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rdkit/INSTALL
Greg Landrum d37d45f297 update install instructions
2011-07-01 09:34:17 +00:00

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The most recent version of the build instructions can always be found
linked from the RDKit wiki:
http://code.google.com/p/rdkit/wiki/GettingStarted
The instructions below are for the Q2 2011 release and subsequent releases.
= Building on Linux or the Mac =
== Getting Ready ==
* Required packages:
* cmake. You need at least version 2.6. http://www.cmake.org if
your linux distribution doesn't have an appropriate
package. _Update: It seems that v2.8 is a better bet than
v2.6. It might be worth compiling your own copy of v2.8 even if
v2.6 is already installed._
* flex and bison. These are frequently already installed if you
have the various pieces of the development environment
installed. Note that some Redhat-based systems have an extremely
ancient version of flex (v2.5.4, from 1997) installed; in order
to build the RDKit on these systems you need to compile and
install a more recent version. The source is available at
http://flex.sourceforge.net.
* 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.
* Optional packages
* If you would like to install the RDKit InChI support (first
available in the Q2 2011 release), follow the instructions in
$RDBASE/External/INCHI-API to get a copy of the InChI source and
put it in the appropriate place.
== Installing Boost ==
* *NOTE*: if your linux distribution has a boost-devel package
including the python and regex libraries, you can use that and
save yourself the steps below. _Update: if you *do* have a
version of the boost libraries pre-installed and you want to use
your own version, be careful when you build the code. We've seen
at least one example on a Fedora system where cmake compiled
using a user-installed version of boost and then linked against
the system version. This led to segmentation faults. There is a
workaround for this below in the
[#Frequently_Encountered_Problems Frequently Encountered
Problems] section._
* download the boost source distribution from [http://www.boost.org
the boost web site]
* extract the source somewhere on your machine
(e.g. `/usr/local/src/boost_1_45_0`)
* build the required boost libraries:
* `cd $BOOST`
* If you want to use the python wrappers: `./bootstrap.sh --with-libraries=python,regex`
* If not using the python wrappers: `./bootstrap.sh --with-libraries=regex`
* Building on 32 bit systems: `./bjam install`
* Building on 64 bit systems: `./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install`
If you have any problems with this step, check the boost
[http://www.boost.org/more/getting_started/unix-variants.html
installation instructions].
== Building the Code ==
* follow the Installing Boost instructions above.
* environment variables:
* RDBASE: the root directory of the RDKit distribution (e.g. ~/RDKit)
* *Linux:* LD_LIBRARY_PATH: make sure it includes $RDBASE/lib and
wherever the boost shared libraries were installed
* *Mac:* DYLD_LIBRARY_PATH: make sure it includes $RDBASE/lib and
wherever the boost shared libraries were installed
* The following are required if you are planning on using the
* Python wrappers: PYTHONPATH: make sure it includes $RDBASE
* Building:
* cd to $RDBASE
* `mkdir build`
* `cd build`
* `cmake ..` : See the section below on configuring the build if
you need to specify a non-default version of python or if you
have boost in a non-standard location
* `make` : this builds all libraries, regression tests, and
wrappers (by default).
* `make install`
See below for a list of [#Frequently_Encountered_Problems frequently
encountered problems] and solutions.
== Testing the Build (optional, but recommended) ==
* cd to $RDBASE/build and do `ctest`
* you're done!
== Advanced ==
=== Specifying an alternate Boost installation ===
You need to tell cmake where to find the boost libraries and header files:
If you have put boost in /opt/local, the cmake invocation would look like:
{{{cmake -DBOOST_ROOT=/opt/local ..}}}
=== Specifying an alternate Python installation ===
You need to tell cmake where to find the python library it should link
against and the python header files.
Here's a sample command line:
{{{cmake -D PYTHON_LIBRARY=/usr/lib/python2.5/config/libpython2.5.a -D PYTHON_INCLUDE_DIR=/usr/include/python2.5/ -D PYTHON_EXECUTABLE=/usr/bin/python ..}}}
The `PYTHON_EXECUTABLE` part is optional if the correct python is the
first version in your PATH.
