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FD3D installation instruction

System requirements

  • Operating system

    UNIX-like operating system (e.g., LINUX or OS X)

  • PETSc (version 3.5 or higher)

  • MaxwellFDFD

    MaxwellFDFD is a companion MATLAB package to create the input files for FD3D and analyze the solution files. MaxwellFDFD (and MATLAB) does not have to be installed on the same machine you install FD3D. In fact, FD3D is typically installed on a LINUX cluster, whereas MaxwellFDFD is installed on your local machine, such as your laptop.

How to install PETSc

  1. Download the PETSc library source code from the PETSc download page.

  2. Unarchive the PETSc package, and move it to the directory where you want to install the library.

    For example, you can create a directory petsc under your home directory and move the package there. Then, the contents of the PETSc package will be at $HOME/petsc/petsc-X.Y.Z/, where X.Y.Z is the version number.

  3. Define the environment variables PETSC_DIR and PETSC_ARCH.

    If your LINUX SHELL is bash, you can open .bash_profile file in your home directory (or create one if there is not), and add the following two lines to the file:

     export PETSC_DIR=YOUR_PETSC_DIRECTORY
 export PETSC_ARCH=petscfd3d

    where YOUR_PETSC_DIRECTORY is where your PETSc package exists, e.g., $HOME/petsc/petsc-X.Y.Z in Step 2.

  4. Make the environment variables effective.

    If your LINUX shell is bash and you followed Step 3, this can be done by executing:

     source `$HOME/.bash_profile`.

  5. Copy the PETSc configuration script from FD3D.

    In your FD3D directory, you will find petscfd3d.py script. Copy this to $PETSC_DIR/config/ directory.

  6. Make the configuration script executable.

    This can be done by executing:

     cd $PETSC_DIR/config
 chmod u+x petscfd3d.py

  7. Configure PETSc.

    Execute:

     cd $PETSC_DIR
 config/petscfd3d.py

    Now, you will see a long configuration message.

  8. Build PETSc.

    Execute:

     make all

  9. Test PETSc.

    Execute:

     make test

    If you do not get any error, your PETSc installation is successful. If you have any problem, you may find a solution at PETSc Documentation: Installation.

How to install FD3D

Follow this instruction after you install the PETSc library following the instruction above.

  1. Unarchive the FD3D package, and move it to the directory where you want to install the library.

    For example, you can put the unarchived package in your home directory. Then the contents of the FD3D package will be at $HOME/fd3d/.

  2. Define the environment variable FD3D_ROOT.

    You have to let FD3D know its install location via an environment variable named FD3D_ROOT. If your LINUX shell is bash, you can create $HOME/.fd3d file with the following line using your favorite text editor:

    export FD3D_ROOT=$HOME/fd3d

    Then open $HOME/.bash_profile file with your favorite text editor to append:

    source $HOME/.fd3d
export PATH=$PATH:$FD3D_ROOT/bin

  3. Make the environment variable effective.

    Execute:

     source $HOME/.bash_profile

  4. Build FD3D.

    Move to $FD3D_ROOT/src/ directory by:

     cd $FD3D_ROOT/src

    If this does not place you in $FD3D_ROOT/src/ directory, it means Step 1, 2 are not done correctly.

    Now, copy $FD3D_ROOT/src/makefiles/makefile.tmp file to $FD3D_ROOT/src/ directory and rename it to makefile by:

     cp makefiles/makefile.tmp makefile

    Finally, build fd3d by executing:

     make

    in $FD3D_ROOT/src/ directory.

  5. Test FD3D.

    In $FD3D_ROOT/test/ directory, there are input files pointsrc_2d.h5, poinstsrc_2d.eps.gz, pointsrc_2d.srcJ.gz, pointsrc_2d.srcM.gz. To create these files you need to install MaxwellFDFD, a companion MATLAB package of FD3D, but these input files are provided so that you can test FD3D without installing MaxwellFDFD.

    To test FD3D, execute:

     cd $FD3D_ROOT/test
 gzip -d pointsrc_2d.{eps,srcJ,srcM}.gz
 fd3d -i pointsrc_2d

    If this generates normal standard output without error messages, your FD3D installation is successful.