I just installed RDKit_Q22010_1 on my MacBook Pro running:
OS X 10.6.3
gcc version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659)
Python version 2.6
As usual with RDKit+Boost, it took a long time (about 3-4 hours).
That's in part because Boost-based code seems to take so long
to compile, and in part because I ran into a problem with the
Python part of the installation. I figured a way around the
problem, but it isn't a solution. (Though I don't even know
if I needed to do that work-around.)
Here are the steps I did for installation:
** BOOST **
I installed the latest version of Boost; boost_1_43_0.tar.bz2
1) Downloaded the 33MB file to
~/ftps/boost_1_43_0.tar.bz2
and extracted it (in that directory) as
bzcat boost_1_43_0.tar.bz2 | tar xvf -
I then did a:
sudo ln -s ~/ftps/boost_1_43_0 /usr/local/
so that I have a /usr/local/boost_1_43_0 .
2) I followed the Boost instructions (which are different
than the RDKit ones in INSTALL) which had me do a
% ./bootstrap.sh
-n Building Boost.Jam with toolset darwin...
tools/jam/src/bin.macosxx86_64/bjam
-n Detecting Python version...
2.6
-n Detecting Python root...
/System/Library/Frameworks/Python.framework/Versions/2.6
-n Unicode/ICU support for Boost.Regex?...
not found.
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./bjam
....
3) I then compiled and installed Boost, using:
% sudo ./bjam install
Password:
warning: Building Boost.Regex with the optional Unicode/ICU support disabled.
note: Please refer to the Boost.Regex documentation for more information
note: this is a strictly optional feature.
warning: Graph library does not contain MPI-based parallel components.
note: to enable them, add "using mpi ;" to your user-config.jam
warning: skipping optional Message Passing Interface (MPI) library.
note: to enable MPI support, add "using mpi ;" to user-config.jam.
note: to suppress this message, pass "--without-mpi" to bjam.
note: otherwise, you can safely ignore this message.
....
and waited a *long* time until it finished
4) I checked the installation
% ls -lt /usr/local/lib/libboost_* | head
-rw-r--r-- 1 root wheel 28943960 Jul 3 20:18 /usr/local/lib/libboost_wave.a
-rw-r--r-- 1 root wheel 580848 Jul 3 20:16
/usr/local/lib/libboost_thread.a
-rw-r--r-- 1 root wheel 7834496 Jul 3 20:16
/usr/local/lib/libboost_unit_test_framework.a
...
% ls -lt /usr/local/include/boost/ total 1680
drwxr-xr-x 3 root wheel 102 Jul 3 21:45 compatibility
drwxr-xr-x 49 root wheel 1666 Jul 3 21:44 units
drwxr-xr-x 16 root wheel 544 Jul 3 21:44 tr1
drwxr-xr-x 29 root wheel 986 Jul 3 21:44 spirit
drwxr-xr-x 92 root wheel 3128 Jul 3 21:44 python
...
(The dates are different because I wiped the old include/boost to
make sure that there was no contamination from an old Boost.)
** RDKit **
1) Download RDKit_Q22010_1.tgz into my ~/ftps/ directory then
tar xZvf RDKit_Q22010_1.tgz
2) Set up the environment variables
PATH= ..elided..:/Users/dalke/ftps/RDKit_Q22010_1/bin
PYTHONPATH=/Users/dalke/ftps/RDKit_Q22010_1
RDBASE=/Users/dalke/ftps/RDKit_Q22010_1
BOOST_ROOT=/usr/local/boost_1_43_0
DYLD_LIBRARY_PATH=/Users/dalke/ftps/RDKit_Q22010_1/bin
LD_LIBRARY_PATH=/Users/dalke/ftps/RDKit_Q22010_1/bin
(Do I need to do all these? I'm still not sure about the Mac's
use of DYLD_LIBRARY_PATH vs. LD_LIBRARY_PATH )
3) Follow the build steps
[gateway:~/ftps/RDKit_Q22010_1] dalke% mkdir build
[gateway:~/ftps/RDKit_Q22010_1] dalke% cd build
[gateway:~/ftps/RDKit_Q22010_1/build] dalke% cmake ..
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PythonLibs: -framework Python
-- Found PythonInterp: /usr/bin/python2.6
-- Boost version: 1.43.0
-- Found the following Boost libraries:
-- python
-- Found BISON: /usr/bin/bison
-- Found FLEX: /usr/bin/flex
-- Boost version: 1.43.0
-- Found the following Boost libraries:
-- regex
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/dalke/ftps/RDKit_Q22010_1/build
[gateway:~/ftps/RDKit_Q22010_1/build] dalke% make
Scanning dependencies of target fastentropy
[ 1%] Building CXX object
External/cmim-1.0/CMakeFiles/fastentropy.dir/fastentropy.cc.o
[ 1%] Building CXX object
External/cmim-1.0/CMakeFiles/fastentropy.dir/misc.cc.o
Linking CXX static library libfastentropy.a
...
Linking CXX shared library libRDGeneral.dylib
ld: warning: directory '-framework Python' following -L not found
[ 3%] Built target RDGeneral
Scanning dependencies of target testDict
[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o
Linking CXX executable testDict
ld: warning: directory '-framework Python' following -L not found
[ 3%] Built target testDict
...
Notice the "directory '-framework Python' following -L not found"?
