Informatique / Python / Building Python 2.7.x/3.6.x with Mayavi 4.5.0 on centOS 7

Required packages

Python : compilation and installation

Installing VTK

Installing PyQt

Installing matplotlib, numpy, ...

Installing mayavi

pict pict

In this section I explain how to install Mayavi 4.5.0 on Python 2.7.x, 3.5.x or 3.6.x (not tested with other versions) on CentOS 7.
The steps are the following:

installing some required packages
compiling and installing Python
compiling and installing VTK Python wrapper
compiling and installing PyQt version 4 Python package (version 5 not supported by Mayavi)
installing Mayavi 4.5.0 Python package

The installation process described here was succesfully tested with Python 2.7.14, 3.5.5 and 3.6.0.

Required packages

On my CentOS 7 computer, I need to install (as root) the following packages to compile Python/VTK/PyQt4

sudo yum install gcc gcc-c++ gcc-gfortran ncurses-devel tk-devel gdbm-devel \ 
         readline-devel sqlite-devel bzip2-devel openssl-devel xz-devel

To compile VTK, one must use cmake version 3 but only version 2.8.12 can be installed by default.

Download the latest epel-release rpm from http://dl.fedoraproject.org/pub/epel/7/x86_64/. On march 2018, file is epel-release-7-11.noarch.rpm so
```
wget http://dl.fedoraproject.org/pub/epel/7/x86_64/Packages/e/epel-release-7-11.noarch.rpm
```
Install epel-release rpm:
```
sudo rpm -Uvh epel-release*rpm
```
Install cmake3 rpm package:
```
sudo yum install cmake3
```
On march 2018, the version 3.6.3 of cmake is then installed. Take care, commands are /usr/bin/cmake3, /usr/bin/ccmake3, ...

For VTK compilation some other packages are required:

sudo yum install mesa-libGL-devel libXt-devel

For PyQt version 4, the package qt4-devel must be installed

sudo yum install qt4-devel

Python : compilation and installation

I assume the installation directory to be /fcopt. This directory is writable for me, otherwise one has to be root for install process. The directory ~/compil is used as working directory.
The following compilation/installation commands are given for Python 3.6.4 version. To use another version, one only has to set PYVER variable. The PYDIR variable contains /fcopt/PYTHON/3.6.4 which is the installation directory and the CDIR variable contains ~/compil which is the compilation directory.

PYVER=3.6.4 
CDIR=~/compil 
DIR=/fcopt 
PYDIR=$DIR/PYTHON/$PYVER 
mkdir -p $CDIR 
cd $CDIR 
wget https://www.python.org/ftp/python/$PYVER/Python-$PYVER.tar.xz 
tar -Jxf Python-$PYVER.tar.xz 
cd Python-$PYVER 
./configure --enable-shared --enable-optimizations  --with-ensurepip=install --prefix=$PYDIR

The option –enable-shared is needed when building VTK python wrapper.
The option –enable-optimizations ensure to have an optimized version of Python. This option is time consuming as it requires running a lot of tests (approximatively 30 minutes on my computer). To quickly try Python compilation process, do not use this option!
The option –with-ensurepip=install permits the installation of setuptools and pip packages.

Thereafter the make command is used by using 8 threads (ususally use as maximum the number of core of your computer)

 make -j 8

it is important to ensure that there are no important missing modules by reading last lines (before tests starting with –enable-optimizations option) of the output of previous make command. There is what I obtain on my computer:

... 
Python build finished, but the necessary bits to build these modules were not found: 
_bsddb             bsddb185           dl 
imageop            sunaudiodev 
To find the necessary bits, look in setup.py in detect_modules() for the module’s name. 
...

These missing modules are not not needed in the following (and they are obsolete!). Some other missing modules can be found. There are some of them and the corresponding CentOS packages to install with sudo yum install <package_name> command:

missing modules	packages


_tkinter	tk-devel
_gdbm and _dbm	gdbm-devel
_sqlite3	sqlite-devel
_lzma	xz-devel

If some CentOS packages are installed to prevent missing modules one has to rerun the configure command the make command.
At last one can install Python under $PYDIR directory

make install

On March 2018, packages installed with this Python installation are pip-9.0.1 and setuptools-28.8.0.
To correctly use and test this installed python version

export PATH=$PYDIR/bin:/usr/bin:/bin 
export PYTHONPATH=$PYDIR/lib/python${PYVER%.*}/site-packages 
export LD_LIBRARY_PATH=$PYDIR/lib

With PYVER=3.6.4, ${PYVER%.*} is 3.6 and ${PYVER%%.*} is 3.
To test the installation, I use pip to install ipython package:

pip${PYVER%%.*} install ipython

The mayavi package requires VTK (with ccmake command) and PyQt package to be installed.

