<commit_before>###
#
# Install instructions for a custom Python installation on LISA. 
# Python 2.7.7 + modules and custom parallel (MPI enabled) hdf5 version. 
# Modules: numpy scipy matplotlib yaml h5py skimage
#
# <NAME> 
#


#keep old values  
export OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
export OLD_PATH=$PATH
export OLD_PYTHONPATH=$PYTHONPATH

unset LD_LIBRARY_PATH
unset PYTHONPATH

###
### Python 2.7(.7) from source
###

tar -zxvf Python-2.7.7.tgz
cd Python-2.7.7
./configure --prefix=$HOME/opt/python-2.7.7 

make 
make install 

ln -s $HOME/opt/python-2.7.7 $HOME/opt/python-2.7

PYTHON_INSTALL=$HOME/opt/python-2.7
export PATH=$PYTHON_INSTALL/bin:$PATH
export PYTHONPATH=$PYTHON_INSTALL/lib/python2.7/site-packages:$PYTHONPATH

###
### pip 
### 

wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py

###
### YAML 
### 

wget http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz
tar -zxvf PyYAML-3.11.tar.gz

cd PyYAML-3.11 

python setup.py install 

###
### Python modules 
###

pip install numpy scipy 
pip install matplotlib 
pip install scikit-image

###
### hdf5-1.8.12 
###
#
# note: hdf5-1.8.13 got errorz!
# hdf5 with mpi, enable parallel and shared ! 

tar -zxvf hdf5-1.8.12.tar.gz
cd hdf5-1.8.12

#enable MPI 

module load mpich2/gnu/64
./configure --prefix=$HOME/opt/hdf5-1.8.12/  --enable-parallel --enable-shared 

make 
make install 

ln -s $HOME/opt/hdf5-1.8.12 $HOME/opt/hdf5-1.8    

# don't forget: module load  mpich2/gnu/64 here: 
# env vars: 
export HDF5_INSTALL=$HOME/opt/hdf5-1.8
export LDFLAGS="-L${HDF5_INSTALL}/lib"
export  CFLAGS="-I${HDF5_INSTALL}/include"
export PATH=$HDF5_INSTALL/bin:$PATH 
LD_LIBRARY_PATH=$HDF5_INSTALL/lib:$LD_LIBRARY_PATH   

pip install h5py<commit_msg>updated version. <commit_after>###
#
# Install instructions for a custom Python installation on LISA. 
# Python 2.7.7 + modules and custom parallel (MPI enabled) hdf5 version. 
# Modules: numpy scipy matplotlib yaml h5py skimage
#
# <NAME> 
#


#keep old values  
export OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
export OLD_PATH=$PATH
export OLD_PYTHONPATH=$PYTHONPATH

unset LD_LIBRARY_PATH
unset PYTHONPATH


###
### Python 2.7(.7) from source
###

tar -zxvf Python-2.7.7.tgz
cd Python-2.7.7
./configure --prefix=$HOME/opt/python-2.7.7 

make 
make install 

ln -s $HOME/opt/python-2.7.7 $HOME/opt/python-2.7

PYTHON_INSTALL=$HOME/opt/python-2.7
export PATH=$PYTHON_INSTALL/bin:$PATH
export PYTHONPATH=$PYTHON_INSTALL/lib/python2.7/site-packages:$PYTHONPATH

###
### pip 
### 

wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py

###
### Python modules 
###

pip install numpy scipy 
pip install matplotlib 
pip install scikit-image

###
### YAML 
### 

wget http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz
tar -zxvf PyYAML-3.11.tar.gz

cd PyYAML-3.11 
python setup.py install 
cd.. 

###
### hdf5-1.8.12 
###
#
# note: hdf5-1.8.13 got errors!
# hdf5 with mpi, enable parallel and shared ! 

wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz
tar -zxvf hdf5-1.8.12.tar.gz
cd hdf5-1.8.12

#enable MPI 
module load mpich2/gnu/64
./configure --prefix=$HOME/opt/hdf5-1.8.12/  --enable-parallel --enable-shared 

make 
make install 
cd .. 

ln -s $HOME/opt/hdf5-1.8.12 $HOME/opt/hdf5-1.8    

# don't forget: module load  mpich2/gnu/64 here when performing rebuild: 
# env vars: 
export HDF5_INSTALL=$HOME/opt/hdf5-1.8
export LDFLAGS="-L${HDF5_INSTALL}/lib"
export  CFLAGS="-I${HDF5_INSTALL}/include"
export PATH=$HDF5_INSTALL/bin:$PATH 
LD_LIBRARY_PATH=$HDF5_INSTALL/lib:$LD_LIBRARY_PATH   

pip install h5py
{'fraction_non_alphanumeric': 0.1495798319327731, 'fraction_numerical': 0.050140056022408966, 'mean_word_length': 3.742363877822045, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 2, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4298721', 'n_tokens_mistral': 1622, 'n_tokens_neox': 1494, 'n_words': 298}