That's because of things like the following, from
Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/link.txt
/usr/bin/c++ -mmacosx-version-min=10.6 -O3 -DNDEBUG -Wl,-search_paths_first
-headerpad_max_install_names
CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o
-o graphmoltestPickler -L"-framework Python"
-L/usr/local/lib SmilesParse/libSmilesParse.dylib
Substruct/libSubstructMatch.dylib
FileParsers/libFileParsers.dylib libGraphMol.dylib
../Geometry/libRDGeometryLib.dylib
../RDGeneral/libRDGeneral.dylib SmilesParse/libSmilesParse.dylib
libGraphMol.dylib
../Geometry/libRDGeometryLib.dylib ../DataStructs/libDataStructs.dylib
../RDGeneral/libRDGeneral.dylib
The part which is
-L"-framework Python"
should be
-framework Python
I don't know cmake but it looks like the problem comes from the
link_directories() part of CMakeLists.txt, in the following
...
endif(CMAKE_MAJOR_VERSION EQUAL 2 AND CMAKE_MINOR_VERSION EQUAL 6)
link_directories(${PYTHON_LIBRARIES})
find_package(NumPy REQUIRED)
...
I don't know how to fix it for real, and I don't know if it
makes a difference, but here's my hack fix, which simply
removes the '-L"' and the closing '"' from the wrong text.
% pwd
/Users/dalke/ftps/RDKit_Q22010_1/build
% perl -i -pe 's/-L"-framework Python"/-framework Python/g' `find . -name
link.txt`
% rm `find . -name 'lib*.dylib'`
[ 1%] Built target fastentropy
Linking CXX shared library libRDGeneral.dylib
[ 3%] Built target RDGeneral
Linking CXX executable testDict
[ 3%] Built target testDict
Linking CXX shared library libRDBoost.dylib
[ 3%] Built target RDBoost
Linking CXX shared module rdBase.so
...
You can see that those warning messages have disappeared.
4) Run the self-tests
% make testRunning tests...
Test project /Users/dalke/ftps/RDKit_Q22010_1/build
Start 1: testDict
1/76 Test #1: testDict ......................... Passed 0.00 sec
Start 2: testDataStructs
2/76 Test #2: testDataStructs .................. Passed 0.00 sec
Start 3: pyBV
3/76 Test #3: pyBV .............................***Failed 0.00 sec
Start 4: pyDiscreteValueVect
4/76 Test #4: pyDiscreteValueVect ..............***Failed 0.00 sec
Start 5: pySparseIntVect
5/76 Test #5: pySparseIntVect ..................***Failed 0.00 sec
Start 6: testTransforms
...
You see how all of the Python examples fail? This is because
I didn't understand the testing well enough. I assumed that
I could run the tests in-place, without doing an install first.
According to Testing/Temporary/LastTest.log
----------------------------------------------------------
Traceback (most recent call last):
File "/Users/dalke/ftps/RDKit_Q22010_1/Code/DataStructs/Wrap/testBV.py", line
1, in <module>
from rdkit import DataStructs
File "/Users/dalke/ftps/RDKit_Q22010_1/rdkit/DataStructs/__init__.py", line
7, in <module>
from rdkit import rdBase
ImportError: cannot import name rdBase
<end of output>
Test time = 1.00 sec
----------------------------------------------------------
which means the Python search path isn't right. A quick look at
the build setup shows that it's not set up for that, so once
I did a
sudo make install
then followed the INSTALL steps to build the test databases
(in RDKit_Q22010_1 and not RDKit_Q22010_1/build )
sqlite3 $RDBASE/Data/RDData.sqlt < $RDBASE/rdkit/Dbase/test_data/RDData.s
sqlite3 $RDBASE/Data/RDData.sqlt < $RDBASE/rdkit/Dbase/test_data/RDData.sqlite
then did a "make test" (I did that out of force of habit. The
INSTALL says to run "ctest" and "make test" does
"ctest --force-new-ctest-process" so I don't see the need to
change my habits.)
I ended up with a single error
The following tests FAILED:
71 - pythonTestDirML (Failed)
Errors while running CTest
from the error log
71/76 Testing: pythonTestDirML
71/76 Test: pythonTestDirML
Command: "/usr/bin/python2.6" "/Users/dalke/ftps/RDKit_Q22010_1/rdkit/ML/test_li
st.py" "--testDir" "/Users/dalke/ftps/RDKit_Q22010_1/rdkit/ML"
Directory: /Users/dalke/ftps/RDKit_Q22010_1/build/rdkit
"pythonTestDirML" start time: Jul 03 22:33 CDT
Output:
...
FAIL: testMurtaghUPGMA (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "UnitTestCluster.py", line 70, in testMurtaghUPGMA
assert not newClust.Compare(newClust2,ignoreExtras=0),'equality failed3'
AssertionError: equality failed3
I'll, ummm, leave that to Greg to figure out. :)
BTW,
Boost's Getting Started says
The path to the boost root directory (often /usr/local/boost_1_43_0)
is sometimes referred to as $BOOST_ROOT in documentation and
mailing lists .
The RDKit INSTALL says
* The following are required if you are planning on using the Python wrappers:
* build and install the required boost shared libraries:
* `cd $BOOST`
For consistency, should RDKit use "$BOOST_ROOT" instead of "$BOOST" ?
Andrew
da...@dalkescientific.com
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