Installing VTK

On march 2018, The lastest version of VTK is 8.1.0. I choose as installation directory /fcopt/VTK/vtk8.1.0-py$PYVER which is writeable for me. In the following commands, the DIR, CDIR, PYVER, PYDIR variables are those used for the previously Python installation. There are some remarks on the following commands:

${VTKVER%.*} contains the characters before last point in $VTKVER variable so if $VTKVER is 8.1.0, ${VTKYVER%%.*} contains 8.1.
The -DVTK_LEGACY_SILENT:BOOL=ON is used to avoid some warning messages when using vtk python package as Generic Warning: ...was deprecated for VTK 8.1 and will be removed in a future version.

cd $CDIR 
VTKVER=8.1.0 
VTKDIR=$DIR/VTK/vtk$VTKVER-py$PYVER 
wget http://www.vtk.org/files/release/${VTKVER%.*}/VTK-$VTKVER.tar.gz 
tar zxvf VTK-$VTKVER.tar.gz 
mkdir VTK-$VTKVER-py$PYVER 
mkdir -p $DIR/VTK 
cd VTK-$VTKVER-py$PYVER 
if [ ${PYVER%%.*} -eq 2 ] 
then 
  EXT= 
else 
  EXT=m 
fi 
ccmake3 -DCMAKE_INSTALL_PREFIX:PATH=$VTKDIR \ 
     -DBUILD_SHARED_LIBS:BOOL=ON \ 
     -DVTK_WRAP_PYTHON:BOOL=ON \ 
     -DVTK_PYTHON_VERSION:STRING=${PYVER%%.*} \ 
     -DPYTHON_EXECUTABLE:PATH=$PYDIR/bin/python${PYVER%%.*} \ 
     -DPYTHON_INCLUDE_DIR:PATH=$PYDIR/include/python${PYVER%.*}$EXT \ 
     -DPYTHON_LIBRARY:PATH=$PYDIR/lib/libpython${PYVER%.*}$EXT.so \ 
     -DVTK_USE_GL2PS:BOOL=ON\ 
     -DVTK_LEGACY_SILENT:BOOL=ON\ 
     ../VTK-$VTKVER

In the ccmake3 windows, I press :

configure key [c] a first time and waiting one minute configuring finished...
configure key [c] a second time and waiting 30 seconds configuring finished...
generate key [g]

Thereafter one can run compilation and installation process ( 5 minutes on my computer) :

make -j 8 
make -j 8 install

To test the VTK python wrapper, one have to add paths to the previously initialized environment variables PYTHONPATH and LD_LIBRARY_PATH:

export PATH=$PYDIR/bin:/usr/bin:/bin 
export PYTHONPATH=$PYDIR/lib/python${PYVER%.*}/site-packages:$VTKDIR/lib/python${PYVER%.*}/site-packages 
export LD_LIBRARY_PATH=$VTKDIR/lib:$PYDIR/lib

and run the python code sphere.py (700 bytes) :

wget http://www.math.univ-paris13.fr/~cuvelier/docs/Informatique/Python/sphere.py 
$PYDIR/bin/python${PYVER%%.*} sphere.py

If you have errors as

... 
ERROR: In .../Rendering/OpenGL2/vtkShaderProgram.cxx, line 430 
vtkShaderProgram (0x1145600): 1: #version 120 
...

Your graphic driver does not supported shader so you can try to add the option -DVTK_RENDERING_BACKEND:STRING=OpenGL to cmake3 command:

ccmake3 -DCMAKE_INSTALL_PREFIX:PATH=$VTKDIR \ 
     -DBUILD_SHARED_LIBS:BOOL=ON \ 
     -DVTK_WRAP_PYTHON:BOOL=ON \ 
     -DVTK_PYTHON_VERSION:STRING=${PYVER%%.*} \ 
     -DPYTHON_EXECUTABLE:PATH=$PYDIR/bin/python${PYVER%%.*} \ 
     -DPYTHON_INCLUDE_DIR:PATH=$PYDIR/include/python${PYVER%.*}$EXT \ 
     -DPYTHON_LIBRARY:PATH=$PYDIR/lib/libpython${PYVER%.*}$EXT.so \ 
     -DVTK_LEGACY_SILENT:BOOL=ON\ 
     -DVTK_RENDERING_BACKEND:STRING=OpenGL\ 
     ../VTK-$VTKVER 
make -j 8 install

