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installation-linux-sources-0.9.9.html
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<!DOCTYPE html>
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<meta name="keywords" content="TTK, Topology ToolKit, Topological Data
Analysis, Visualization, Reeb graph, Reeb Space, Morse-Smale complex, contour
tree, persistence diagram, persistence curve, continuous scatterplot, fiber
surface, contour forests, jacobi set, mandatory critical points, topological
simplification, VTK, ParaView, Python" />
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<h1>Topology ToolKit</h1>
<hr class="small">
<span class="subheading">Installation</span>
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Please find below detailed instructions for the
installation of TTK from sources, under Linux (default target platform). <br><br>
TTK is also supported on other operating systems:<br>
·
<a href="installation-windows-sources.html">
Windows installation instructions</a>;
<br>
·
<a href="installation-osx-sources.html">
MacOS installation instructions</a>.<br><br>
These specific notes describe the installation procedure for a
<a
href="http://releases.ubuntu.com/20.04.1/ubuntu-20.04.1-desktop-amd64.iso"
target="new">
Ubuntu Linux 20.04.1</a> operating system (but the process should be very
similar
for other Linux distributions).
<br><a href="tutorials.html#installation" target="new">A video from our
tutorial page</a>
also shows how to proceed on a step-by-step basis.<br> <br>
If you are an advanced user and you do not wish to install ParaView (TTK's
main user interface), you
still
have the possibility to install TTK without ParaView support (although we
highly recommend to activate it).<br>
In that case, simply
download TTK as describded in section 1, install the dependencies as detailed
in
section 2 and finally, directly jump to
<a href="#ttkConfig">
section 6
</a>
(<i>"Configuring, building
and installing TTK"</i>). <br>
Examples showing how to use TTK libraries from your
own VTK code can be found
<a target="new"
href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/vtk-c%2B%2B"
>on this page</a>.<br><br>
If you are an advanced user and you do not even wish to install VTK, you still
have the possibility to install TTK without VTK support (although we
highly recommend to activate it).<br>
In that case, simply download TTK as describded in section 1, install the
<b>optional</b> dependencies as detailed in
section 2 and finally, directly jump to section 6 (<i>"Configuring, building
and
installing TTK"</i>). <br>
Examples showing how to use TTK libraries from your own
C++ code can be found
<a target="new"
href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/c%2B%2B"
>on this page</a>.<br>
<br>
<b>Most users will want to activate TTK's ParaView support.</b><br><br>
The remainder of these notes
describe
the installation of the
<a href="downloads.html" target="new">
version 0.9.9 of
TTK</a> along with the
<a
href="http://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.8&type=source&os=all&downloadFile=ParaView-v5.8.1.tar.xz"
target="new">
version 5.8.1 of ParaView</a>. Other versions of either software packages
may require slight variations in the installation procedure.
For earlier versions of both software packages, you may want to check out
previous versions of our installation notes: <br>
·
<a href="installation-0.9.8.html">TTK 0.9.8 with ParaView 5.6.1</a>,<br>
·
<a href="installation-0.9.7.html">TTK 0.9.7 with ParaView 5.6.0</a>,<br>
·
<a href="installation-0.9.6.html">TTK 0.9.6 with ParaView 5.5.2</a>,<br>
·
<a href="installation-0.9.5.html">TTK 0.9.5 with ParaView 5.5.0</a>,<br>
·
<a href="installation-0.9.4.html">TTK 0.9.4 with ParaView 5.4.1</a>,<br>
·
<a href="installation-0.9.3.html">TTK 0.9.3 with ParaView 5.4.1</a>,<br>
·
<a href="installation-0.9.2.html">TTK 0.9.2 with ParaView 5.4.0</a>,<br>
·
<a href="installation-0.9.1.html">TTK 0.9.1 with ParaView 5.3.0</a>,<br>
·
<a href="installation-0.9.html">TTK 0.9 with ParaView 5.2.0</a>.<br><br>
<!--The following video also shows how to proceed on a
step-by-step basis:<br> <br>
<video width="100%" controls>
<source src="video/test.mov" type="video/mp4">
Your browser does not support the video tag.
