Informatique / Python / (11/03/2018) Build Python 2.7.x/3.6.x with Mayavi 4.5.0 on Ubuntu 16.04 LTS

Required packages

Python : compilation and installation

Installing VTK

Installing PyQt

Installing matplotlib, numpy, ...

Installing mayavi

Troubles

In this section I explain how to install Mayavi 4.5.0 on Python 2.7.x or Python 3.6.x on Ubuntu 16.04 LTS.
The steps are the following :

installing some required packages
compiling and installing Python
compiling and installing VTK Python wrapper
compiling and installing PyQt4 Python package
installing Mayavi 4.5.0 Python package

Required packages

On my Ubuntu 16.04 LTS computer, I need to install (as root) the folowing packages to compile Python

sudo apt install libncurses5-dev libreadline-dev libsqlite3-dev libbz2-dev tix-dev \
libssl-dev libgdbm-dev liblzma-dev libffi-dev tk8.5-dev

Python : compilation and installation

I assume the installation directory /fcopt I choose is writeable (for me), otherwise one have to install as root. The directory ~/compil is used as working directory.

  PYVER=3.6.4
  DIR=/fcopt
  PYDIR=$DIR/PYTHON/$PYVER
  mkdir -p ~/compil
  cd ~/compil
  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.

In the following example PYDIR variable contains /fcopt/PYTHON/3.6.4.
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 !). There are some other missing modules which can be found and the Ubuntu packages to install with sudo apt install command :

_tkinter	tk8.5-dev
_gdbm and _dbm	libgdbm-dev
_sqlite3	libsqlite3-dev sqlite3
_lzma	liblzma-dev

If some Ubuntu 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

Installed versions 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${PYVER:0:3}/site-packages
  export LD_LIBRARY_PATH=$PYDIR/lib

With PYVER=3.6.4, ${PYVER:0:3} is 3.6 and ${PYVER:0:1} is 3

To test the installation, I use pip to install ipython package :

pip${PYVER:0:1} 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.

  cd ~/compil
  wget http://www.vtk.org/files/release/8.1/VTK-8.1.0.tar.gz
  tar zxvf VTK-8.1.0.tar.gz
  mkdir VTK-8.1.0-py$PYVER
  mkdir -p $DIR/VTK
  cd VTK-8.1.0-py$PYVER
  if [ ${PYVER:0:1} -eq 2 ]; then EXT=; else EXT=m; fi
  ccmake -DCMAKE_INSTALL_PREFIX:PATH=$DIR/VTK/vtk8.1.0-py$PYVER \
       -DBUILD_SHARED_LIBS:BOOL=ON \
       -DVTK_WRAP_PYTHON:BOOL=ON \
       -DVTK_PYTHON_VERSION:STRING=${PYVER:0:1} \
       -DPYTHON_EXECUTABLE:PATH=$PYDIR/bin/python${PYVER:0:1} \
       -DPYTHON_INCLUDE_DIR:PATH=$PYDIR/include/python${PYVER:0:3}$EXT \
       -DPYTHON_LIBRARY:PATH=$PYDIR/lib/libpython${PYVER:0:3}$EXT.so \
       ../VTK-8.1.0

Then in the ccmake 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 compile and install process ( 5 minutes on my computer) :

make -j 8
make install

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

export PYTHONPATH=$PYTHONPATH:$DIR/VTK/vtk8.1.0-py$PYVER/lib/python${PYVER:0:3}/site-packages
export LD_LIBRARY_PATH=$DIR/VTK/vtk8.1.0-py$PYVER/lib:$LD_LIBRARY_PATH

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:0:1} sphere.py

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:0:1}" >> $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

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.

  cd ~/compil
  wget https://sourceforge.net/projects/pyqt/files/sip/sip-4.19.8/sip-4.19.8.tar.gz
  tar zxvf sip-4.19.8.tar.gz
  cd sip-4.19.8/
  $PYTHON configure.py
  make -j 8
  make install

Then we can install PyQt4 package (PyQt5 is not compatible with Mayavi)

  cd ~/compil
  wget https://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.12.1/PyQt4_gpl_x11-4.12.1.tar.gz
  tar zxf PyQt4_gpl_x11-4.12.1.tar.gz
  cd PyQt4_gpl_x11-4.12.1
  $PYTHON configure-ng.py
  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

Installing matplotlib, numpy, ...

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

pip3 install numpy scipy matplotlib

Installing mayavi

pip3 install mayavi

The mayavi-4.5.0 python package is now installed.

To quickly test the mayavi package, one can run the python code mayavi_boy.py (774 bytes) .

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

With this installation, I set the environment variables PATH, PYTHONPATH and LD_LIBRARY_PATH before to use python3, ipython3, ... as follows

  export PATH=/fcopt/python3.6.0/bin:/usr/bin:/bin
  export PYTHONPATH=/fcopt/python3.6.0/lib/python3.6/site-packages:/fcopt/VTK/vtk7.0-py3.6.0/lib/python3.6/site-packages
  export LD_LIBRARY_PATH=/fcopt/python3.6.0/lib:/fcopt/VTK/vtk7.0-py3.6.0/lib
  export MPLBACKEND=Qt4Agg

The MPLBACKEND environment variable is used to set matplotlib backend.

Troubles

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), \
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.

In this section I explain how to install Mayavi 4.5.1 (development version) for Python 3 on Ubuntu 17.10 by using PyQt 5.

To use Mayavi 4.5.0 python package, the version 4 of PyQt is needed : version 5 is not supported in this version of Mayavi. To use PyQt version 5 one has to install Mayavi 4.5.1 (development version on march 2018), pyface (>= 5.2.0) and traitsui (>=5.2.0)

Firstly we install (as root) python3, python3-pip and python3-env Ubuntu packages. The last one will be used to create Python virtual environments.

sudo apt-get install python3 python3-pip python3-venv

As first step, we create a virtual environment in /python-env/python3 directory

python3 -m venv ~/python-env/python3/Mayavi

We can now load this virtual environment :

source ~/python-env/python3/Mayavi/bin/activate

All the following commands will be execute in this environment. I have somme trouble when using pip3 for installing some packages :
error : invalid command ’bdist_wheel’ ... To avoid this trouble, I use the –no-cache-dir option. There are the command to install some usefull packages (for me)

pip3 install numpy scipy matplotlib ipython3 --no-cache-dir

Then we classicaly install the VTK Python wrapper, PyQt version 5 and Mayavi 4.5.0

  pip3 install VTK --no-cache-dir
  pip3 install pyQt5 --no-cache-dir
  pip3 install mayavi  --no-cache-dir

And finally, one can upgrade the Mayavi pyface and traitsui from their git repository

  pip3 install git+https://github.com/enthought/mayavi.git
  pip3 install git+https://github.com/enthought/pyface.git
  pip3 install git+https://github.com/enthought/traitsui.git

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
python3 mayavi_boy.py