Linux_install.txt

Local installation on Linux CentOS6 


Compilers:

The version of the C compiler matters. My default system 
(CentOS5) has an old version gcc 4.1.2 and this does not support
c++11/c++0x. These arguments require gcc v.4.3 and higher and the
most recent version available is 4.8.1.

Newer versions of the Armadillo library use features from the chromo namespace that are defined
in C++11. Unfortunately, these features were not defined in the system library header that comes
with g++ 4.6. These are not needed for carma_pack, and if you want to use g++ 4.6 then you will
have to revert to v3.920.4 of the Armadillo library (thanks to Eric Morganson for pointing this 
out).

I decided to use the system gcc compiler on CentOS6 version 4.4.7

1/ Building BOOST libraries:

* get the tar file from 
http://www.boost.org/doc/libs/1_54_0/more/getting_started/unix-variants.html#get-boost)

and follow the installation instruction in "Sec.5.1 Easy Build and Install" on the same web 
page. This step can take about an hour.

cd /data/qednew/Software/boost_source/boost_1_54_0

Make sure the python version is correct. I'm using the anaconda version installed on a local disk

set path=(/data/waimea2/Software/anaconda/bin $path)

The first command ./bootstrap.sh builds the project-config.jam file
which can be edited. Before the build step which is long this file should be checked for
the correct versions of all the directories.

./bootstrap.sh --prefix=/data/qednew/Software/boost

# bootstrap creates a config jam file - can be checked and edited
# b2 builds boost and option install copies the files to the installation location.
Now build and install

./b2 install

setenv BOOST_DIR /data/qednew/Software/boost

2/Download and install Armadillo 
http://arma.sourceforge.net/download.html

cmake -DCMAKE_INSTALL_PREFIX=/data/qednew/Software/armadillo -DBOOST_ROOT=$BOOST_DIR/  .
make install

setenv ARMADILLO_DIR /data/qednew/Software/armadillo

3/ In order to check if BOOST libraries work I needed to run tests described 
in this web page:

http://www.boost.org/doc/libs/1_41_0/more/getting_started/unix-variants.html#library-naming

It was good to check "boost_regexe example". It is not python library, so this checks the basic system links etc.
LD_LIBRARY_PATH has to be set for both BOOST and Armadillo. 

setenv LD_LIBRARY_PATH /data/qednew/Software/boost/lib:${LD_LIBRARY_PATH}
setenv LD_LIBRARY_PATH /data/qednew/Software/armadillo/lib:${LD_LIBRARY_PATH}


4/ Build and install carma_pack

First setup the variables if they are not set. Check if they point to /lib and /include.
These variables are used in setup.py to locate libraries

setenv BOOST_DIR /data/qednew/Software/boost
setenv ARMADILLO_DIR /data/qednew/Software/armadillo

Numpy is used at compile stage, so this is also needed:

setenv NUMPY_DIR /data/waimea2/Software/anaconda

Download ZIP file from the GitHub repository and unzip the file.

Install carmcmc python module by going to the src directory of carpack 

cd /data/qednew/Software/carma_pack-master/src
python setup.py install

>>> I tried the trick below, but it did not work
>>> setenv LD_RUN_PATH /data/qednew/Software/boost/lib:/data/qednew/Software/armadillo/lib
>>> It needs some more work with setup.py

5/ need to install "acor"
pip install acor

6/ try the example testCarmcmc.py

setenv LD_LIBRARY_PATH /data/qednew/Software/boost/lib:${LD_LIBRARY_PATH}
setenv LD_LIBRARY_PATH /data/qednew/Software/armadillo/lib:${LD_LIBRARY_PATH}

cd tests
python testCarmcmc.py