=== Disabling the Python wrappers ==
You can completely disable building of the python wrappers by setting
the configuration variable RDK_BUILD_PYTHON_WRAPPERS to nil:
{{{cmake -D RDK_BUILD_PYTHON_WRAPPERS= ..}}}
=== Building the Java wrappers ===
*Additional Requirements*
* SWIG v2.0.x: http://www.swig.org
* Junit: get a copy of the junit .jar file from
https://github.com/KentBeck/junit/downloads and put it in the
directory `$RDBASE/External/java_lib` (you will need to create the
directory) and rename it to junit.jar.
*Building*
* When you invoke cmake add `-D RDK_BUILD_SWIG_WRAPPERS=ON` to the
arguments. For example: {{{cmake -D RDK_BUILD_SWIG_WRAPPERS=ON ..}}}
* Build and install normally using `make`. The directory
`$RDBASE/Code/JavaWrappers/gmwrapper` will contain the three
required files: libGraphMolWrap.so (libGraphMolWrap.jnilib on the
Mac), org.RDKit.jar, and org.RDKitDoc.jar.
*Using the wrappers*
To use the wrappers, the three files need to be in the same directory,
and that should be on your CLASSPATH and in the java.library.path. An
example using jython:
{{{
% CLASSPATH=$CLASSPATH:$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar; jython -Djava.library.path=$RDBASE/Code/JavaWrappers/gmwrapper
Jython 2.2.1 on java1.6.0_20
Type "copyright", "credits" or "license" for more information.
>>> from org.RDKit import *
>>> from java import lang
>>> lang.System.loadLibrary('GraphMolWrap')
>>> m = RWMol.MolFromSmiles('c1ccccc1')
>>> m.getNumAtoms()
6L
}}}
== Frequently Encountered Problems ==
In each case I've replaced specific pieces of the path with `...`.
*Problem:*
{{{
Linking CXX shared library libSLNParse.so
/usr/bin/ld: .../libboost_regex.a(cpp_regex_traits.o): relocation R_X86_64_32S against `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage' can not be used when making a shared object; recompile with -fPIC
.../libboost_regex.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
make: *** [all] Error 2
}}}
*Solution:*
Add this to the arguments when you call cmake:
`-DBoost_USE_STATIC_LIBS=OFF`
[http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html more information here]
----
*Problem:*
{{{
.../Code/GraphMol/Wrap/EditableMol.cpp:114: instantiated from here
.../boost/type_traits/detail/cv_traits_impl.hpp:37: internal compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccgSaXge.out file, please attach this to your bugreport.
make[2]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o] Error 1
make[1]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all] Error 2
make: *** [all] Error 2
}}}
*Solution:*
Add `#define BOOST_PYTHON_NO_PY_SIGNATURES` at the top of
`Code/GraphMol/Wrap/EditableMol.cpp`
[http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01178.html
more information here]
----
*Problem:*
Your system has a version of boost installed in /usr/lib, but you
would like to force the RDKit to use a more recent one.
*Solution:*
This can be solved by using cmake version 2.8.3 (or more recent) and
providing the `-D Boost_NO_SYSTEM_PATHS=ON` argument :
{{{
cmake -D BOOST_ROOT=/usr/local -D Boost_NO_SYSTEM_PATHS=ON ..
}}}
#------------------------------------------------
= Building on Windows =
#------------------------------------------------
== Software to Install ==
* Microsoft Visual C++ : The Express version has everything
necessary and can be downloaded for free
[http://www.microsoft.com/express/download/ from Microsoft]. This
is a big installation and will take a while. The RDKit has been
successfully built with all version of visual c++ since 6.0, so
the current version of VC++ (2008 as of this writing) should be
fine.
* flex and bison : these are easily installed as part of a
[http://www.cygwin.com cygwin] installation, but one can also find
flex and bison binaries for windows elsewhere. Cygwin is not
required to build the RDKit, but it's very useful to have (a
minimal cygwin installation is fine). *Note* if you install flex
and bison without cygwin, be sure to read
[http://eli.thegreenplace.net/2007/07/27/bison-looking-for-bisonsimple-on-windows/
this web page] about environment variables and set the
BISON_SIMPLE environment variable to the appropriate value.
* cmake : [http://www.cmake.org/cmake/resources/software.html cmake] should be installed.
* python : [http://www.python.org/download python] should be installed
* numpy : the
[http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103
current version of numpy] should be installed. It's fine to use
the binary installer.
