Peter - This is great! I've only browsed through the script you have, but I
do see a few differences. I'll give it a shot now and report back. Thank
you so much for posting this.
Greg - I ran ldd on rdBase.so, and here's the output:
libRDGeneral.so.1 => /opt/RDKit_svn_20101115/lib/libRDGeneral.so.1
(0x00002ad72659b000)
libRDBoost.so.1 => /opt/RDKit_svn_20101115/lib/libRDBoost.so.1
(0x00002ad7267d6000)
libboost_python.so.1.44.0 =>
/usr/local/lib/libboost_python.so.1.44.0 (0x00002ad726ba5000)
libstdc++.so.6 => /usr/local/lib64/libstdc++.so.6
(0x00002ad726df7000)
libm.so.6 => /lib64/libm.so.6 (0x00002ad72712f000)
libgcc_s.so.1 => /usr/local/lib64/libgcc_s.so.1 (0x00002ad7273b2000)
libc.so.6 => /lib64/libc.so.6 (0x00002ad7275c9000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002ad727920000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ad727b23000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002ad727d3f000)
librt.so.1 => /lib64/librt.so.1 (0x00002ad727f43000)
/lib64/ld-linux-x86-64.so.2 (0x00000031f7000000)
It does look like it is refering to the correct instances of what I've
built. There are a few system level C/C++ library references, but I'm not
seeing anything odd here. What's your take on it?
-Kirk
On Wed, Nov 17, 2010 at 6:34 AM, Peter Schmidtke <[email protected]> wrote:
> 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
>
>
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