Dear Peter, Thanks for posting these very detailed instructions. Do you mind if I post them to the wiki (with credit of course) to make them easier to find?
I made a few comments and suggestions below: On Wed, Nov 17, 2010 at 11:19 AM, Peter Schmidtke <[email protected]> wrote: > Dear Robert, > I recently ran also into several problems while installing rdkit on a fresh > Centos 5.3. It's a real headache. Anyway, this time I've written up a guide > of how to do it step by step, I hope I didn't forget anything in the end. > However, now it works just fine on our Centos machines. Here's the step by > step installing guide : > > Centos is a stable but not very userfriendly OS. This becomes obvious when > one wants to install python packages like pycuda etc...Centos comes with a > very old python version, 2.4, but lots of newer features, like pycuda > require a newer python version. Lets start the lengthy install process under > Centos : > > Installing Python 2.6 or newer > > If you already have python2.7 installed, please check that it was installed > with --enabled-shared. If this is the case you should have libpython2.7.so > in /usr/local/lib. If not, you should have libpython2.7.a. If the second is > the case, you have to install python2.7 with the following way : > > Download the current version from python (source code). Like with 2.6 or 2.7 > (don't grab the 3.x for now) : > > wget http://www.python.org/ftp/python/2.7/Python-2.7.tgz > > Next untar and unzip the file, go to Python-2.7 directory and issue : > > ./configure --enable-shared; make; sudo make install > > This installs python in the /usr/local/ directory. > > Add the RPMForge repo to yum : > > wget > http://packages.sw.be/rpmforge-release/rpmforge-release-0.5.1-1.el5.rf.x86_64.rpm > > su -c 'rpm -Uvh rpmforge-release-0.5.1-1.el5.rf.x86_64.rpm' > > Then install atlas, lapack, blas : > > yum install atlas-c++.x86_64 atlas-c++-devel.x86_64 lapack.x86_64 > lapack-devel.x86_64 blas.x86_64 blas-devel.x86_64 > > Now we can install fftw3 : > > yum install fftw3.x86_64 fftw3-devel.x86_64 > > > > Now we could potentially install numpy 1.3 or 1.4, but as python2.7 is brand > new there are some problems. I downloaded : > > wget http://sourceforge.net/projects/numpy/files/NumPy/1.3.0/numpy-1.3.0.tar.gz/download > > then untar and unzip this whole thing and go to the numpy directory > > Download the following patch : > > wget http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/dev-python/numpy/files/numpy-1.4.0-python-2.7.patch > > and apply it in this directory using : > > patch -p0 < numpy-1.4.0-python-2.7.patch > > Now build numpy using python setup.py build; python setup.py install > > Numpy should now be accessible from python2.7, simply try a import numpy > after launching python to check. > > First we need to install the boost libraries and their python bindings. > Download boost to your downloads directory using, here I use the version > 1.41 of boost. : > > wget > http://sourceforge.net/projects/boost/files/boost/1.41.0/boost_1_41_0.tar.gz/download > > untar and unzip this file and go to the directory. > > Then issue the following commands : > > ./bootstrap.sh --with-libraries=python,regex,signals,thread signals should not be necessary for the rdkit. > > Then you can issue the boost build command : > > ./bjam -j24 variant=release address-model=64 cflags=-fPIC cxxflags=-fPIC > link=shared install > > Then add the line "export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}" > to your .bashrc file and source it. > > If you have the default flex and bison packages installed from the yum > repositories erase them using yum erase flex and yum erase bison. Those are > extremely old and Rdkit needs newer ones, we have to build them by hand now. > > wget http://prdownloads.sourceforge.net/flex/flex-2.5.35.tar.gz?download > > untar and unzip, cd flex-2.5.35 and then do a classic : > > ./configure; make; make install > > Now grab and install bison using the same procedure as for flex : > > wget http://ftp.gnu.org/gnu/bison/bison-2.4.2.tar.gz > > ... > > Now we have to upgrade cmake, because Centos uses, as usual an old and a bit > buggy on. Download cmake 2.8 from here and untar and unzip it and go to the > directory. Previously uninstall the existing (if existing) cmake version on > your Centos platform using "yum erase cmake". > > The installation should be easy using : > > ./bootstrap; make; make install > > Finally we can go to the Rdkit part: > > > > > Download RDKit from here. > > wget https://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/RDKit_Q22010_1.tgz/download > > wget http://mathema.tician.de/news.tiker.net/download/software/boost-bindings/boost-numeric-bindings-20081116.tar.gz The above part is no longer necessary (the boost numeric bindings aren't used anymore). > > and follow instructions on boost numeric bindings here . > > cp -r boost_1_41_0 /usr/local > cp -r RDKit_Q22010 /usr/local > > define environment variables in /etc/bashrc as follows : > > export RDBASE=/usr/local/RDKit_Q22010_1 > export BOOSTHOME=/usr/local/boost_1_41_0 > export BOOST_BUILD_PATH=/usr/local > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/bin > export PYTHON_ROOT=/usr/local > export PYTHON_VERSION=2.7 > export PYTHONPATH=$PYTHONPATH:$RDBASE > > > > > got to the /usr/local/RDKit_Q22010 directory and do : > > mkdir build; cd build > > Add #define BOOST_PYTHON_NO_PY_SIGNATURES at the top of > ../Code/GraphMol/Wrap/EditableMol.cpp > > then issue the command : > > cmake -D PYTHON_LIBRARY=/usr/local/lib/libpython2.7.so -D > PYTHON_INCLUDE_DIR=/usr/local/include/python2.7/ -D > PYTHON_EXECUTABLE=/usr/local/bin/python -D BOOST_ROOT=/usr/local/ > -DBoost_USE_STATIC_LIBS=OFF .. > > make > > make install > > Next you should install the test databases for rdkit, like said in the > documentation. Installing the test databases is also no longer required. Best Regards, -greg ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
