-devel qt-assistant \
    mpfr-devel gmp-devel
     
    #This one is useful, but not crucial
    yum upgrade
  3. In addition to this, we need the EPEL repository, so that we can install the package qtwebkit-devel needed for building ParaView 4.1.0. The latest RPM link is usually available here: EPEL FAQ: How can I install the packages from the EPEL software repository? The commands we'll use for this are as follows (the first one you might have to get the latest RPM link from the FAQ indicated above):
    rpm -Uvh http://download.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-5.noarch.rpm
     
    #disable the EPEL repository from being turned on by default
    sed -i -e 's/enabled=1/enabled=0/' /etc/yum.repos.d/epel.repo
     
    #now install the packages we need from EPEL
    yum install --enablerepo=epel qtwebkit-devel
  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/foam/OpenFOAM-2.4.0.tgz?use_mirror=mesh" -O OpenFOAM-2.4.0.tgz
    wget "http://downloads.sourceforge.net/foam/ThirdParty-2.4.0.tgz?use_mirror=mesh" -O ThirdParty-2.4.0.tgz
     
    tar -xzf OpenFOAM-2.4.0.tgz 
    tar -xzf ThirdParty-2.4.0.tgz
  7. A few details need to be fixed, namely switching to a custom built Boost version:
    sed -i -e 's=boost-system=boost_1_54_0=' OpenFOAM-2.4.0/etc/config/CGAL.sh
  8. For building OpenFOAM itself, you'll need to source the correct environment settings:
    #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 mpi/openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin 
     
    #ignore any error messages given by the command above
     
    #here you can change 4 to the number of cores you've got
    source $HOME/OpenFOAM/OpenFOAM-2.4.0/etc/bashrc WM_NCOMPPROCS=4 WM_MPLIB=SYSTEMOPENMPI

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

    echo "alias of240='module load mpi/openmpi-x86_64; source \$HOME/OpenFOAM/OpenFOAM-2.4.0/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 2.4.0 shell environment. In other words, whenever you start a new terminal, you should run:
    of240
    
    For more information on this topic, read section Using aliases to help manage multiple OpenFOAM versions in the page Installation/Working with the Shell.
  9. Now let's get and unpack Boost and fix the version in makeCGAL:
    cd $WM_THIRD_PARTY_DIR
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getBoost"
    chmod +x get*
    ./getBoost
    sed -i -e 's=boost-system=boost_1_54_0=' makeCGAL
  10. 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 > log.mkcgal 2>&1
     
    #update the shell environment
    wmSET $FOAM_SETTINGS
  11. Now let's build OpenFOAM:
    #Go into OpenFOAM's main source folder
    cd $WM_PROJECT_DIR
     
    # This next command will take a while... somewhere between 30 minutes to 3-6 hours.
    ./Allwmake > log.make 2>&1
     
    #Run it a second time for getting a summary of the installation
    ./Allwmake > log.make 2>&1
  12. 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.
  13. Now, in order to build ParaView 4.1.0 that comes with OpenFOAM:
    1. We need to first apply a fix and then we can build with both MPI and Python support:
      cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0
      wget http://www.paraview.org/pipermail/paraview/attachments/20140210/464496cc/attachment.bin -O Fix.patch
      patch -p1 < Fix.patch
      cd ..
    2. Now we can build ParaView:
      ./makeParaView4 -qmake $(which qmake-qt4) -mpi -python > log.makePV 2>&1

      While ParaView is being built, you might want to check the file log.makePV to check how it's coming along with the build and to check if there were any major errors; there could be some error messages, but some of them will not stop the build from concluding with success.

    3. Now let's build the official OpenFOAM reader for ParaView:
      cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers 
      wmSET $FOAM_SETTINGS
      ./Allwclean 
      ./Allwmake
  14. 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 the OpenFOAM environment is possibly not properly activated.
    2. You can also find the more recent OpenFOAM Foundation User Guides online at the following page: official OpenFOAM User Guide - but be careful if you use the version that is too much ahead of the version you are currently using, given that some features have changed overtime.


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:
of240
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.


2.4 CentOS 7.1 (on ARMv8 64-bit architecture)

NOTE: The following instructions are for building OpenFOAM 2.4.0 on the ARMv8 64-bit architecture. The work was done on ARM's Versatile Express Juno Development Platform. A description of the hardware is at http://www.arm.com/products/tools/development-boards/versatile-express/juno-arm-development-platform.php. The operating system is an aarch64 build of CentOS Linux 7 (release 7.1.1503).