</video>-->
<p>
<h3>1. Downloads</h3>
TTK builds on top of <a href="http://www.paraview.org"
target="new">ParaView</a> for its main user interface. Thus, you will first
need to download
<a
href="https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.8&type=source&os=Sources&downloadFile=ParaView-v5.8.1.tar.xz"
target="new">
ParaView's source code</a>.
Note
that TTK plugins for ParaView will only work with a version of ParaView
compiled from source. Thus, if you already installed ParaView with a binary
copy, you may need to un-install it before proceeding.
Next, download TTK from our <a
href="downloads.html">download page</a>.</p>
<p>
<h3>2. Installing the dependencies</h3>
Several dependencies will need to be installed in order to
compile ParaView and TTK from source. Please enter the following commands
(omit the <code>$</code> character) in a terminal to install them (please see
the documentation of your package manager if your operating system is not
Ubuntu Linux):<br><code><br>
$ sudo apt-get install cmake-qt-gui libboost-system-dev libpython3.8-dev libxt-dev<br>
<!-- $ sudo apt-get install libvtk7-dev<br> -->
<!-- $ sudo apt-get install protobuf-compiler<br> -->
$ sudo apt-get install qt5-default qttools5-dev libqt5x11extras5-dev
libqt5svg5-dev qtxmlpatterns5-dev-tools
</code><br><br>
Note that these commands will also trigger the installation of the (numerous)
dependencies of these components.</p>
<h4>Optional dependencies</h4>
In order to enjoy the complete set of TTK features, we also recommend to
install the following, <i>optional</i> dependencies:<br><br>
·
<a href="https://www.embree.org/" target="new">embree</a>
(in-situ ray-tracing support for TTK's cinema features, version 3.4.0 or later). See the
<a target=="new" href="https://www.embree.org/">
following page</a> for installation
instructions.<br><br>
·
<a target="new"
href="http://eigen.tuxfamily.org/">eigen</a> (for scalar field design, version 3.3.7 or later).
Under
<a
href="http://releases.ubuntu.com/20.04.1/ubuntu-20.04.1-desktop-amd64.iso"
target="new">
Ubuntu Linux 20.04.1</a>, enter the following command:
<code><br><br>
$ sudo apt-get install libeigen3-dev
</code><br><br>
·
<a target="new"
href="https://www.graphviz.org/">graphviz</a> (for graph
drawing features, version 2.40.1 or later). Under
<a
href="http://releases.ubuntu.com/20.04.1/ubuntu-20.04.1-desktop-amd64.iso"
target="new">
Ubuntu Linux 20.04.1</a>, enter the following command:
<code><br><br>
$ sudo apt-get install graphviz-dev
</code><br><br>
·
<a target="new"
href="https://scikit-learn.org/stable/index.html">scikit-learn</a> (for data
reduction features, version 0.19.0 or later). Under
<a
href="http://releases.ubuntu.com/20.04.1/ubuntu-20.04.1-desktop-amd64.iso"
target="new">
Ubuntu Linux 20.04.1</a>, enter the following command:
<code><br><br>
$ sudo apt-get install python3-sklearn
</code><br><br>
·
<a href="https://github.com/yixuan/spectra/archive/v0.8.1.tar.gz" target="new">Spectra</a>
(for the computation of the eigenfunctions of the Laplace-Beltrami operator, version 0.8.1 or later). See the
<a target=="new" href="https://spectralib.org/">
following page</a> for installation
instructions.<br><br>
·
<a href="https://www.sqlite.org/" target="new">sqlite</a> (for cinema query
features, version 3.24.0 or later).
Under
<a
href="http://releases.ubuntu.com/20.04.1/ubuntu-20.04.1-desktop-amd64.iso"
target="new">
Ubuntu Linux 20.04.1</a>, enter the following command:
<code><br><br>
$ sudo apt-get install libsqlite3-dev
</code><br><br>
·
<a href="https://github.com/LLNL/zfp/archive/master.zip" target="new">ZFP</a>
(for advanced compression support, version 0.5.4 or later). See the
<a target=="new" href="https://github.com/LLNL/zfp">
following page</a> for installation
instructions.<br><br>
·
<a href="https://zlib.net/" target="new">
zlib</a> (for further compression support, version 1.2.11 or later).
