Skip to content

Latest commit

 

History

History
executable file
·
250 lines (149 loc) · 10.3 KB

mydoc_installation_source_100.md

File metadata and controls

executable file
·
250 lines (149 loc) · 10.3 KB
Raw
title keywords summary sidebar permalink folder
Installation guide for DAFoam v1.0.0
dafoam, installation, compile
mydoc_sidebar
mydoc_installation_source_100.html
mydoc

This section assumes you want to compile the DAFoam optimization package from the source on a Linux system. If you use the pre-compiled version, skip this section.

DAFoam runs on Linux systems and is based on OpenFOAM-v1812. You must install OpenFOAM and verify that it is working correctly. You also need to install the 3rd party and MDOLab packages before using DAFoam for optimization. Other dependencies include:

  • C/C++ compilers (gcc/g++ or icc/icpc)

  • Fortran compiler (gfortran or ifort)

  • MPI software (openmpi, mvapich2, or impi)

  • Swig

  • cmake

To compile the documentation, you also need:

  • Doxygen

  • Graphviz

  • Sphinx

NOTE: Always try to use the system provided C/Fortran compiler and MPI software to compile DAFoam and all its dependencies. Using self-built C/Fortran and MPI may cause linking issues

NOTE: For Ubuntu 18.04 users, you need to compile your own OpenMPI since the Ubuntu 18.04 comes with OpenMPI-2.1 which is known to have compatibility issues with the MDOLab packages. Please follow this page and use version OpenMPI-1.10.7. Make sure you compile OpenMPI before the following steps. After it is done, add this to your bashrc file and source it::

 export LD_PRELOAD=/change_this_to_your_compiled_openmpi_lib_path/libmpi.so

Note that the above is needed only for Ubuntu 18.04 because we compile our own OpenMPI.

NOTE: The following steps assume you use GNU compilers. For Intel compilers, users need to adjust settings in OpenFOAM and PETSc, and use configuration file config/defaults/config.LINUX_INTEL_OPENMPI.mk for each MDOLab repo.

|

To install the DAFoam package:

  1. Create a "OpenFOAM" folder in your home directory ($HOME). Go into the "OpenFOAM" directory and install OpenFOAM-v1812 following this website: http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-v1806/Ubuntu NOTE: DAFoam does not support long integer, so in OpenFOAM/OpenFOAM-v1812/etc/bashrc, use 32bit integer (WM_LABEL_SIZE=32), and double precision scalar (WM_PRECISION_OPTION=DP). After the OpenFOAM installation is done, start a new session to install the rest packages; DO NOT load the OpenFOAM environment. This is to prevent environmental variable conflict between OpenFOAM and other packages.

  2. Create a "packages" folder in your home directory. Go into the "packages" directory and install the following 3rd party packages:

  • Anaconda Python. NOTE: Anaconda2-2.4.0 is recommended since the newer version may have libgfortran conflict. Download https://repo.continuum.io/archive/Anaconda2-2.4.0-Linux-x86_64.sh and run::

    chmod 755 Anaconda2-2.4.0-Linux-x86_64.sh && ./Anaconda2-2.4.0-Linux-x86_64.sh

    When asked, put $HOME/packages/anaconda2 as the prefix for the installation path. At the end of the installation, reply "yes" to add the anaconda bin path to your bashrc.

  • PETSc v3.6.4. Download http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.4.tar.gz and untar it in the $HOME/packages folder, go into $HOME/packages/petsc-3.6.4, and run::

    sed -i 's/ierr = MPI_Finalize();CHKERRQ(ierr);/\/\/ierr = MPI_Finalize();CHKERRQ(ierr);/g' src/sys/objects/pinit.c

    This will comment out line 1367 in src/sys/objects/pinit.c to prevent Petsc from conflicting with OpenFOAM MPI. After this, run::

    ./configure --with-shared-libraries --download-superlu_dist --download-parmetis --download-metis --with-fortran-interfaces --with-debugging=no --with-scalar-type=real --PETSC_ARCH=real-opt --download-fblaslapack

    and after this, run::

     make PETSC_DIR=$HOME/packages/petsc-3.6.4 PETSC_ARCH=real-opt all

    Add the following into your bashrc and source it::

     export PETSC_DIR=$HOME/packages/petsc-3.6.4
 export PETSC_ARCH=real-opt
 export PATH=$PETSC_DIR/$PETSC_ARCH/bin:$PATH
 export PATH=$PETSC_DIR/$PETSC_ARCH/include:$PATH
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PETSC_DIR/$PETSC_ARCH/lib
 export PETSC_LIB=$PETSC_DIR/$PETSC_ARCH/lib

  • cgnslib_3.2.1 (http://cgns.sourceforge.net/download.html). Download cgnslib_3.2.1.tar.gz, put it in the $HOME/packages/ folder, and untar it. NOTE: The 3.2.1 version fortran include file is bad, so you need to manually edit the cgnslib_f.h file in the src directory and remove all the comment lines at the beginning of the file starting with "C". Then run::

     cmake .

    and::

     ccmake .

    A “GUI” appears and toggle ENABLE_FORTRAN by pressing [enter] (should be OFF when entering the screen for the first time, hence set it to ON). Type ‘c’ to reconfigure and ‘g’ to generate and exit. Then run::

     make

    Now add this into your bashrc and source it::

     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/packages/cgnslib_3.2.1/src

  • mpi4py-1.3.1 (http://bitbucket.org/mpi4py/mpi4py/downloads/). Untar and run::

     python setup.py install --user

    This will install the package to the .local directory.

