Ensure that the following dependencies are installed before compiling PetIBM:
- GNU C++ Compiler(
g++) version 4.6 or above - Git distributed version control system (
git) - PETSc version 3.5.0 or above (use branch
petsc-3.4-compatibleto run with PETSc 3.4) - Boost version 1.55.0 or above
PetIBM has been tested and run on Ubuntu 12.04, Ubuntu 14.10 and Mac OS X 10.9.
On Ubuntu, install g++ using the following command:
> sudo apt-get install g++
Check the version of G++ installed:
> g++ --version
Other development and version control tools can be installed by following the instructions under Step 1 in the CompilingEasyHowTo page on the Ubuntu Community Help Wiki. Software developers will find it useful to install all of them.
g++ can be installed on Mac OS X by installing XCode through the App Store.
Install git. On Ubuntu, this can be done via the Terminal using the following command:
> sudo apt-get install git-core
You can download and install git on OS X from here.
Install PETSc-3.5.2 in the optimized mode by running the following:
> cd $HOME
> mkdir src
> cd src
> wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.5.2.tar.gz
> tar -xvzf petsc-lite-3.5.2.tar.gz
> cd petsc-3.5.2
> ./configure --with-debugging=0 --COPTFLAGS=-O3 --FOPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --download-fblaslapack --download-mpich
> make all test
All production runs must be compiled and run using the optimized mode.
The debug mode is recommended during development. To install PETSc in debug mode, use the following flags in the configure step:
> ./configure --download-fblaslapack --download-mpich
When running the code on an external cluster, make sure that you compile PETSc with the MPI that has been configured to
work with the cluster. Hence, do not use the --download-mpich flag, and instead point to the folder with the MPI
compilers and executables using the --with-mpi-dir flag. If BLAS and LAPACK are already installed in the system, you
can point to the libraries using the --with-blas-lib and --with-lapack-lib flags.
If you are installing PETSc-3.4, use the option --download-f-blas-lapack instead of --download-fblaslapack.
Detailed instructions with more options to customize
your installation can be found on the PETSc website. Run ./configure --help in the PETSc root directory to list all
the available configure flags.
The PETSc Users Manual and the Manual Pages can be found on their documentation page.
Before compiling PetIBM, set the environment variables PETSC_DIR and PETSC_ARCH. These will be displayed at the
end of the configure step during PETSc installation. You can either set them through the command line or insert the
following lines in your ~/.bashrc or ~/.bash_profile files:
> export PETSC_DIR=$HOME/src/petsc-3.5.2
> export PETSC_ARCH=arch-linux2-c-opt
Set the environment variable BOOST_INCLUDE in your ~/.bashrc or ~/.bash_profile files:
> export BOOST_INCLUDE=/path/to/boost/include
Replace the values above with the version and mode specific to your installation. Use the setenv command to do
the same in C shell. Restart the terminal or source the file:
> source $HOME/.bashrc
Create a local copy of the PetIBM repository:
> cd $HOME/src
> git clone https://github.com/barbagroup/PetIBM.git
Compile all the files:
> cd PetIBM
> make
The following case simulates flow over an impulsively started 2-D circular cylinder at Reynolds number 40. It runs with 2 MPI processes.
> cd $HOME/src/PetIBM
> make cylinderRe40
Postprocess the results:
The Python script plotFields2d.py generates the contour of the velocity components, the pressure and the vorticity at saved time-steps. The following command-line displays the list of options available:
> python scripts/python/plotFields2d.py --help
For example, the contours, for the 2-D circular cylinder at Reynolds number 40, are generated with:
> python scripts/python/plotFields2d.py --case cases/2d/cylinder/Re40 --bottom-left -2.0 -2.0 --top-right 4.0 2.0
To generate .vtk files, readable by open-source visualization tools such as Paraview or VisIt, use the Python scripts: generateVTKFiles2d.py (2-D cases) and generateVTKFiles3d.py (3-D cases).
Please e-mail Anush Krishnan, Olivier Mesnard if you have any questions, suggestions or feedback.