Under
<a
href="http://releases.ubuntu.com/20.04.1/ubuntu-20.04.1-desktop-amd64.iso"
target="new">
Ubuntu Linux 20.04.1</a>, enter the following command:
<code><br><br>
$ sudo apt-get install zlib1g-dev
</code><br><br>
<!-- · Other optional dependencies should already be installed by
default under <a
href="http://releases.ubuntu.com/20.04.1/ubuntu-20.04.1-desktop-amd64.iso"
target="new">
Ubuntu Linux</a>, such as:<br>-->
<!-- TODO optional dep libsqlite3-dev to install (not pulled by pv) -->
<!--<h4>Note to non-Ubuntu users</h4>
We recommend in general to install the version 8 of the VTK library
instead of the version described above (which
is only recommended for Ubuntu users).
<br><br>-->
<h4>Note to Fedora users</h4>
You can install the different required packages as follows:
<code><br><br>
$ sudo dnf install vtk-devel<br>
$ sudo dnf install cmake-gui <br>
$ sudo dnf install qt5-qttools-devel <br>
$ sudo dnf install qt5-qtx11extras <br>
$ sudo dnf install cgnslib <br>
$ sudo dnf install eigen3-devel <br>
$ sudo dnf install graphviz-devel
</code><br><br>
It has also been reported that the following packages may need to be installed
under Fedora (as of version 30):
<code>lz4</code>,
<code>protobuf</code>,
<code>pugixml</code>,
<code>cgnslib-devel</code>,
<code>zfp-devel</code>.
<p>
<h3>3. Preparing the sources</h3>
Move the tarballs to a working directory (for instance called
<code>~/ttk</code>) and decompress them by entering the following commands in
a terminal (this assumes that you downloaded the tarballs to the
<code>~/Downloads</code> directory):<br><br>
<code>$ mkdir ~/ttk</code><br>
<code>$ mv ~/Downloads/ParaView-v5.8.1.tar.xz ~/ttk/</code><br>
<code>$ mv ~/Downloads/ttk-0.9.9.tar.gz ~/ttk/</code><br>
<code>$ cd ~/ttk</code><br>
<code>$ tar xvJf ParaView-v5.8.1.tar.xz</code><br>
<code>$ tar xvzf ttk-0.9.9.tar.gz</code><br><br>
You can delete the tarballs after the source trees have been decompressed by
entering the following commands:<br><br>
<code>$ rm ParaView-v5.8.1.tar.xz</code><br>
<code>$ rm ttk-0.9.9.tar.gz</code></p>
<p>
<h3>4. Patching the ParaView source tree</h3>
In order to enjoy the complete set of TTK features, we
recommend at this stage to patch the ParaView source tree.
This step is
optional.
To proceed, go to
the patch directory and apply it as follows:<br><br>
<code>$ cd ~/ttk/ttk-0.9.9/paraview/patch</code><br>
<code>$ ./patch-paraview-5.8.1.sh
~/ttk/ParaView-v5.8.1/</code></p>
<!-- <code style="color: #ef2929; font-weight: bold;">root #</code> -->
<!-- <code>emerge --ask --unmerge -->
<!-- sys-kernel/genkernel</code> -->
<p>
<h3>5.
Configuring, building and installing ParaView</h3>
<h4>a) Configuration</h4>
To enter the configuration menu of ParaView's build, enter
the following commands:<br><br>
<code>$ cd ~/ttk/ParaView-v5.8.1/</code><br>
<code>$ mkdir build</code><br>
<code>$ cd build</code><br>
<code>$ cmake-gui ../</code><br><br>
The configuration window opens. Click on the "Configure" button to proceed.