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: Use the package-management utility 'yum' to install dependencies. The main packages required are: GNU c/c++ compiler; the multi-precision library GMP and MPFR; the Boost libraries; Qt and its dependencies. Many of these packages are pre-installed. The main steps performed were:
    yum install boost-devel
    yum install gmp-devel
    yum install mpfr-devel
    yum install qt-devel
    yum install readline-devel

    Note that on CentOs (or RHEL/Fedora type of operating systems), it is the development packages that are to be installed.

    Also note that CMake is required to build several OpenFOAM dependencies. However, do not use the CMake 3.x distributed with the system. Use CMake 2.8.12 distributed with OpenFOAM instead.

  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://downloads.sourceforge.net/foam/OpenFOAM-2.4.0.tgz?use_mirror=mesh" -O OpenFOAM-2.4.0.tgz
    wget "http://downloads.sourceforge.net/foam/ThirdParty-2.4.0.tgz?use_mirror=mesh" -O ThirdParty-2.4.0.tgz
     
    tar -xzf OpenFOAM-2.4.0.tgz 
    tar -xzf ThirdParty-2.4.0.tgz
  6. CentOs 7 only comes with OpenMPI 1.6.x. If this is a problem, one can optionally compile from source OpenMPI 1.8.5 (which matches the version distributed with OpenFOAM 2.4.0). This is done by the standard ./configure; make; make install procedure. Make sure the OpenMPI binaries are in PATH to be found by the OpenFOAM installer.
  7. Modify OpenFOAM configuration files: Modify the following three sets of configuration files before compiling OpenFOAM. Assuming Bash shell is used:
    • Open OpenFOAM-2.4.0/etc/bashrc in an editor, comment out line 45 so that it reads '#foamInstall=$HOME/$WM_PROJECT'. Later the $FOAM_INST_DIR variable will be set to specify the installation directory. The rest of this file normally should not be touched.
    • Open OpenFOAM-2.4.0/etc/config/settings.sh, go to the section starting at line 67 and add the following:
             aarch64)
              WM_ARCH=linux64
              export WM_COMPILER_LIB_ARCH=64
              export WM_CC='gcc'
              export WM_CXX='g++'
              export WM_CFLAGS='-fPIC'
              export WM_CXXFLAGS='-fPIC'
              export WM_LDFLAGS=''
              ;;
      This supplies the basic system information to the OpenFOAM installer. Note there is an existing 'armv7l' section for the old ARM systems.
    • Go to OpenFOAM-2.4.0/wmake/rules. This is where the compiler flags, among other settings, are located. Back up the linux64Gcc sub-directory. Reuse this folder for simplicity. Of course it would be much more elegant to create a new set of settings for the ARMv8 system. Create a new empty linux64Gcc sub-directory. Then copy the contents from linuxARM7Gcc. Edit the cOpt and c++Opt files and specify the following flags that need to be passed to the GNU C/C++ compiler:
         -O3 -floop-optimize -falign-loops -falign-labels -falign-functions
       -falign-jumps -march=armv8-a -mtune=cortex-a57 -mcpu=cortex-a57

      Note the hardware specific flags.

  8. Now run the following commands to initialize OpenFOAM's environment:
    export FOAM_INST_DIR=/path/to/OpenFOAM/   # adjust the installation directory
    export PATH=/path/to/openmpi-1.8.5/bin:$PATH  # adjust path to OpenMPI
    source $FOAM_INST_DIR/OpenFOAM-2.4.0/etc/bashrc
    export WM_NCOMPPROCS=4  # set the number of cores used to compile 
     

    Note the OpenMPI built earlier is added to $PATH. This is sufficient for OpenFOAM's build system.

  9. Build CMake: As mentioned earlier, build CMake 2.8.12 first as the one with the system is not compatible.
    cd $WM_THIRD_PARTY_DIR
    ./makeCmake 2>&1 | tee log.makeCmake
    wmSET $FOAM_SETTINGS
  10. Build other third-party libraries:
    cd $WM_THIRD_PARTY_DIR
    ./Allwmake 2>&1 | tee log.make
    wmSET $FOAM_SETTINGS
  11. Build OpenFOAM:
    cd $WM_PROJECT_DIR
    ./Allwmake 2>&1 | tee log.make.1
    ./Allwmake 2>&1 | tee log.make.2

    Note the the main build script is run a second time to generate a clean log file, which should contain no errors for a successful build. Note that by design, ARM hardware is considerably slower than x86 hardware. So compiling OpenFOAM, in particular this step, takes many hours to complete. For this reason, we did not attempt to compile ParaView.

  12. 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 the OpenFOAM environment is possibly not properly activated.
    2. You can also find the more recent OpenFOAM Foundation User Guides online at the following page: official OpenFOAM User Guide - but be careful if you use the version that is too much ahead of the version you are currently using, given that some features have changed overtime.