From 8252be8c4b53a47ea7465f9f64987274325e6c0a Mon Sep 17 00:00:00 2001
From: David <forenkram@gmx.de>
Date: Mon, 12 Oct 2020 09:41:56 +0200
Subject: [PATCH] expand explanation. Add doc links
---
Setup/README.md | 71 +++++++++++++++++++++++++++++++++++++------------
1 file changed, 54 insertions(+), 17 deletions(-)
diff --git a/Setup/README.md b/Setup/README.md
index 5e1de4e..9075fe0 100644
--- a/Setup/README.md
+++ b/Setup/README.md
@@ -29,18 +29,27 @@ in the command line.
Note: If you don't have admistrative rights on your system, ask your systemadmin
to perform these steps for you. The user that wants to run `docker` needs to
be in the docker group. If you have added yourself to the docker group, don't
-forget to log out and back in again. A reboot might be required, so if in doubt,
-do that.
+forget to log out and back in again.
## Manual how to set up latest fenix image in Docker
Pull the latest `Fenics` Docker image
docker pull quay.io/fenicsproject/stable:latest
-This code as been tested on the latest docker version, which is as of October 2020 `Fenics 2019`. The above explains how to pull the latest `Fenics` docker image. Drastic changes to Fenics are envisioned for the next release, notably abandoning the mesh tool `mshr` which this code heavily relies on. Therefore, before even starting, check on the `Fenics` [website](https://fenicsproject.org/download/) if another version of `Fenics` has come out.
-If yes, you are free to check whether or not this code still works under the latest version, but things might have broken.
+This code as been tested on the latest docker version, which is as of October
+2020 `Fenics 2019`.
+The above explains how to pull the latest `Fenics` docker image.
+Drastic changes to Fenics are envisioned for the next release, notably
+abandoning the mesh tool `mshr` which this code heavily relies on.
+Therefore, before even starting, check on the `Fenics`
+[website](https://fenicsproject.org/download/) if another version of `Fenics`
+has come out.
+If yes, you are free to check whether or not this code still works under the
+latest version, but things might have broken.
In that case, the code needs to be adapted first.
-Alternatively, look on [the release cite](https://quay.io/repository/fenicsproject/stable?tab=tags) for the latest 2019 tag and pull the 2019 image.
+Alternatively, look on
+[the release cite](https://quay.io/repository/fenicsproject/stable?tab=tags)
+for the latest 2019 tag and pull the 2019 image.
So assuming `2019.1.0` was the latest tag for the 2019 version, you would run
docker pull quay.io/fenicsproject/stable:2019.1.0
@@ -52,14 +61,18 @@ Move into the folder in which you cloned this directory and run
docker run --dns=129.69.252.252 -it --env HOST_UID=$(id -u $USER) --env HOST_GID=$(id -g $USER) --env DISPLAY=unix$DISPLAY --device /dev/dri --volume /tmp/.X11-unix:/tmp/.X11-unix:rw --volume $(pwd):/home/fenics/shared --name LDD-TPR-fenics2019 quay.io/fenicsproject/stable:latest /bin/bash
This will setup your current folder as shared directory for the `Fenics` docker
-image.
+image. Once you stepped into the docker image (see below), this shared
+directory can be found in `~/shared`.
+This directory is used to share files between your system and the docker
+container. As you most likely will be programming on your system and only step
+into the docker container to run a simulation, this is a necessary mechanism.
+
Note: If you pulled a version of docker with a fixed tag, you need to adapt
the line `quay.io/fenicsproject/stable:latest` in the above to
`quay.io/fenicsproject/stable:2019.1.0`.
If you want the container do be automatically deleted after exiting add `--rm` option.
-
If you have trouble with internet connection inside the container use
--dns=YOUR_DNS_SERVER
@@ -89,11 +102,13 @@ example:
python3 demo_poisson.py
```
-
It is good practice to update the system in your `docker image` so run
sudo apt-get update && sudo apt-get upgrade
+Have a look around running `ls`. You should see the folder `shared` from where
+you are, which should be the fenics home directoy.
+
## Install missing python3 modules
Once you are in the container navigate into the `Setup` of the cloned repository.
This should be achieved by running
@@ -146,26 +161,48 @@ Remove image
**Solution**
-1. If the package is not found first `apt-get update` and then try again. If there is no connection
-check your dns settings.
+1. If the package is not found first `apt-get update` and then try again.
+If there is no connection check your dns settings.
-2. In the container, execute once the script `Rechtesetup/setpermissions.sh` to gain write access in `/home/fenics/shared`
+2. In the container, execute once the script `Rechtesetup/setpermissions.sh` to
+gain write access in `/home/fenics/shared`
cd /home/fenics/shared/Rechtesetup & sudo ./setpermissions.sh
-## Nützliche FEniCS Links
+## Usefull FEniCS Links
+The dolphin documentation including introductory documentation and demos
+can be found here
-- Fenics based forums:
+ [Dolphin (latest)](https://fenicsproject.org/docs/dolfin/latest/python/index.html)
- https://www.allanswered.com/community/s/fenics-project/
+ [Dolfin (2019.1.0)](https://fenicsproject.org/docs/dolfin/2019.1.0/python/index.html)
+
+ [Dolfin (2018.1.0)](https://fenicsproject.org/docs/dolfin/2018.1.0/python/index.html)
+
+It is sometimes usefull to look at older docs to find the right answers.
+- Python API references:
+An index for API references of dolphin (both cpp and python) can be found
+[here](https://fenicsproject.org/docs/dolfin/).
+The python API references can be found here
-- Python API reference (die von der neuesten Version existiert quasi noch nicht):
+ [Dolphin (Fenics latest)](https://fenicsproject.org/docs/dolfin/latest/python/api.html)
- https://fenicsproject.org/docs/dolfin/2017.2.0/python/programmers-reference/index.html
+ [Dolphin (Fenics 2019.1.0)](https://fenicsproject.org/docs/dolfin/2019.1.0/python/)
+ [Dolphin (Fenics 2018.1.0)](https://fenicsproject.org/docs/dolfin/2018.1.0/python/index.html)
-- Fenics git wenn man wirklich mal in die source files schauen möchte:
+ [Dolphin (Fenics 2017.2.0)](https://fenicsproject.org/docs/dolfin/2017.2.0/python/programmers-reference/index.html)
+
+It is sometimes necessary to have a look at older versions because some details
+are better explained there and the docs have not been updated yet.
+
+- Fenics git in case you want to view the source files:
https://bitbucket.org/fenics-project/
+
+
+- Fenics based forums:
+
+ https://www.allanswered.com/community/s/fenics-project/
--
GitLab