Once the configuration is finished, please
tick the "Advanced" check box and
set the following variables as follows (required
for TTK's
installation):<br><br>
<code> · CMAKE_BUILD_TYPE=Release</code><br>
<code> · PARAVIEW_USE_PYTHON=ON</code><br>
<code> · PARAVIEW_INSTALL_DEVELOPMENT_FILES=ON</code><br>
<code> · PARAVIEW_PYTHON_VERSION=3</code>
<br>
<!-- <code> · VTK_USE_SYSTEM_PROTOBUF=ON</code><br> -->
<!-- <code> · PARAVIEW_QT_VERSION=4</code><br> -->
<!-- <code> · VTK_RENDERING_BACKEND=OpenGL2</code><br> -->
<!-- <code> · VTK_SMP_IMPLEMENTATION_TYPE=OpenMP</code><br>-->
<br>
<!--<h4>Note to non-Ubuntu users</h4>
We recommend in general to use the version 5 of the Qt library, instead of the
version 4 as described above (which is only recommended for Ubuntu
users).<br><br>-->
Optionally, you may want to turn on additional features. See the
<a
href="http://www.paraview.org/Wiki/ParaView:
Build_And_Install#Configure_ParaView_With_CMake"
target="new">
ParaView
build documentation</a> for further details if needed.<br><br>
Next, click on the "Generate" button and close the configuration window when
the generation is completed.<br><br>
<h4>Note to Linux Mint users</h4>
It has been reported that the following CMake variables need to be updated as follows (as of version 19):
<br>
<code> · CMAKE_C_FLAGS=-luuid</code><br>
<code> · CMAKE_CXX_FLAGS=-luuid</code>
<br><br>
<h4>b) Build</h4>
Now you can start the compilation process by entering the following command,
where <code>N</code> is the number of available cores on your system (this will
take a <b>LONG</b> time):<br><br>
<code>$ make -jN</code><br><br>
<h4>c) Installation</h4>
Once the build is finished,
enter the following
command
to install your build of ParaView on your system:<br><br>
<code>$ sudo make install</code><br><br>
<!--<h4>Note to MacOS users</h4>
It seems that the support of ParaView's development framework is currently not
as mature under MacOS than it is under Linux. We recommend MacOS users to omit
the above command (to use ParaView then, simply invoke the output binary
located in the source tree).<br><br>-->
<!--<h4>c) Post-installation</h4>
Once the installation of ParaView is finished,
enter the following command to enable the build of TTK plugins:<br><br>
<code>$ sudo chmod 777 -R /usr/local/lib/cmake/paraview-5.5</code>
</p>-->
<p>
<h3><a name="ttkConfig">6.</a> Configuring, building and installing TTK</h3>
<h4>a) Configuration</h4>
To enter the configuration menu of TTK's build, enter the following
commands:<br><br>
<code>$ cd ~/ttk/ttk-0.9.9/</code><br>
<code>$ mkdir build</code><br>
<code>$ cd build</code><br>
<code>$ cmake-gui ../</code><br><br>
The configuration window opens. Click on the "Configure" button to proceed.
At this stage, under Linux, TTK's build should be automatically configured
correctly
by default and Linux users can click on the "Generate" button.<br>
<!--For MacOS users, the variable <code>ParaView_DIR</code> may need to be
adjusted prior to clicking the "Generate" button. In particular, this variable
needs to be set to the path to the
directory containing the file <code>ParaViewConfig.cmake</code>.-->
Once the generation is completed, close the configuration window.<br><br>
If you are an advanced user and you do not wish to activate TTK's ParaView
support, set the CMake variable <code>TTK_BUILD_PARAVIEW_PLUGINS</code> to
<code>OFF</code>.
Examples showing how to use TTK libraries from your
own VTK code can be found
<a target="new"
href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/vtk-c%2B%2B"
>on this page</a>.<br><br>
If you are an advanced user and you do not even wish to activate TTK's VTK
support, set the CMake variables
<!-- NOT NEEDED AFTER RELEASE 0.9.9 -->
<code>TTK_BUILD_STANDALONE_APPS</code> and
<!-- END OF NOT NEEDED -->
<code>TTK_BUILD_VTK_WRAPPERS</code> to <code>OFF</code>.
