I have been able to reproducibly build RDKit on CentOS 5.5, but it required
a significant amount of updating of the build components. The attached
walk-through script should get you there. I do not recall ever seeing that
particular error, however.
-Kirk
On Wed, Jan 5, 2011 at 1:15 PM, Igor Filippov [Contr]
<[email protected]>wrote:
> Dear All,
>
> Has anyone successfully compiled RDKit on CentOs 5? I'm running into the
> following error message:
> [ 15%] Building CXX object
>
> Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o
>
> /root/RDKit_2010_09_1/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:14:31:
> error: numpy/arrayobject.h: No such file or directory
>
> On CentOs 5 arrayobject.h is part of python-numeric package and it's
> located in:
> /usr/include/python2.4/Numeric/arrayobject.h
>
> I'm attempting to compile RDKit_2010_09_1, using boost version 1.39.0,
> x86_64 system.
>
> Regards,
> Igor
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Learn how Oracle Real Application Clusters (RAC) One Node allows customers
> to consolidate database storage, standardize their database environment,
> and,
> should the need arise, upgrade to a full multi-node Oracle RAC database
> without downtime or disruption
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> _______________________________________________
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>
RDKit build walk through for CentOS 5.5
***************************************
You may want to remove old versions of cmake, flex, and bison as these will be
rebuilt with the latest versions. I've completed the process with and without
the old versions present and not had any problems with version conflicts.
Build steps can be done as user or as root, but all install steps must be done
as root.
***************************
install atlas, atlas-devel, blas, blas-devel, lapack, lapack-devel through yum.
These linear algebra libraries are required by NumPy
yum install atlas, atlas-devel, blas blas-devel lapack lapack-devel
***************************
GCC with MPFR 2.4.1
I have upgraded GCC on my LINUX install to version 4.5.5. Previously, I found
the version of GCC on CentOS (4.1.2-48) to have many bugs, in particular
template handling errors which prevented it from properly compiling boost and
ultimately breaking the entire process at the last step. The only remedy I've
found is to completely rebuild GCC. MPFR is a multi-precision floating point
math library required for other libraries, so I've simply included it in this
build. I don't know if the newest version of CentOS' GCC (v4.1.2) has this
problem, so I rebuilt as a precaution.
For MPFR 2.4.1, copy the expanded mpfr directory into the top level gcc
directory tree as 'mpfr' (no version numbers or dates). The build process
takes care of it after that so you don't have to build and link it on your own.
Create a build directory OUTSIDE the gcc directory structure and do all build
steps from there - the build process will take a few hours.
mkdir gcc-build
cd gcc-build
../gcc-4.4.5/configure
make
make install
***************************
CMake 2.8.2
./configure
make
make install
***************************
flex 2.5.35
./configure
make
make install
***************************
bison 2.4.2
./configure
make
make install
***************************
python 2.7
Install with -fPIC flags set
Enable Unicode UCS4 support.
Enable shared library support.
./configure CFLAGS=-fPIC --enable-unicode=ucs4 --enable-shared
make
make install
I also made sure Python was built with the newly compiled GCC, and not the
system GCC. On the command line, you should see this:
[GCC 4.4.5] on linux2
At this point you will probably need to add
/usr/local:/usr/local/lib:/usr/local/lib64 to the front of LD_LIBRARY_PATH in
order for the system to know which version of Python and various libraries
should be preferred.
***************************
NumPy 1.5.0
python setup.py build
python setup.py install
Test this by:
python
>>> import numpy
>>>
If you get an error, you've done something wrong.
***************************
Boost 1.44.0
./bootstrap.sh --with-libraries=python,regex
./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install
***************************
RDKit
Make sure all envvars are set properly:
$RDBASE = <the directory where you have installed the RDKit code>
$LD_LIBRARY_PATH = /usr/local/lib:/$RDBASE/lib
$PYTHONPATH = $RDBASE
cd $RDBASE
mkdir build
cd build
cmake -D BOOST_USE_STATIC_LIBS=OFF -D BOOST_ROOT=/usr/local ..
make
make install
***************************
FreeType 2.4.3
./configure
make
make install
***************************
PIL 1.1.7
Modify the FREETYPE_ROOT environment variable (line 40) to point to the
directory in which FreeType was built. In my case, /opt/freetype-2.4.3.
python setup.py build
python setup.py install
***************************
Aggdraw
If you use the standard aggdraw package
(http://effbot.org/zone/aggdraw-index.htm) you have to use the following
compiler flag on 64-bit systems.
export CFLAGS="-fpermissive"
On option is to modify the one line of code for 64-bit as discussed here:
http://www.mail-archive.com/[email protected]/msg01107.html
In /agg2/include/agg_array.h
change line #523 from this:
unsigned align = (alignment - unsigned(ptr) % > alignment) % alignment;
to this:
unsigned align = (alignment - (unsigned long)(ptr) % alignment) % alignment;
You will also need to modify aggdraw's setup.py line 21 to point to your
freetype directory. Mine:
FREETYPE_ROOT="/opt/freetype-2.4.3"
I can then get aggdraw to build, but running the selftest.py gives a
segmentation fault. If I go ahead and install, it seems to work just fine and
the images produced from RDKit are much improved. The full build process is:
export CFLAGS="-fpermissive"
python setup.py build_ext -i
python setup.py install
------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