To save environment variables in a file one can do:

FILE=~/setmyPython$PYVER.sh 
echo "export PATH=$PATH" > $FILE 
echo "export PYTHONPATH=$PYTHONPATH"  >> $FILE 
echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> $FILE 
echo "export PYTHON=$PYDIR/bin/python${PYVER%.*}" >> $FILE 
echo "export MPLBACKEND=Qt4Agg" >> FILE 
echo "Writing environment variables in $FILE" 
echo "To load set environment variables do:" 
echo "  source $FILE"

Thereafter one can source the created file to reload them in any terminal

source ~/setmyPython3.6.4.sh

Installing PyQt

We first have to install sip package. The environment variables PATH, PYTHONPATH and LD_LIBRARY_PATH must be correctly set and PYTHON is either python3 (version 3 of Python) or python2 (version 2 of Python) depending on previously installed version.

PYTHON=$PYDIR/bin/python${PYVER%.*} 
SIPVER=4.19.8 
cd $CDIR 
wget https://sourceforge.net/projects/pyqt/files/sip/sip-$SIPVER/sip-$SIPVER.tar.gz 
tar zxvf sip-$SIPVER.tar.gz 
cd sip-$SIPVER/ 
$PYTHON configure.py 
make -j 8 
make install

Then we can install PyQt4 package (PyQt5 is not compatible with Mayavi). For my usage, I don’t need to install QT designer plugin (must be root for that) so I use the --no-designer-plugin option with configure-ng.py

QT4VER=4.12.1 
cd $DIR 
export PATH=$PATH:/usr/lib64/qt4/bin 
wget https://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-$QT4VER/PyQt4_gpl_x11-$QT4VER.tar.gz 
tar zxf PyQt4_gpl_x11-$QT4VER.tar.gz 
cd PyQt4_gpl_x11-$QT4VER 
$PYTHON configure-ng.py --confirm-license --no-designer-plugin 
make -j 8 
make install

To quickly test the PyQt4 package, one can run the python code pyqt4_window.py (339 bytes) .

export MPLBACKEND=Qt4Agg 
wget http://www.math.univ-paris13.fr/~cuvelier/docs/Informatique/Python/pyqt4_window.py 
$PYTHON pyqt4_window.py

In the following we suppose the environment variables PATH, PYTHONPATH, LD_LIBRARY_PATH and MPLBACKEND set as

export PATH=$PYDIR/bin:/usr/bin:/bin 
export PYTHONPATH=$PYDIR/lib/python${PYVER%.*}/site-packages:$VTKDIR/lib/python${PYVER%.*}/site-packages 
export LD_LIBRARY_PATH=$VTKDIR/lib:$PYDIR/lib 
export MPLBACKEND=Qt4Agg

Installing matplotlib, numpy, ...

I choose to install matplotlib package after the installation of PyQt.

$PYDIR/bin/pip${PYVER%%.*} install numpy scipy matplotlib

Installing mayavi

$PYDIR/bin/pip${PYVER%%.*} install mayavi

The mayavi-4.5.0 python package is now installed (march 2018).
To quickly test the mayavi package, one can run the python code mayavi_boy.py (774 bytes) .

wget http://www.math.univ-paris13.fr/~cuvelier/docs/Informatique/Python/mayavi_boy.py 
$PYTHON mayavi_boy.py

When running mayavi_boy.py script, if you have the following warning:

..../site-packages/tvtk/array_handler.py:268: FutureWarning: Conversion of the second argument of issubdtype from ‘complex‘ to ‘np.complexfloating‘ is deprecated. In future, it will be treated as ‘np.complex128 == np.dtype(complex).type‘. 
  assert not numpy.issubdtype(z.dtype, complex), \

then change the line 268 of file ..../site-packages/tvtk/array_handler.py by
assert not numpy.issubdtype(z.dtype, numpy.complexfloating), \
(Take care to respect identation).
See https://github.com/enthought/mayavi/pull/588/files.

When saving a mlab figure in pdf format , I have the following error:
Saving as a vector PS/EPS/PDF/TeX file using GL2PS is either not supported by your version of VTK or you have not configured VTK to work with GL2PS -- read the documentation for the vtkGL2PSExporter class.