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Update installation doc (#1183)
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Description
This PR follows #1181 and updates documentation related to the installation of Lethe. More specifically, it corrects the version of p4est to be installed to 2.3.6.

Co-authored-by: Olivier Guévremont <guevremont.o@gmail.com>
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@AmishgaAlphonius @oguevremont
AmishgaAlphonius and oguevremont authored Jul 1, 2024
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30 changes: 25 additions & 5 deletions doc/source/installation/apple_arm.rst
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Expand Up @@ -24,7 +24,27 @@ To install the dependencies (mpi, p4est, trilinos and METIS) all together using
sudo apt-get install libmuparser-dev
Clone the candi git repository in a folder of your choice (e.g. ``$HOME/sofware/``). You can edit the ``candi.cfg`` file if you want to force the installation of the deal.II master version instead of the current stable version by setting the ``STABLE_BUILD=false``. Under Apple ARM, we only recommend the installation of the required libraries, namely parmetis, trilinos and p4est.
Clone the candi git repository in a folder of your choice (e.g. ``$HOME/software/``). You can edit the ``candi.cfg`` file if you want to force the installation of the deal.II master version instead of the current stable version by setting ``DEAL_II_VERSION=master`` on line 97. Under Apple ARM, we only recommend the installation of the required libraries, namely parmetis, trilinos and p4est.

To ensure that the Lethe test suite works, deal.II must be configured with p4est version 2.3.6. In the subfolder ``deal.II-toolchain/packages/``, open the ``p4est.package`` file with a text editor and change the following lines:

+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| line # | initial line | changed line |
+========+================================================+===============================================================================+
| 9 | ``VERSION=2.3.2`` | ``#VERSION=2.3.2`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 10 | ``CHECKSUM=076df9e...`` | ``#CHECKSUM=076df9e...`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 11 | ``CHECKSUM="${CHECKSUM} b41c8ef29ca...`` | ``#CHECKSUM="${CHECKSUM} b41c8ef29ca...`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 12 | ``CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` | ``#CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 13 | | .. code-block:: text |
| | | :class: copy-button |
| | | |
| | | VERSION=2.3.6 |
| | | CHECKSUM=4b35d9cc374e3b05cd29c552070940124f04af8f8e5e01ff046e39833de5e153 |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+

From the candi folder, the installation of candi can be launched using:

Expand All @@ -45,18 +65,18 @@ After installation, add an environment variable to your ``~/.zshrc`` either manu
Setting the Library and Include Paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The deal.II installation procedure might not set the correct path for the libraries agaisnt which it needs to link. These include parmetis, p4est and trilinos. To fix this issue, the include and library path must be manually added by appending the following lines to the ``~/.zshrc`` file.
The deal.II installation procedure might not set the correct path for the libraries towards which it needs to link. These include parmetis, p4est and trilinos. To fix this issue, the include and library path must be manually added by appending the following lines to the ``~/.zshrc`` file.

.. code-block::
:class: copy-button
export PATH=/opt/homebrew/bin:$PATH
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:path/to/candi/install/trilinos-release-12-18-1/lib/
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:path/to/candi/install/p4est-2.3.2/FAST/lib
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:path/to/candi/install/p4est-2.3.2/DEBUG/lib
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:path/to/candi/install/p4est-2.3.6/FAST/lib
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:path/to/candi/install/p4est-2.3.6/DEBUG/lib
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:path/to/candi/install//parmetis-4.0.3/lib
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:path/to/candi/install/trilinos-release-12-18-1/include/
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:path/to/candi/install/p4est-2.3.2/FAST/include/
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:path/to/candi/install/p4est-2.3.6/FAST/include/
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:path/to/candi/install/parmetis-4.0.3/lib/
.. note::
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56 changes: 25 additions & 31 deletions doc/source/installation/regular_installation.rst
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Expand Up @@ -72,7 +72,7 @@ Installing deal.II using Candi

To install the dependencies (MPI, p4est, trilinos and METIS) all together using candi, the `procedure <https://github.com/dealii/candi.git>`_ on the candi repository can be followed.

Clone the candi git repository in a folder of your choice (e.g. ``/home/username/software``). Edit the ``candi.cfg`` file to alter which dependencies are compiled. This should notably be used to force the installation of the deal.II master version directly instead of the current stable version by setting the ``STABLE_BUILD=false``.
Clone the candi git repository in a folder of your choice (e.g. ``/home/username/software``). Edit the ``candi.cfg`` file to alter which dependencies are compiled. This file should notably be used to force the installation of the deal.II master version directly instead of the current stable version by setting ``DEAL_II_VERSION=master`` on line 97.

