Difference between revisions of "Installation/Linux/OpenFOAM-3.0.1/CentOS SL RHEL"

From OpenFOAMWiki
m (added override for ul)
m (fixed typo)
Line 308: Line 308:
 
</bash></li>
 
</bash></li>
  
<li>A few details need to be fixed, because proceeding, which will change the default Boost version:
+
<li>A few details need to be fixed, before proceeding, which will change the default Boost version:
 
<bash>sed -i -e 's=boost-system=boost_1_55_0=' OpenFOAM-3.0.1/etc/config/CGAL.sh
 
<bash>sed -i -e 's=boost-system=boost_1_55_0=' OpenFOAM-3.0.1/etc/config/CGAL.sh
 
</bash>
 
</bash>

Revision as of 15:43, 28 April 2016

1 Introduction

This page is dedicated to explaining how to install OpenFOAM OF Version 301.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 6.7.

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

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 4.4.0 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-3.0.1.tgz?use_mirror=mesh" -O OpenFOAM-3.0.1.tgz
    wget "http://downloads.sourceforge.net/foam/ThirdParty-3.0.1.tgz?use_mirror=mesh" -O ThirdParty-3.0.1.tgz
     
    tar -xzf OpenFOAM-3.0.1.tgz 
    tar -xzf ThirdParty-3.0.1.tgz
  8. A few details need to be fixed, before proceeding, which switching to a custom built Boost version:
    sed -i -e 's=boost-system=boost_1_55_0=' OpenFOAM-3.0.1/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-3.0.1/etc/bashrc foamCompiler=ThirdParty WM_ARCH_OPTION=32

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

      echo "alias of301='source \$HOME/OpenFOAM/OpenFOAM-3.0.1/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 3.0.1 shell environment. In other words, whenever you start a new terminal, you should run:
      of301
      
      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, make sure you start a new terminal window!!
      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-3.0.1/etc/bashrc foamCompiler=ThirdParty
      • For building with the normal 64-bit integer support (maximum 9.22×1018 cells, faces or points):
        source $HOME/OpenFOAM/OpenFOAM-3.0.1/etc/bashrc WM_LABEL_SIZE=64 foamCompiler=ThirdParty

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

      echo "alias of301='source \$HOME/OpenFOAM/OpenFOAM-3.0.1/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 3.0.1 shell environment. In other words, whenever you start a new terminal, you should run:
      of301
      
      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-3.0.1/etc/config/settings.sh:
        Cannot find /home/user/OpenFOAM/ThirdParty-3.0.1/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 3.0 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 4.4.0 needs a one of the versions from a 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"
    sed -i -e 's=2\.8=3.2=' -e 's=version}\.3=version}.1=' getCmake
    chmod +x getCmake
    ./getCmake
    ./makeCmake > mkcmake.log 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 > mkcmake.log 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 > mkgcc.log 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 > mkbinutils.log 2>&1
  14. Now let's get and unpack Boost and fix the version in makeCGAL:
    sed -i -e 's=boost_1_54_0=boost_1_55_0=' getBoost
    ./getBoost
    sed -i -e 's=boost-system=boost_1_55_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 > mkcgal.log 2>&1
     
    #update the shell environment
    wmSET $FOAM_SETTINGS
  16. Now let's build OpenFOAM:
    1. Go into OpenFOAM's main source folder:
      cd $WM_PROJECT_DIR

      And apply a little hack for using libncurses for setSet:

      sed -i -e 's/LINK_FLAGS="\-lreadline"/LINK_FLAGS="-lreadline -lncurses"/' \
        $FOAM_UTILITIES/mesh/manipulation/setSet/Allwmake
    2. This next command will take a while... somewhere between 30 minutes to 3-6 hours:
      ./Allwmake -j 4 > make.log 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 > make.log 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.


  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 4.4.0 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
    wget https://github.com/OpenFOAM/ThirdParty-3.0.x/raw/master/makeQt
    wget -P etc/tools/ https://github.com/OpenFOAM/ThirdParty-3.0.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 > mkqt.log 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 4.4.0 that comes with OpenFOAM:
    1. We need to first apply a fix and then we can build with Python support:
      cd $WM_THIRD_PARTY_DIR
      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: official OpenFOAM User Guide


Reminder: Whenever you start a new terminal window or tab, you should run the alias command associated to the OpenFOAM 3.0.1 shell environment. In other words, run the following command whenever you start a new terminal:
of301
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 6.7

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://downloads.sourceforge.net/foam/OpenFOAM-3.0.1.tgz?use_mirror=mesh" -O OpenFOAM-3.0.1.tgz
    wget "http://downloads.sourceforge.net/foam/ThirdParty-3.0.1.tgz?use_mirror=mesh" -O ThirdParty-3.0.1.tgz
     
    tar -xzf OpenFOAM-3.0.1.tgz 
    tar -xzf ThirdParty-3.0.1.tgz
  6. A few details need to be fixed, before proceeding, which will change the default Boost version:
    sed -i -e 's=boost-system=boost_1_55_0=' OpenFOAM-3.0.1/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
       
      source $HOME/OpenFOAM/OpenFOAM-3.0.1/etc/bashrc foamCompiler=ThirdParty WM_ARCH_OPTION=32

