ZJLi2013 / PetIBM

Parallel immersed boundary method code.

PetIBM - A PETSc-based Immersed Boundary Method code

Installation instructions

Dependencies

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-compatible to run with PETSc 3.4)

PetIBM has been tested and run on Ubuntu 12.04 and Mac OS X 10.9.

GNU C++ Compiler (g++)

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.

Git (git)

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.

PETSc

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 --downloadfblaslapack --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.

Set environment variables

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

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

Compiling PetIBM

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

Run a test case

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:

> python scripts/python/plot.py -folder cases/2d/cylinder/Re40 -xmin -2 -xmax 4 -ymin -2 -ymax 2

Contour plots of the x and y components of velocity, the pressure and the vorticity will be written to the folder cases/2d/cylinder/Re40/output.

Contact

Please e-mail Anush Krishnan if you have any questions, suggestions or feedback.