LinuxDevelEnvironment: CentOS6.x_Install.txt

#
# instrucciones para compilar tol/tolbase en centos 6.x X86_64,
# concretamente:
#
# Linux brw07.localbayes.es 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
#

# Se recomienda hacer un update para evitar posibles conflictos entre
# los paquetes x86_64 y i686

sudo yum update

# asumimos que existe una variable de entorno TOLROOT debajo de la cual 
# compilaremos TOL
#

export TOLROOT=${HOME}/TOL

# para asegurar que en siguientes sesiones este creada la variable
# ejecutamos

echo export TOLROOT=${HOME}/TOL >> ${HOME}/.bash_profile

#
# creamos directorios de trabajo
#
mkdir -p ${TOLROOT}/tools
mkdir -p ${TOLROOT}/contribs
mkdir -p ${TOLROOT}/contribs/rpms

#
# incorporamos el repositorio EPEL
#
sudo rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm

# para poder hacer X11 remoto
sudo yum install xauth

sudo yum install rlwrap

# Instalamos los paquetes base
sudo yum install bc unzip wget cvs subversion gcc-c++ gcc-c++.i686 libgcc.i686 glibc.i686 glibc-devel.i686 gcc-gfortran.i686 libstdc++-devel libstdc++-devel.i686 autoconf make bzip2-devel.i686 gsl-devel.i686 boost-devel.i686 mysql-devel.i686 postgresql-devel.i686 openssl-devel.i686 zlib-devel.i686 libtool-ltdl-devel.i686 libX11-devel.i686 libX11.i686  libXt.i686 libXt-devel.i686

# No package gcc-c++.i686 available.
# No package gcc-gfortran.i686 available.

# unixODBC-devel.i686, no ya que usamos el fuente unixODBC-2.3.0
cd ${TOLROOT}/contribs
wget ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-2.3.2.tar.gz
tar zxf unixODBC-2.3.2.tar.gz
cd unixODBC-2.3.2
mkdir build
cd build
CC='gcc -m32' CXX='g++ -m32' ../configure --prefix=/usr/local/unixODBC-2.3.0
make
sudo make install


# tcl-devel.i686 tk-devel.i686 tk.i686 no ya que compilamos desde el fuente el 8.4
cd ${TOLROOT}/contribs
wget http://downloads.sourceforge.net/project/tcl/Tcl/8.4.20/tcl8.4.20-src.tar.gz
tar zxf tcl8.4.20-src.tar.gz
cd tcl8.4.20
mkdir build
cd build
CC='gcc -m32' CXX='g++ -m32' ../unix/configure --prefix=/usr/local/tcl8.4.20 --enable-threads --enable-shared 
make
sudo make install install-private-headers
cd ${TOLROOT}/contribs
wget http://downloads.sourceforge.net/project/tcl/Tcl/8.4.20/tk8.4.20-src.tar.gz
tar zxf tk8.4.20-src.tar.gz
cd tk8.4.20
mkdir build
cd build
CC='gcc -m32' CXX='g++ -m32' ../unix/configure --prefix=/usr/local/tcl8.4.20 --enable-threads --enable-shared --with-tcl=/usr/local/tcl8.4.20/lib
make
sudo make install install-private-headers

#
# instalamos atlas/blas/lapack, estos pasos parten de la base que el
# procesador implementa las extensiones sse2, algo que puede saberse
# ejecutando:
#
# cat /proc/cpuinfo | grep flags
#
# en nuestro caso las extensiones son sse2
sudo yum install atlas-sse2.i686 atlas-sse2-devel.i686

# bash_profile
export BLAPI_BLAS_LIB=/usr/lib/atlas-sse2/libf77blas
export BLAPI_LAPACK_LIB=/usr/lib/atlas-sse2/liblapack