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

      echo "alias of301='module load openmpi-i386; source \$HOME/OpenFOAM/OpenFOAM-3.0.1/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 3.0.1 shell environment. In other words, whenever you start a new terminal, you should run:
      of301
      
      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-3.0.1/etc/bashrc foamCompiler=ThirdParty
      • For building with the normal 64-bit integer support (maximum 9.22×1018 cells, faces or points):
        source $HOME/OpenFOAM/OpenFOAM-3.0.1/etc/bashrc WM_LABEL_SIZE=64 foamCompiler=ThirdParty

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

      echo "alias of301='module load openmpi-x86_64; source \$HOME/OpenFOAM/OpenFOAM-3.0.1/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 3.0.1 shell environment. In other words, whenever you start a new terminal, you should run:
      of301
      
      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-3.0.1/etc/config/settings.sh:
        Cannot find /home/user/OpenFOAM/ThirdParty-3.0.1/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-3.0.1 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*
     
    #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 4.4.0 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: [2]):
    cd $WM_THIRD_PARTY_DIR
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getCmake"
    chmod +x getCmake
    sed -i -e 's=2\.8=3.2=' -e 's=version}\.3=version}.1=' getCmake
    ./getCmake
    ./makeCmake > log.makeCM 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 > mkcmake.log 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 > mkgcc.log 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 > mkbinutils.log 2>&1
  12. Now let's get Boost and fix the Boost version in makeCGAL:
    wget "https://raw.github.com/wyldckat/scripts4OpenFOAM3rdParty/master/getBoost"
    chmod +x getBoost
    sed -i -e 's=boost_1_54_0=boost_1_55_0=' getBoost
    ./getBoost
     
    sed -i -e 's=boost-system=boost_1_55_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 > mkcgal.log 2>&1
     
    #update the shell environment
    wmSET $FOAM_SETTINGS
  14. CentOS 6.7 comes with Qt 4.6.2, but ParaView 4.4.0 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
    wget https://github.com/OpenFOAM/ThirdParty-3.0.x/raw/master/makeQt
    wget -P etc/tools/ https://github.com/OpenFOAM/ThirdParty-3.0.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 > mkqt.log 2>&1
  15. Now, in order to build ParaView 4.4.0 that comes with OpenFOAM:
    1. For building ParaView 4.4.0 with Python and MPI, run:
      cd $WM_THIRD_PARTY_DIR
       
      #this will take a while... somewhere between 30 minutes to 2 hours or more
      ./makeParaView4 -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 makeParaView4 script is finished running, make sure to check the contents of the file log.makePV and check if there are any errors.
    3. Finally, update the shell environment:
      wmSET $FOAM_SETTINGS
  16. 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 > make.log 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 > make.log 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.

  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. 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 3.0.1 shell environment. In other words, run the following command whenever you start a new terminal:
of301
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.


2.3 CentOS 7.1

NOTE: 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 4.4.0. 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-3.0.1.tgz?use_mirror=mesh" -O OpenFOAM-3.0.1.tgz
    wget "http://downloads.sourceforge.net/foam/ThirdParty-3.0.1.tgz?use_mirror=mesh" -O ThirdParty-3.0.1.tgz
     
    tar -xzf OpenFOAM-3.0.1.tgz 
    tar -xzf ThirdParty-3.0.1.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_55_0=' OpenFOAM-3.0.1/etc/config/CGAL.sh
  8. Now it will depend 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):
    #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

    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-3.0.1/etc/bashrc
    • For building with the normal 64-bit integer support (maximum 9.22×1018 cells, faces or points):
      source $HOME/OpenFOAM/OpenFOAM-3.0.1/etc/bashrc WM_LABEL_SIZE=64

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

    echo "alias of301='module load openmpi-x86_64; source \$HOME/OpenFOAM/OpenFOAM-3.0.1/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 3.0.1 shell environment. In other words, whenever you start a new terminal, you should run:
    of301
    
    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*
    sed -i -e 's=boost_1_54_0=boost_1_55_0=' getBoost
    ./getBoost
    sed -i -e 's=boost-system=boost_1_55_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 > mkcgal.log 2>&1
     
    #update the shell environment
    wmSET $FOAM_SETTINGS
  11. 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 > make.log 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 > make.log 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.

  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 4.4.0 that comes with OpenFOAM:
    1. Now we can build ParaView with both MPI and Python support:
      cd $WM_THIRD_PARTY_DIR
      ./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.

    2. 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: official OpenFOAM User Guide


Reminder: Whenever you start a new terminal window or tab, you should run the alias command associated to the OpenFOAM 3.0.1 shell environment. In other words, run the following command whenever you start a new terminal:
of301
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.