Downloading and Installing¶

Downloading bemio¶

bemio is distributed through the bemio GitHub repositiory.

Note

The folder that contains the bemio source code will be referred to as $BEMIO_SOURE.

Dependencies¶

Python: Python 2.7.x and the following Python packages are required to run bemio. These packages can easily be installed using using pip or your preferred package instillation method:

numpy

scipy

matplotlib

progressbar2

astropy

h5py

Visualization Toolkit (VTK): If you would like to use the bemio.mesh_utilities, that allow you to manipulate simple mesh files, you will also have to install VTK and the Python 2.7.x bindings. Instructions for how to install VTK are provided in the Installing VTK with Python Bindings section.

HDFVIEW: Although not required, bemio users will benefit from installing HDFVIEW. HDFVIEW allows bemio users to view and interact with the bemio output files.

Installing: Quick Start for Python Beginners¶

Step 1 - Install Python: It can be a pain to install Python, NumPy, SciPy, Matplotlib, h5py and other dependencies that are needed to run bemio. If you’re new to Python, the easiest approach is to start by installing one of the science and engineering oriented Python distributions:

Anaconda (Linux, Mac, Windows)

PythonXY (Windows)

Note

If you are using Anaconda, PythonXY or another non-Python.org distribution, you may need to install one of the packages identified in the Dependencies section. If you need to do so, you should install any needed packages via your distribution’s package manager.

Step 2 - Download bemio: Download bemio from the GitHub repositiory

Step 3 - Install bemio: Open a command window (Windows) or terminal window (OSX and Linux) and navigate to $BEMIO_SOURCE. Once inside the $BEMIO_SOURCE folder, execute the following command to install bemio:

python setup.py install --user

Step 4 - Test the instillation: Test the bemio by running the following command from a command prompt inside the $BEMIO_SOURCE folder:

python install_test.py

If the tutorial cases (located in $BEMIO_SOURCE/tutorials) run successfully you will receive a success messages.

Installing: For Experienced Python Users¶

These instructions assume the user has an advanced level of Python knowledge.

Step 1 - Install Python: Install Python 2.7.x and the Python modules identified in the Dependencies section.

Step 2 - Download bemio: Download bemio from the GitHub repositiory

Step 3 - Install bemio: Add the $BEMIO_SOURCE folder to your PYTHONPATH.

Step 4 - Test the instillation: Test bemio by running the following command from a command prompt inside the $BEMIO_SOURCE folder:

python install_test.py

If the tutorial cases (located in $BEMIO_SOURCE/tutorials) run successfully you will receive a success messages.

Installing VTK with Python Bindings¶

In order to use bemio.mesh_utilities packaged with bemio you must have the Visualization Toolkit (VTK) and the VTK Python 2.7.x bindings installed on your system. Installing VTK with the Python bindings is optional and is only required to use the bemio.mesh_utilities.

Note

Installing the VTK Python bindings is only required if you would like to use bemio’s bemio.mesh_utilities features.

Note

Some Python distributions, such as Anaconda and PythonXY, may include VTK bindings, however, it is recommended that bemio users install VTK using the instructions in this section because the VTK versions distributed with Anaconda and PythonXY are not kept current.

OSX¶

Method 1: Simple¶

Install VTK using MacPorts, Fink, or HomeBrew. If you would like to install VTK using this method you should also install Python and other bemio dependencies using this method.

Method 2: Complex¶

Pre-Installation Tasks¶

Step 1: Insure the following software is installed on your system:

Python is preloaded on OSX systems and XCode can be installed through the OSX App Store . The other packages can easily be installed using MacPorts, Fink, or HomeBrew. Here is an example of how to install cmake, tck, and tk using MacPorts:

sudo port install cmake
sudo port install tcl
sudo port install tk

Step 2: Download and unzip the latest version of VTK from here - http://www.vtk.org/download.

Note

The folder that contains the VTK source code will be referred to as $VTK_SOURCE

Install¶

Open a terminal window and use the following procedure to compile VTK and the Python bindings.

# Move to the VTK source directory
mlawson@mbp:~$ cd $VTK_SOURCE

# Make a directory for the build and move into the build directory
mlawson@mbp:VTK-6.2.0$ mkdir build
mlawson@mbp:VTK-6.2.0$ cd build

# Run cmake in interactive mode. Insure that the ``PYTHON_VERSION`` is set to ``2``, the
# ``VTK_WRAP_PYTHON`` is set to ``ON, and ``BUILD_SHARED_LIBS`` is set to ON. ``BUILD_SHARED_LIBS``
# is not always visable and you may need to enter the "advnacec mode" by pressing ``t`` to confirm this option is
# correctly set. After the options are properly set, press ``c`` to configure and then ``g``
# to generate the required make files.
mlawson@mbp:VTK-6.2.0$ sudo ccmake ..

    BUILD_DOCUMENTATION              OFF
    BUILD_EXAMPLES                   OFF
    BUILD_SHARED_LIBS                ON       # May need to toggle advanced mode to view this option
    BUILD_TESTING                    OFF
    BUILD_USER_DEFINED_LIBS          OFF
    CMAKE_BUILD_TYPE                 Release
    CMAKE_FRAMEWORK_INSTALL_PREFIX   /usr/local/frameworks
    IOS_DEVICE_ARCHITECTURES         arm64;armv7;armv7s
    IOS_SIMULATOR_ARCHITECTURES      i386;x86_64
    OPENGL_ES_VERSION                2.0
    VTK_ANDROID_BUILD                OFF
    VTK_Group_Imaging                OFF
    VTK_Group_MPI                    OFF
    VTK_Group_Qt                     OFF
    VTK_Group_Rendering              ON
    VTK_Group_StandAlone             ON
    VTK_Group_Tk                     OFF
    VTK_Group_Views                  OFF
    VTK_Group_Web                    OFF
    VTK_IOS_BUILD                    OFF
    VTK_PYTHON_VERSION               2
    VTK_SMP_IMPLEMENTATION_TYPE      Sequential
    VTK_USE_LARGE_DATA               OFF
    VTK_WRAP_JAVA                    OFF
    VTK_WRAP_PYTHON                  ON
    VTK_WRAP_TCL                     OFF

    BUILD_DOCUMENTATION: Build the VTK documentation
    Press [enter] to edit option                                                 CMake Version 3.2.2
    Press [c] to configure
    Press [h] for help           Press [q] to quit without generating
    Press [t] to toggle advanced mode (Currently Off)

# Build VTK using make - this will take a while :(
mlawson@mbp:VTK-6.2.0$ sudo make

Linux¶

Install VTK and the VTK Python bindings using your system’s package manager or adapt the OSX instructions described above.

Windows¶

No instructions available at this time.