#
# instalamos R-project
# quizas se puede instalar el R de 64 bits, ya que se usa en modo comando
sudo yum install R-core.i686 R-devel.i686 glpk-devel.i686
echo 'options(repos="http://cran.r-project.org")' > /tmp/Rinstall.R
echo 'install.packages("coda")' >> /tmp/Rinstall.R
echo 'install.packages("quadprog")' >> /tmp/Rinstall.R
echo 'install.packages("Rglpk")' >> /tmp/Rinstall.R
sudo R BATCH -f /tmp/Rinstall.R
rm /tmp/Rinstall.R

#
# instalo Boost Build 2: bjam
#
cd ${TOLROOT}/tools
wget http://www.boost.org/boost-build2/boost-build.tar.bz2
tar jxf boost-build.tar.bz2
cd boost-build/engine
./build.sh
# lo copio en bin pues su debe encontrarlo para hacer tareas de instalacion
sudo cp bin.linuxx86_64/bjam /usr/bin/.
cd ..
export BOOST_BUILD_PATH=`pwd`
echo export BOOST_BUILD_PATH=`pwd` >> ${HOME}/.bash_profile

#
# instalo google sparse hash
#
sudo yum install sparsehash-devel

#
# compilo ZipArchive
#
cd ${TOLROOT}/contribs
mkdir ZipArchive
cd ZipArchive
wget http://packages.tol-prj.org/linux/sources/ziparchive_src.zip
unzip ziparchive_src.zip
cp _projects/Linux/Makefile ZipArchive/.
cd ZipArchive
sed -e 's/$(CC)/g++ -m32 -fPIC/' -e 's/$(CCC)/gcc -m32 -fPIC/' < Makefile > Makefile.fix
make -e -f Makefile.fix

#
# compilo fftw3
cd ${TOLROOT}/contribs
wget http://packages.tol-prj.org/linux/sources/fftw-3.3.1.tar.gz
tar zxf fftw-3.3.1.tar.gz
cd fftw-3.3.1
CC='gcc -m32' CXX='g++ -m32' ./configure --prefix=/usr/local/fftw-3.3.1
make
sudo make install

#
# compilamos ANN
#
cd ${TOLROOT}/contribs/
#wget http://www.cs.umd.edu/%7Emount/ANN/Files/1.1.2/ann_1.1.2.tar.gz
wget http://packages.tol-prj.org/linux/sources/ann_1.1.2.tar.gz
tar zxf ann_1.1.2.tar.gz
cd ann_1.1.2
cp Make-config Make-config.original
sed 's/"C++ = g++"/"C++ = g++ -m32"/' < Make-config.original > Make-config
make -e linux-g++

#
# instalamos Cint: C interpretado
#
sudo yum install root-cint.i686

#
#
# compilamos GBLA
#
cd ${TOLROOT}
svn co https://www.tol-prj.org/svn/gbla
cd gbla/trunk/libltdl
chmod +x configure
CC='gcc -m32' CXX='g++ -m32' ./configure
cd ..
bjam address-model=32 release
# verificamos que el codigo generado funciona, pasamos los test de blas
cd examples/blas
bjam address-model=32 release
bin/gcc-4.4.7/release/address-model-32/blas1_check
bin/gcc-4.4.7/release/address-model-32/blas2_check
bin/gcc-4.4.7/release/address-model-32/blas3_check
cd ${TOLROOT}/gbla/trunk
sudo BOOST_BUILD_PATH=`echo $BOOST_BUILD_PATH` bjam address-model=32 release install

#
# compilamos SuiteSparse_TOL
#
cd ${TOLROOT}/contribs/
wget http://packages.tol-prj.org/linux/sources/SuiteSparse_TOL.tar.bz2
tar jxf SuiteSparse_TOL.tar.bz2
cd SuiteSparse_TOL/BB2/CHOLMOD
===========================================================================
edit the metis-4.0/Lib/rename.h file and replace the last line in the file:

#define log2    __log2

with the following:

#define log2    METIS__log2
===========================================================================

bjam address-model=32 release
sudo BOOST_BUILD_PATH=`echo $BOOST_BUILD_PATH` bjam address-model=32 release install

sudo yum install libcurl-devel.i686
# compilamos tclcurl, observar que se compila con -m32
cd ${TOLROOT}/contribs
wget http://packages.tol-prj.org/linux/sources/TclCurl-7.19.6.tar.gz
tar zxf TclCurl-7.19.6.tar.gz
cd TclCurl-7.19.6
PKG_CONFIG_PATH=/usr/lib/pkgconfig CC='gcc -m32' CXX='g++ -m32' ./configure --with-tcl=/usr/local/tcl8.4.20/lib
make -e
sudo make install


#
# Compilamos TOL: vamos a por tol!!!!
#
cd ${TOLROOT}
#sudo ln -s /usr/include /usr/include/postgresql
svn co https://www.tol-prj.org/svn/tolp/trunk
cd trunk/tol
cp prj-config.jam.CentOS6x prj-config.jam
./bjam-gcc-release address-model=32
./sudo_install address-model=32

# script de arranque de tolcon
sudo mv /usr/local/tol32/bin/tolcon /usr/local/tol32/bin/tolcon.bin 
echo '#!/bin/bash' > /tmp/tolcon
echo 'LD_LIBRARY_PATH=/usr/local/lib:/usr/local/unixODBC-2.3.0 BLAPI_BLAS_LIB=/usr/lib/atlas-sse2/libf77blas BLAPI_LAPACK_LIB=/usr/lib/atlas-sse2/liblapack /usr/local/tol32/bin/tolcon.bin  ${1+"$@"}' >> /tmp/tolcon
chmod a+x /tmp/tolcon
sudo mv /tmp/tolcon /usr/local/tol32/bin/tolcon

# verificamos que arranca bien 
cd ..
/usr/local/tol32/bin/tolcon -ndp -i -c"WriteLn(\"Hola soy TOL \")"

# puede dar problemas al arrancar
# cannot restore segment prot after reloc: Permission denied
# sudo /usr/sbin/setenforce 0
# vease http://www.appistry.com/community/forums/content/cannot-restore-segment-prot-after-reloc-permission-denied

#
# compilamos toltcl: el puente con tcl.
#
cd ${TOLROOT}/trunk/toltcl/release
CC='gcc -m32' CXX='g++ -m32' ./default_config.sh --with-tol=/usr/local/tol32 --with-tcl=/usr/local/tcl8.4.20/lib
make
sudo make install

# instalamos tcllib

cd ${TOLROOT}/contribs
wget https://github.com/tcltk/tcllib/archive/tcllib_1_16.tar.gz
tar zxf tcllib_1_16.tar.gz
cd tcllib-tcllib_1_16/
./configure --prefix=/usr/local/tcl8.4.20
sudo make install

# 
# compilamos tolsh: la consola de tol con Tcl_EvalEx
#
cd ${TOLROOT}/trunk/tolsh
sudo cp -r tolsh.vfs/lib/app-tolsh /usr/local/tcl8.4.20/lib/.
sudo cp -r tolsh.vfs/lib/tequila /usr/local/tcl8.4.20/lib/.
sudo cp -r tolsh.vfs/lib/tlogger /usr/local/tcl8.4.20/lib/.
sudo cp -r tolsh.vfs/lib/tolcomm /usr/local/tcl8.4.20/lib/.
echo '#!/bin/bash' > /tmp/tolsh
echo 'LD_LIBRARY_PATH=/usr/local/lib:/usr/local/unixODBC-2.3.0/lib BLAPI_BLAS_LIB=/usr/lib/atlas-sse2/libf77blas BLAPI_LAPACK_LIB=/usr/lib/atlas-sse2/liblapack TOLSessionPath=/usr/local/tol32/bin/tolsh /usr/local/tcl8.4.20/bin/tclsh8.4 /usr/local/tcl8.4.20/lib/app-tolsh/tolsh.tcl ${1+"$@"}' >> /tmp/tolsh
chmod a+x /tmp/tolsh
sudo mv /tmp/tolsh /usr/local/tol32/bin/tolsh