Hey Greg, yep that would be great, as right now they are only on a group internal blog ;) I saw that you recently changed you linux build instructions (concerning database things, boost numerical bindings etc...), but I did this before this came out ;)
First lets see if Robert comes through the install process without major problems and then you can post it on your wiki (I might have forgotten some stuff). Some things are based on installing pycuda on those machines, this is why signals and things like that are compiled with boost (might be worth to mention somehow in case people need both). ++ Peter On 17/11/2010, at 14:25, Greg Landrum wrote: > 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 Peter Schmidtke ----------------- PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain ------------------------------------------------------------------------------ Beautiful is writing same markup. 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