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Chapter 2: Installation

The Python Distutils are used to build and install PyTables, so it is fairly simple to get the application up and running. If you want to install the package from sources go to the next section. But if you are running Windows and want to install precompiled binaries jump to section 2.2). In addition, packages are starting to appear in different Linux distributions, for instance RockLinux, Debian, Fedora or Gentoo. There also packages for other Unices like FreeBSD or MacOSX

2.1 Installation from source

These instructions are for both Unix/Linux and Windows systems. If you are using Windows, it is assumed that you have a recent version of MS Visual C++ (>= 6.0) compiler installed. A GCC compiler is assumed for Unix, but other compilers should work as well.

Extensions in PyTables have been developed in Pyrex (see ) and C language. You can rebuild everything from scratch if you have Pyrex installed, but this is not necessary, as the Pyrex compiled source is included in the distribution.

To compile PyTables you will need a recent version of the HDF5 (C flavor) library and the numarray (see ) package. Although you won't need Numerical Python (see ) in order to compile PyTables, it is supported; you only need a reasonably recent version of it (>= 21.x) if you plan on using its methods in your applications. PyTables has been successfully tested with Numeric 21.3, 22.0 and 23.0. If you already have Numeric installed, the test driver module will detect it and will run the tests for Numeric automatically.

2.1.1 Prerequisites

First, make sure that you have at least HDF5 1.6.3-patch and numarray 1.1 or higher installed (I'm using HDF5 1.6.3-patch3) and numarray 1.1 currently). If you don't, fetch and install them before proceeding.

Compile and install these packages (but see section 2.2.1 for instructions on how to install precompiled binaries if you are not willing to compile the prerequisites on Windows systems).

For compression (and possibly improved performance), you will need to install the Zlib (see ), which is also required by HDF5 as well. You may also optionally install the excellent LZO and UCL compression libraries (see and section 6.3).

Unix

setup.py will detect HDF5, LZO or UCL libraries and include files under /usr or /usr/local; this will cover most manual installations as well as installations from packages. If setup.py can't find libhdf5 or libz (or liblzo or libucl that you may wish to use) or if you have several versions of a library installed and want to use a particular one, then you can set the path to the resource in the environment, setting the values of the HDF5_DIR, LZO_DIR or UCL_DIR environment variables to the path to the particular resource. You may also specify the locations of the resource root directories on the setup.py command line. For example:

		--hdf5=/stuff/hdf5-1.6.3
		--lzo=/stuff/lzo-1.08
		--ucl=/stuff/ucl-1.03
	      
If your HDF5 library was built as a shared library not in the runtime load path, then you can specify the additional linker flags needed to find the shared library on the command line as well. For example:
		  --lflags="-Xlinker -rpath -Xlinker /stuff/hdf5-1.6.3/lib"
		
or perhaps just
		  --rpath="/stuff/hdf5-1.6.3/lib"
		
Check your compiler and linker documentation as well as the Python Distutils documentation for the correct syntax.
It is also possible to link with specific libraries by setting the LIBS environment variable:
		  LIBS="hdf5-1.6.5"
		  LIBS="hdf5-1.6.5 nsl"
		
Windows

Once you have installed the prerequisites, setup.py needs to know where the necessary library stub (.lib) and header (.h) files are installed. Set the following environment variables:

HDF5_DIR
Points to the root HDF5 directory (where the include/ and dll/ directories can be found). Mandatory.
LZO_DIR
Points to the root LZO directory (where the include/ and lib/ directories can be found). Optional.
UCL_DIR
Points to the root UCL directory (where the include/ and lib/ directories can be found). Optional.
For example:
		  set HDF5_DIR=c:\stuff\5-162-win2k\c\release
		  set UCL_DIR=c:\stuff\ucl-1-02
		  set LZO_DIR=c:\stuff\lzo-1-08
		
Or, you can pass this information to setup.py by setting the appropriate arguments on the command line. For example:
		--hdf5=c:\stuff\5-162-win2k\c\release
		--lzo=c:\stuff\lzo-1-08
		--ucl=c:\stuff\ucl-1-02
	      

2.1.2 PyTables package installation

Once you have installed the HDF5 library and numarray packages, you can proceed with the PyTables package itself:

  1. Run this command from the main PyTables distribution directory, including any extra command line arguments as discussed above:
    		  python setup.py build_ext --inplace
    		