The following packages (which are specified after line 57) should be installed:

Expand All @@ -93,27 +93,27 @@ A dependency required by Lethe, and that deal.II needs to be compiled with, is m
sudo apt-get install libmuparser-dev
Other packages can be disabled by simply commenting out the lines (adding an ``#`` at the beggining of the lines)

To ensure that the the Lethe test suite works, deal.II must be configured with p4est version 2.2.1. In the subfolder ``deal.II-toolchain/packages/``, open the ``p4est.package`` file with a text editor and change the following lines:

.. tip::
We are simply uncommenting line 7, and commenting lines 9 to 12, to change the p4est version.

+--------+------------------------------------------------+-----------------------------------------------+
| line # | initial parameter | changed parameter |
+========+================================================+===============================================+
| 7 | ``#VERSION=2.2;CHECKSUM=6943949a...`` | ``VERSION=2.2;CHECKSUM=6943949a...`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 9 | ``VERSION=2.3.2`` | ``#VERSION=2.3.2`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 10 | ``CHECKSUM=076df9e...`` | ``#CHECKSUM=076df9e...`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 11 | ``CHECKSUM="${CHECKSUM} b41c8ef29ca...`` | ``#CHECKSUM="${CHECKSUM} b41c8ef29ca...`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 12 | ``CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` | ``#CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` |
+--------+------------------------------------------------+-----------------------------------------------+

Other packages can be disabled by simply commenting out the lines (adding a ``#`` at the beginning of the lines)

To ensure that the Lethe test suite works, deal.II must be configured with p4est version 2.3.6. In the subfolder ``deal.II-toolchain/packages/``, open the ``p4est.package`` file with a text editor and change the following lines:

+--------+------------------------------------------------+------------------------------------------------------------------------------+
| line # | initial line | changed line |
+========+================================================+==============================================================================+
| 9 | ``VERSION=2.3.2`` | ``#VERSION=2.3.2`` |
+--------+------------------------------------------------+------------------------------------------------------------------------------+
| 10 | ``CHECKSUM=076df9e...`` | ``#CHECKSUM=076df9e...`` |
+--------+------------------------------------------------+------------------------------------------------------------------------------+
| 11 | ``CHECKSUM="${CHECKSUM} b41c8ef29ca...`` | ``#CHECKSUM="${CHECKSUM} b41c8ef29ca...`` |
+--------+------------------------------------------------+------------------------------------------------------------------------------+
| 12 | ``CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` | ``#CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` |
+--------+------------------------------------------------+------------------------------------------------------------------------------+
| 13 | | .. code-block:: text |
| | | :class: copy-button |
| | | |
| | | VERSION=2.3.6 |
| | | CHECKSUM=4b35d9cc374e3b05cd29c552070940124f04af8f8e5e01ff046e39833de5e153 |
+--------+------------------------------------------------+------------------------------------------------------------------------------+

From the candi folder, the installation of candi can be launched using:

Expand Down Expand Up @@ -268,19 +268,13 @@ The deal.II version supported by Lethe is updated and tested every week or so, s

