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Update installation doc #1183

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Update installation doc #1183

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d4b99b6
Update installation doc
AmishgaAlphonius Jun 29, 2024
5bb35a7
Integrate new lines in the table
oguevremont Jun 30, 2024
9f2eac9
Update doc/source/installation/apple_arm.rst
AmishgaAlphonius Jun 30, 2024
552f054
Update doc/source/installation/regular_installation.rst
AmishgaAlphonius Jun 30, 2024
8c6a264
Apply suggestions from code review
AmishgaAlphonius Jun 30, 2024
5a17a18
Fix table indentation
AmishgaAlphonius Jun 30, 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::
Expand Down
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 |
+--------+------------------------------------------------+-------------------------------------------------------------------------------+
Comment on lines +250 to +255
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I like this format for adding new lines. I suggest we write it the same way for regular installation and Apple ARM

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@AmishgaAlphonius AmishgaAlphonius Jun 30, 2024 •
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I was hesistating between both format, so I thought leaving them both here, the reviewers will tell me their opinion. Thanks for making the change!


* 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).
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The only thing I don't like is that Software here is with a capital letter. Haha. Otherwise, chill


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