Installation

The current version of pDynamo has been tested on machines running the Linux, MAC OS-X 10 and Windows operating systems.

Linux and MAC OS-X

  1. If older versions of pDynamo are installed, the environment variables and Python path definitions corresponding to these versions should be removed. This can be done by undefining the appropriate variables or by overwriting them with the definitions appropriate to the new version (see Step 10 below).
  2. Installation of pDynamo requires Python 2.7 and a C compiler. pDynamo employs some third-party libraries, notably BLAS and LAPACK, Cython and PyYAML, but basic versions of these come in the distribution and so need not be provided separately.
  3. Download the current version of the library, pdynamo-x.y.tgz.
  4. Put the downloaded file, pdynamo-x.y.tgz, in the directory where the library is to be installed.
  5. Type tar -xvzf pdynamo-x.y.tgz to unpack the downloaded file and create the directory pDynamo-x.y.
  6. Go to the directory containing third-party libraries by typing cd pDynamo-x.y/thirdParty.
  7. Install PyYAML and, optionally, Cython. This is done by going to the appropriate directories and typing python setup.py install. It is possible that this requires superuser privileges, in which case contact the system administrator.
  8. Go to the pDynamo installation directory, pDynamo-x.y/installation.
  9. Type python Install.py to install the library. This command can take a little while and will produce a lot of output.
  10. Set up the environment variables that are needed by the library. These are described in the file 00ReadMe.txt in the installation directory and are most conveniently placed in a shell configuration file, such as .bash_profile or .cshrc. As an aid to users, the installation procedure creates files in the installation directory that contain the necessary definitions for certain Unix shells. These are entitled environment_shell.com and can be adapted as appropriate.
  11. To test the library, type cd ../book/examples and then python RunExamples.py --all to run the full suite of examples or python RunExamples.py to run a selection of the shorter cases. The full set of tests take several hours to run and require about a gigabyte of disk space whereas the shorter examples take only a few minutes. Once the jobs are finished type python DifferenceOutputs.py to see the differences between the generated outputs and the reference outputs provided with the installation.
  12. Test cases come with some of pDynamo's packages. If desired, these can be run after the environment variables have been set up (see Step 10). To do so, go back to the installation directory and type python RunPackageTests.py.

By default, installation does not process the Cython/Pyrex files that link the Python and C parts of pDynamo together. Instead, the preprocessed files that are included in the distribution are employed. This may cause problems, such as compilation errors or segmentation faults, on some machines. If this is the case, install the version of Cython included in the source distribution (step 7) and then repeat the installation of pDynamo using the command:

python Install.py -f