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Greg Landrum
2009-02-05 19:43:24 +00:00
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INSTALL
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@@ -1,21 +1,23 @@
The instructions below are for source distributions from Q3 2008 on.
The instructions below are for source distributions from Q1 2009 on.
= Building on Linux =
== Getting Ready ==
* Required packages:
** The python headers. This probably means that you need to install the python-dev package (or whatever it's called) for your linux distribution.
** Blas and lapack. This is also probably just a matter of finding the appropriate package for your linux.
** flex and bison. These are frequently already installed if you have the various pieces of the development environment installed
** sqlite3. You also need the shared libraries. This may require that you install a sqlite3-dev package.
** You need to have numpy (http://www.scipy.org/NumPy) installed. If you do not have python and/or numpy installed in the standard location, you need to edit the Jamroot ($RDBASE/Code/Jamroot) to reflect the location, i.e. replace `<toolset>gcc:<include>/usr/lib/python2.5/site-packages/numpy/core/include` with whatever is appropriate for your python/numpy installation.
** The following are required if you are planning on using the Python wrappers:
*** The python headers. This probably means that you need to install the python-dev package (or whatever it's called) for your linux distribution.
*** sqlite3. You also need the shared libraries. This may require that you install a sqlite3-dev package.
*** You need to have numpy (http://www.scipy.org/NumPy) installed.
== Installing Boost ==
* download the boost source distribution from [http://www.boost.org the boost web site]
* extract the source to a _non-temporary_ location on your machine, you're going to need it to build the RDKit as well as boost. (e.g. `/usr/local/src/boost_1_36_0`)
* build and install the required boost shared libraries:
** `cd $BOOST`
** `bjam --with-thread --with-python release install`
If you have any problems with this step, check the boost [http://www.boost.org/more/getting_started/unix-variants.html installation instructions].
* The following are required if you are planning on using the Python wrappers:
** build and install the required boost shared libraries:
*** `cd $BOOST`
*** `bjam --with-thread --with-python release install`
If you have any problems with this step, check the boost [http://www.boost.org/more/getting_started/unix-variants.html installation instructions].
== Installing the boost numeric bindings ==
* download the most recent version of the boost numeric bindings from [http://mathema.tician.de/dl/software/boost-bindings http://mathema.tician.de/dl/software/boost-bindings].
@@ -30,20 +32,22 @@ The instructions below are for source distributions from Q3 2008 on.
** RDBASE: the root directory of the RDKit distribution (e.g. ~/RDKit)
** BOOSTHOME: should be wherever you extracted the boost source (e.g. /usr/local/src/boost_1_34_1)
** BOOST_BUILD_PATH: should be the same as $BOOSTHOME
** PYTHON_ROOT: wherever python is installed (e.g. /usr)
** PYTHON_VERSION: the first two digits of the python version (e.g. 2.5, *not* 2.5.1)
** PYTHONPATH: make sure it includes $RDBASE/Python
** LD_LIBRARY_PATH: make sure it includes $RDBASE/bin and wherever the boost shared libraries were installed
** The following are required if you are planning on using the Python wrappers:
** PYTHON_ROOT: wherever python is installed (e.g. /usr)
** PYTHON_VERSION: the first two digits of the python version (e.g. 2.5, *not* 2.5.1)
** PYTHONPATH: make sure it includes $RDBASE
* If you are planning on using the Python wrappers:
** cd to $RDBASE/Code and do `python CompleteJamroot.py`
* Building: cd to $RDBASE/Code and do `bjam` (`bjam address-model=64` on 64bit systems), this builds all libraries, wrappers, and regression tests. This command will generate a lot of text (mostly compiler warnings), but it should not generate any errors. At the end you should *not* see any messages about failed or skipped targets.
== Testing the Build (optional, but recommended) ==
* cd to $RDBASE/Code and do `python $RDBASE/Python/TestRunner.py test_list.py`
* cd to $RDBASE/Code/GraphMol and do `python $RDBASE/Python/TestRunner.py test_list.py`
* cd to $RDBASE/Code and do `python $RDBASE/rdkit/TestRunner.py test_list.py`
* create the databases used by the Python tests, requires sqlite3 to be installed:
** `sqlite3 $RDBASE/Data/RDTests.sqlt < $RDBASE/Python/Dbase/testData/RDTests.sqlite`
** `sqlite3 $RDBASE/Data/RDData.sqlt < $RDBASE/Python/Dbase/testData/RDData.sqlite`
* cd to $RDBASE/Python and do: `find . -name 'test_list.py' -exec python $RDBASE/Python/TestRunner.py \{\} >> pytests.out 2>&1 \;`
* cd to $RDBASE/Projects and do: `python $RDBASE/Python/TestRunner.py test_list.py`
** `sqlite3 $RDBASE/Data/RDTests.sqlt < $RDBASE/rdkit/Dbase/testData/RDTests.sqlite`
** `sqlite3 $RDBASE/Data/RDData.sqlt < $RDBASE/rdkit/Dbase/testData/RDData.sqlite`
* cd to $RDBASE/Python and do: `python $RDBASE/rdkit/TestRunner.py test_list.py`
* cd to $RDBASE/Projects and do: `python $RDBASE/rdkit/TestRunner.py test_list.py`
= Building on Windows =
@@ -79,10 +83,11 @@ This section assumes that python is installed in c:\Python25, that the boost lib
* Make sure that the directory c:\Python25 is in your PATH
* Make sure that the directory c:\RDKit\bin is in your PATH
* Make sure that the directory c:\boost\lib is in your PATH
* Make sure that the directory c:\RDKit\Python is in your PYTHONPATH
* Make sure that the directory c:\RDKit is in your PYTHONPATH
== Building the RDKit ==
* cd to your $RDBASE\Code directory
* run : `python CompleteJamroot.py`
* run : `c:\boost\boost_1_36_0\bjam.exe --toolset=msvc`. This will take a while and will generate a lot of text (including many warnings), but it should finish without errors.
If the last step above completed without errors, you have succeeded in building the RDKit C++ libraries and Python wrappers. Congratulations!
@@ -91,16 +96,14 @@ If the last step above completed without errors, you have succeeded in building
It's a good idea to test your build to make sure everything is ok. Here's how to do so.
* cd to your $RDBASE\Code directory
* run `python c:/RDKit/Python/TestRunner.py test_list.py`. After this completes (less than 30 seconds), you should see a message like this:
* run `python c:/RDKit/rdkit/TestRunner.py test_list.py`. After this completes (a minute or so), you should see a message like this:
{{{
-----------------
Script: test_list.py. Passed 14 tests in 9.63 seconds
}}}
Note that the number of tests passed and time required to run will change as the code itself changes. The important thing is that no failures are reported.
* cd to your $RDBASE\Code\GraphMol directory
* run `python c:/RDKit/Python/TestRunner.py test_list.py`. After this completes (less than 60 seconds), you should see a message like the one above.
* cd to your $RDBASE\Python\Chem directory
* run `python c:/RDKit/Python/TestRunner.py test_list.py`. After this completes (less than 60 seconds), you should see a message like the one above.
* cd to your $RDBASE\rdkit\Chem directory
* run `python c:/RDKit/rdkit/TestRunner.py test_list.py`. After this completes (less than 60 seconds), you should see a message like the one above.
If these three test suites pass without failures, your RDKit installation is in good shape and you are ready to go.