* boost : download a copy of the current versions of the
[http://www.boost.org/users/download/ boost source distribution
and boost-Jam]. Both are available from the same link, be sure to
get the `.ntx86.zip` file for boost-Jam. Extract the source
distribution (to, for example, c:\boost\boost_1_43_0) and copy the
bjam.exe executable from the boost jam zip file to the same
directory. *Note:* it is also possible to download and use a
precompiled version of the boost libraries from
http://www.boostpro.com/download/ . When you run the installer,
the only binary libraries you need are python and regex.
* a subversion client : _This is only necessary if you are planning
on building development versions of the RDKit_. A command line
client for subversion can be installed as part of the cygwin
installation, or a very nice graphical client that integrates well
with windows explorer can be downloaded from the
[http://tortoisesvn.tigris.org/ Tortoise SVN home page].
* Optional packages
* If you would like to install the RDKit InChI support (first
available in the Q2 2011 release), follow the instructions in
$RDBASE/External/INCHI-API to get a copy of the InChI source and
put it in the appropriate place.
== Setup and Preparation ==
This section assumes that python is installed in c:\Python26, that the
boost libraries have been extracted to c:\boost\boost_1_43_0, and that
you will build the RDKit from a directory named c:\RDKit. If any of
these conditions is not true, just change the corresponding paths.
_Notes_ :
# If you install things in paths that have spaces in their names,
be sure to use quotes properly in your environment variable
definitions.
# If you have more than one version of visual studio installed,
the instructions below may not use the correct compiler. In this
case you need to use a different `--toolset` argument to specify
the version of the compiler used in all commands. Information
for this situation is covered in
[http://www.boost.org/doc/libs/1_43_0/more/getting_started/windows.html
the boost.build documentation].
* Make sure that boost builds properly by going to the directory
c:\boost\boost_1_43_0 and executing the command: `.\bjam.exe
--toolset=msvc --with-regex --with-python release install`. This
may take a while, but it should finish without errors. _This step
is not required if you are using a pre-compiled version of boost._
* If you are planning on using a development version of the RDKit:
get a copy of the current RDKit source using subversion. If you're
using the command-line client the command is: `svn co
http://rdkit.svn.sourceforge.net/svnroot/rdkit/trunk c:\RDKit`
* If you are planning on using a released version of the RDKit : get
a copy of the most recent release and extract it into the directory c:\RDKit
* Set the required environment variables (you can set this in cygwin
or in windows. If you set them in windows, be sure to restart your
cygwin window):
* RDBASE = c:\RDKit *Note* this variable is optional for the Q3
2010 release and later releases.
* Make sure that the directory c:\Python26 is in your PATH
* Make sure that the directory c:\RDKit\lib is in your PATH
* Make sure that the directory c:\boost\lib is in your PATH _If you
are using a precompiled version of boost, make sure the directory
containing its DLLs is in your path._
* Make sure that the directory c:\RDKit is in your PYTHONPATH
== Building the Code ==
* follow the Installing Boost instructions above.
* environment variables:
* if you built your own version of boost and cmake complains about
not being able to find it, define the environment variable
BOOST_ROOT to point to the directory containing the boost
source.
* Configure the build:
* Start the cmake gui
* tell it where the source code is (e.g. c:/RDKit) and where to
build the binaries (recommended: c:/RDKit/build)
* click "Configure", select your compiler, and wait until the
basic configuration is complete, you'll see a bunch of red lines
entries in the main windows.
* click "Configure" again
* click "Generate"
* Build:
* open the solution file that cmake created
(c:/RDKit/build/RDKit.sln) with Visual Studio.
* check to be sure that you're building a Release build (for some
reason CMake produces solution files that default to doing a
Debug build)
* build the "ALL_BUILD" target; this will take a while and
generate warnings, but there should be no errors. *Note:* if you
are building the SWIG wrappers you may get an error the first
time you try to build them. If you see this error, try building
ALL_BUILD again; it should work the second time.
* build the "INSTALL" target
== Testing the Build (optional, but recommended) ==
* cd to $RDBASE/build and run `ctest`
* you're done!
== Additional notes ==
* There is a bug in boost v1.44 that causes link errors related to
boost-serialization on windows. To fix this you need to edit one
of the boost header
files. [https://groups.google.com/group/boost-list/msg/066897d43d9ca27a?hl=en
This post] contains instructions on what needs to be done.
=======
# $Id$
# Copyright (C) 2008-2010 Greg Landrum
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