  • petsc4py-3.6.0 (http://bitbucket.org/petsc/petsc4py/downloads/). Untar and run::

     python setup.py install --user

    This will install the package to the .local directory.

  1. Create a "repos" folder in your home directory. Go into the "repos" directory and download and install the following MDOLab packages (use small cases for all the repository names):

  • First add this to your bashrc and source it::

      export PYTHONPATH=$PYTHONPATH:$HOME/repos/

  • Get baseClasses. In the "repos" folder, Run::

      git clone https://github.com/mdolab/baseclasses && cd baseclasses && git checkout 298ac94 && cd ../

  • Get pyGeo. In the "repos" folder, Run::

      git clone https://github.com/mdolab/pygeo && cd pygeo && git checkout 90f4b90 && cd ../

  • Get openFoamMeshReader. In the "repos" folder, Run::

      git clone https://github.com/mdolab/openfoammeshreader && cd openfoammeshreader && git checkout d53d72d && cd ../

  • Get multipoint. In the "repos" folder, Run::

      git clone https://github.com/mdolab/multipoint && cd multipoint && git checkout 6818887 && cd ../

  • Get pySpline. In the "repos" folder, Run::

      git clone https://github.com/mdolab/pyspline && cd pyspline && git checkout 30f2340 && cd ../

    and in the "pyspline" folder, run::

      cp config/defaults/config.LINUX_GFORTRAN.mk config/config.mk && make

  • Get pyHyp. In the "repos" folder, Run::

      git clone https://github.com/mdolab/pyhyp && cd pyhyp && git checkout 926b3f7 && cd ../

    and in the "pyhyp" folder, run::

      cp -r config/defaults/config.LINUX_GFORTRAN_OPENMPI.mk config/config.mk && make

  • Get cgnsUtilities. In the "repos" folder, Run::

      git clone https://github.com/mdolab/cgnsutilities && cd cgnsutilities && git checkout 3430e04 && cd ../

    and in the "cgnsutilities" folder, run::

      cp config.mk.info config.mk && make

    Add this to your bashrc and source it::

      export PATH=$PATH:$HOME/repos/cgnsutilities/bin

  • Get IDWarp. In the "repos" folder, Run::

      git clone https://github.com/mdolab/idwarp && cd idwarp && git checkout 0149681 && cd ../

    and in the "idwarp" folder, run::

      cp -r config/defaults/config.LINUX_GFORTRAN_OPENMPI.mk config/config.mk && make

  • Get pyOptSparse. In the "repos" folder, Run::

      git clone https://github.com/mdolab/pyoptsparse && cd pyoptsparse && git checkout 6d2ae0a  && cd ../

    and in the "pyoptsparse" folder, run::

      python setup.py install --user

  1. Download DAFoam. In the "repos" folder, Run::

     git clone https://github.com/mdolab/dafoam

    Then, source the OpenFOAM environmental variables and compile ::

     source $HOME/OpenFOAM/OpenFOAM-v1812/etc/bashrc && ./Allwmake

    Next, go to $HOME/repos/dafoam/python/reg_tests, download input.tar.gz <https://github.com/mdolab/dafoam/raw/master/python/reg_tests/input.tar.gz>_ and untar it. Finally, run the regression test there::

     python run_reg_tests.py

    The regression tests should take less than 30 minutes. You should see something like::

     dafoam buoyantBoussinesqSimpleDAFoam: Success!
 dafoam buoyantSimpleDAFoam: Success!
 dafoam calcDeltaVolPointMat: Success!
 dafoam rhoSimpleCDAFoam: Success!
 dafoam rhoSimpleDAFoam: Success!
 dafoam simpleDAFoam: Success!
 dafoam simpleTDAFoam: Success!
 dafoam solidDisplacementDAFoam: Success!
 dafoam turboDAFoam: Success!

    You should see the first "Success" in less than 5 minute. If any of these tests fails or they take more than 30 minutes, check the error in the generated dafoam_reg_* files. Make sure all the tests pass before running DAFoam. NOTE: The regression tests verify the latest version of DAFoam on Github. However, we use specific old versions for DAFoam's dependencies (e.g., pyGeo, IDWarp).

|

In summary, here is the folder structures for all the installed packages::

 $HOME
   - OpenFOAM
     - OpenFOAM-v1812
     - ThirdParty-v1812
   - packages
     - anaconda2
     - cgnslib_3.2.1
     - mpi4py-1.3.1
     - petsc-3.6.4
     - petsc4py-3.6.0
   - repos
     - baseclasses
     - cgnsutilities
     - dafoam
     - idwarp
     - multipoint
     - openfoammeshreader
     - pygeo
     - pyhyp
     - pyoptsparse
     - pyspline

Here is the DAFoam related environmental variable setup that should appear in your bashrc file::

 # PETSC
 export PETSC_DIR=$HOME/packages/petsc-3.6.4
 export PETSC_ARCH=real-opt
 export PATH=$PETSC_DIR/$PETSC_ARCH/bin:$PATH
 export PATH=$PETSC_DIR/$PETSC_ARCH/include:$PATH
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PETSC_DIR/$PETSC_ARCH/lib
 export PETSC_LIB=$PETSC_DIR/$PETSC_ARCH/lib
 
 # cgns lib
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/packages/cgnslib_3.2.1/src

 # cgns utilities
 export PATH=$PATH:$HOME/repos/cgnsutilities/bin

 # Python path
 export PYTHONPATH=$PYTHONPATH:$HOME/repos

 # Anaconda2
 export PATH="$HOME/packages/anaconda2/bin:$PATH"

{% include links.html %}