With Candi
~~~~~~~~~~~~~
In the candi folder (for instance, ``/home/username/software/candi``), modify the ``candi.cfg`` to get the latest dealii version, by changing the ``DEAL_II_VERSION`` variable in the case of an official release, or by changing the ``STABLE_BUILD`` in the case of a development release. The ``candi.cfg`` should contain:
In the candi folder (for instance, ``/home/username/software/candi``), modify the ``candi.cfg`` to get the latest dealii version, by changing the ``DEAL_II_VERSION`` variable in the case of an official release with its number (e.g. ``v9.5.2``), or by changing it to ``master`` in the case of a development release. The ``candi.cfg`` file should contain on lines 96-97:

.. code-block:: text
:class: copy-button
# Install the following deal.II version:
DEAL_II_VERSION=v9.5.0
# Would you like to build stable version of deal.II?
# If STABLE_BUILD=false, then the development version of deal.II will be
# installed.
STABLE_BUILD=true
#STABLE_BUILD=false
# Install the following deal.II version (choose master, v9.3.0, v9.2.0, ...)
DEAL_II_VERSION=master
Run the command ``./candi.sh`` to install the new version of dealii.

Expand Down
42 changes: 23 additions & 19 deletions doc/source/installation/windows_wsl.rst
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Expand Up @@ -70,7 +70,7 @@ When prompted "do you want to continue?", proceed by typing ``y`` and hitting ``
5. |win_shell| (optional) For better ease in the Linux terminal (better coloring, multiple tabs), change the default terminal:

* in the microsoft store, download ``Windows Terminal``
* in the ``parameters`` of ``Windows Terminal``, select on the left pannel "start": change default profile with ``Ubuntu-22.04``
* in the ``parameters`` of ``Windows Terminal``, select on the left panel "start": change default profile with ``Ubuntu-22.04``
* from now on, you can use this application instead to launch Ubuntu terminal

.. tip::
Expand Down Expand Up @@ -202,7 +202,7 @@ Do not forget the ``.`` at the end of the command, which means "here".
* open the ``candi.cfg`` file with notepad (or other text editor) and change the following lines:

+--------+------------------------------------------+----------------------------------------+
| line # | initial parameter | changed parameter |
| line # | initial line | changed line |
+========+==========================================+========================================+
| 7 | ``CLEAN_BUILD=OFF`` | ``CLEAN_BUILD=ON`` |
+--------+------------------------------------------+----------------------------------------+
Expand All @@ -219,7 +219,7 @@ Do not forget the ``.`` at the end of the command, which means "here".
The prefix ``#`` is used to comment a line. Here we are simply commenting lines 44 and 45, and uncommenting lines 50 and 51, to change the trilinos version.

+--------+------------------------------------------------+-----------------------------------------------+
| line # | initial parameter | changed parameter |
| line # | initial line | changed line |
+========+================================================+===============================================+
| 44 | ``VERSION=12-18-1`` | ``#VERSION=12-18-1`` |
+--------+------------------------------------------------+-----------------------------------------------+
Expand All @@ -234,21 +234,25 @@ Do not forget the ``.`` at the end of the command, which means "here".
* still in the subfolder ``deal.II-toolchain/packages/``, open the ``p4est.package`` file with notepad and change the following lines:

.. tip::
The prefix ``#`` is used to comment a line. Here we are simply uncommenting line 7, and commenting lines 9 to 12, to change the p4est version.

+--------+------------------------------------------------+-----------------------------------------------+
| line # | initial parameter | changed parameter |
+========+================================================+===============================================+
| 7 | ``#VERSION=2.2;CHECKSUM=6943949a...`` | ``VERSION=2.2;CHECKSUM=6943949a...`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 9 | ``VERSION=2.3.2`` | ``#VERSION=2.3.2`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 10 | ``CHECKSUM=076df9e...`` | ``#CHECKSUM=076df9e...`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 11 | ``CHECKSUM="${CHECKSUM} b41c8ef29ca...`` | ``#CHECKSUM="${CHECKSUM} b41c8ef29ca...`` |
+--------+------------------------------------------------+-----------------------------------------------+
| 12 | ``CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` | ``#CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` |
+--------+------------------------------------------------+-----------------------------------------------+
The prefix ``#`` is used to comment a line. Here we are commenting lines 9 to 12 and adding 2 new lines to change the p4est version.

+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| line # | initial line | changed line |
+========+================================================+===============================================================================+
| 9 | ``VERSION=2.3.2`` | ``#VERSION=2.3.2`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 10 | ``CHECKSUM=076df9e...`` | ``#CHECKSUM=076df9e...`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 11 | ``CHECKSUM="${CHECKSUM} b41c8ef29ca...`` | ``#CHECKSUM="${CHECKSUM} b41c8ef29ca...`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 12 | ``CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` | ``#CHECKSUM="${CHECKSUM} 0ea6e4806b6...`` |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
| 13 | | .. code-block:: text |
| | | :class: copy-button |
| | | |
| | | VERSION=2.3.6 |
| | | CHECKSUM=4b35d9cc374e3b05cd29c552070940124f04af8f8e5e01ff046e39833de5e153 |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+

* save and close

Expand Down Expand Up @@ -297,7 +301,7 @@ Where ``$numprocs`` corresponds to the number of processors used for the compila
Installing Lethe (Step #2)
-------------------------------------

1. |linux_shell| Set-up the folder structure. Create the ``Software`` folder (if you are doing the candi installation, this folder should alredy exist from Step #1).
1. |linux_shell| Set-up the folder structure. Create the ``Software`` folder (if you are doing the candi installation, this folder should already exist from Step #1).

.. code-block:: text
:class: copy-button
Expand Down

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