Examples showing how to use TTK libraries from your own
C++ code can be found
<a target="new"
href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/c%2B%2B"
>on this page</a>.<br><br>
<h4>b) Build</h4>
Now you can start the compilation process by entering the following command,
where <code>N</code> is the number of available cores on your system (this will
take a <b>LONG</b> time):<br><br>
<code>$ make -jN</code><br><br>
<h4>c) Installation</h4>
Once the build is finished,
enter the following
command to install your build of TTK on your system:<br><br>
<code>$ sudo make install</code>
<!--as mentioned previously, it seems that the support of paraview's
development
framework is currently not as mature under macos than it is under linux. we
recommend macos users to omit the above command.
then, in order to use ttk plugins in paraview, macos users will need to load
them from the paraview plugin manager. see the
<a href="http://www.paraview.org/wiki/paraview/plugin_howto#using_plugins"
target="new">
related documentation page</a> of paraview.-->
</p>
<p>Note that, in addition to the installation of TTK plugins for ParaView,
the above command also installed a collection of standalone TTK programs
that
can be used outside of ParaView,
either as command line tools or VTK-based graphical user interfaces. To list
them, enter the following commands (this assumes that you did not modify the
default TTK installation path, <code>/usr/local/</code>):<br><br>
<code>$ ls /usr/local/bin/*Cmd</code><br>
<code>$ ls /usr/local/bin/*Gui</code>
</p>
<!--<p>
If you wish to disable the build and installation of certain TTK components,
just comment the corresponding lines in the <code>CMakeLists.txt</code> file at
the root of the source tree (<code>~/ttk/ttk-0.9.9/CMakeLists.txt</code> in our
example) prior to entering the configuration step of TTK's build (<a
href="#ttkConfig">section 6.a</a>).
</p>-->
<p>
<h3>7. Setting up environment variables</h3>
At this point, for an optimal user experience, we recommend users to define the following environment variables (in particular, when using TTK with python).
Under Ubuntu Linux, this can be done by entering the following commands (omit the <code>$</code> character):<br><br>
<code>$ echo "export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib" >> ~/.bashrc</code><br>
<code>$ echo "export PV_PLUGIN_PATH=${PV_PLUGIN_PATH}:/usr/local/bin/plugins/"
>> ~/.bashrc</code><br>
<code>$ echo "export PYTHONPATH=${PYTHONPATH}:/usr/local/lib/python3.8/site-packages/" >> ~/.bashrc</code><br>
<code>$ source ~/.bashrc</code><br><br>
Note that if you decided to change the default installation path of ParaView and TTK, you will need in the above commands to replace <code>/usr/local</code> by your custom installation path.
</p>
<p>
<h3>8. Checking your TTK installation</h3>
If you applied all the above steps successfully (including step 4), you
can now open a terminal and type the following command to load your
TTK-patched ParaView:<br><br>
<code>$ paraview</code><br><br>
<!--MacOS users will need to launch the built ParaView
binary from the ParaView source tree and load all the TTK plugins with the
<a href="http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Using_Plugins"
target="new">ParaView Plugin Manager</a> before continuing.<br>-->
At this point, you should see the following TTK startup screen:<br> <br>
<a href="img/ttkStartup.jpg" target="new">
<img align='center'width="95%" src="img/ttkStartup.jpg">
</a>
<br><br>
On this screen, clicking on the "Example Visualizations" link should bring you
to the TTK built-in example screen:
<br> <br>
<a href="img/ttkExamples.jpg" target="new">
<img align='center'width="95%" src="img/ttkExamples.jpg">
</a>
<br><br>
From there, clicking on one of the three buttons should generate one of the
following three visualizations:<br><br>
<a href="img/gallery/builtinExample1.jpg" target="new">
<img align='center'width="95%" src="img/gallery/builtinExample1.jpg" >
</a>
<br><br>
<a href="img/gallery/builtinExample2.jpg" target="new">
<img align='center'width="95%" src="img/gallery/builtinExample2.jpg" >
</a>
<br><br>
<a href="img/gallery/builtinExample3.jpg" target="new">
<img align='center'width="95%" src="img/gallery/builtinExample3.jpg" >
</a>
<br><br>
If this is the case, congratulations!<br> You have just successfully installed
TTK on your system!</p>
<p>
If you have not applied the optional step 4 of this installation procedure,
certain TTK features will not be accessible from ParaView and the above
built-in examples will not be available in your ParaView build. However, most
of TTK features should still work as expected.</p>
<p>
Now, please visit our <a href="tutorials.html">tutorial</a> page to watch video
tutorials showing how to use TTK with ParaView with concrete examples and how to
use it from your own Python or C++ code or how to extend TTK by writing up your
own module!
</p>
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