    Depending on the compiler flags used when compiling your Python executable, there may appear many warnings. Don't worry, almost all of them are caused by variables declared but never used. That's normal in Pyrex extensions.
  2. To run the test suite, change into the test directory and execute this command:

    Unix
    In the shell sh and its variants:
    		    PYTHONPATH=..  
    		    export PYTHONPATH
    		    python test_all.py
    		  
    Windows
    Open a DOS terminal and type:
    		    set PYTHONPATH=..  
    		    python test_all.py
    		  
    If you would like to see verbose output from the tests simply add the flag -v and/or the word verbose to the command line. You can also run only the tests in a particular test module. For example, to execute just the types test:
    		  python test_types.py -v
    		
    If a test fails, please enable verbose output (the -v flag and verbose option), run the failing test module again, and, very important, get your PyTables version information by running the command:
    		  python test_all.py --show-versions-only
    		
    and send back the output to developers so that we may continue improving PyTables.

    If you run into problems because Python can't load the HDF5 library or other shared libraries:

    Unix
    Try setting the LD_LIBRARY_PATH environment variable to point to the directory where the missing libraries can be found.
    Windows
    Put the DLL libraries (hdf5dll.dll and, optionally, lzo.dll and ucl.dll) in a directory listed in your PATH environment variable. The setup.py installation program will print out a warning to that effect if the libraries can't be found.
  3. To install the entire PyTables Python package, change back to the root distribution directory and run the following command (make sure you have sufficient permissions to write to the directories where the PyTables files will be installed):
    		  python setup.py install
    		
    Of course, you will need super-user privileges if you want to install PyTables on a system-protected area. You can select, though, a different place to install the package using the --prefix flag:
    		  python setup.py install --prefix="/home/myuser/mystuff"
    		
    Have in mind, however, that if you use the --prefix flag to install in a non-standard place, you should properly setup your PYTHONPATH environment variable, so that the Python interpreter would be able to find your new PyTables installation.
    You have more installation options available in the distutils package. Issue a:
    		  python setup.py install --help
    		
    for more information on that subject.

That's it! Now you can skip to the next chapter to learn how to use PyTables.

2.2 Binary installation (Windows)

This section is intended for installing precompiled binaries on Windows platforms. You may also find it useful for instructions on how to install binary prerequisites even if you want to compile PyTables itself on Windows.

2.2.1 Windows prerequisites

First, make sure that you have HDF5 1.6.3-patch4) or higher and numarray 1.1 or higher installed (I have built the PyTables binaries using HDF5 1.6.3-patch and numarray 1.1).

For the HDF5 it should be enough to manually copy the hdf5dll.dll, zlib1.dll and szipdll.dll files to a directory in your PATH environment variable (for example C:\WINDOWS\SYSTEM).

To enable compression with optional LZO and UCL libraries (see the section 6.3 for hints about how they may be used to improve performance), fetch and install the LZO and UCL binaries from:
http://gnuwin32.sourceforge.net/. Normally, you will only need to fetch and install the
<package>-<version>-bin.zip file and copy the lzo.dll or ucl.dll files in a directory in the PATH environment variable, so that they can be found by the PyTables extensions.

Note: If you are reading this because you have been redirected from the section 2.1 (Installation from source), some of the headers you will need are in the <package>-<version>-lib.zip file.

2.2.2 PyTables package installation

Download the tables-<version>.win32-py<version>.exe
(tables-<version>-LU.win32-py<version>.exe if you want support for LZO and UCL libraries) file and execute it.

You can (you should) test your installation by unpacking the source tar-ball, changing to the test/ subdirectory and executing the test_all.py script. If all the tests pass (possibly with a few warnings, related to the potential unavailability of LZO and UCL libs) you already have a working, well-tested copy of PyTables installed! If any test fails, please try to locate which test module is failing and execute:
	      python test_<module>.py -v verbose
	    
and also:
	      python test_all.py --show-versions-only
	    
and mail the output to the developers so that the problem can be fixed in future releases.

That's it! Now, proceed to the next chapter to see how to use PyTables.


3) Unfortunately, HDF5 1.6.3 was released with a bug that causes a segmentation fault when an index is deleted. The 1.6.3-patch and higher versions solve this.
4) Unfortunately, HDF5 1.6.3 was released with a bug that causes a segmentation fault when an index is deleted. The 1.6.3-patch and higher versions solve this. You can find a binary version of libraries in ftp://hdf.ncsa.uiuc.edu/HDF5/hdf5-1.6.3/src/patches/bin/WinXP-patch.tar.gz

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