Re: deal.ii in Docker

[luca.heltai]

Dear Chris,

I’m forwarding the mail also to the deal.II usergroup, as many others may find this useful.

> On 4 Jan 2021, at 10:20, Christopher Ham <christo...@gmail.com> wrote:
>
> Dear Both,
>
> I wonder if you might be able to help me. I would really like to try
> out deal.ii. I am a bit of a novice with the computing side of things
> though. I have successfully downloaded Docker and pulled and run some
> of the deal.ii containers. However, I had some problems and I'd be
> really grateful for your help.
>
> I first pulled dealii/dealii:latest. The /home/dealii/ folder was
> empty. I looked around in the file system and then used the find
> command but I could not find the examples folder.

This image is constructed using apt install procedure, which puts deal.II directly under /usr. Examples are *not* installed in this image.

This image is intended to be used by mounting some local volumes in the image, and then compiling using the docker environment. In general, you don’t want to modify the image itself under docker (i.e., compile the examples inside the docker image), since these changes in general get lost when you exit docker.

The library is installed directly in /usr, so you don’t need to specify anything at cmake configuration time, since it is picked up automatically.


> I then pulled dealii/dealii:master-focal. I could find the examples
> folder in this container (I found two places where they were
> actually). However I got an error when I ran 'cmake .' I guess I need
> to specify the directory where deal.ii is installed but I don't know
> this.

The master-focal version is intended for development and developers. It is installed under /usr/local (and not under /usr), and it also includes the source files of the library in /usr/src/dealii (which indeed also include the examples), in order to allow debugging with gdb.

Notice, however, that if you run as the standard dealii user, you don’t have write access to /usr/local, nor to /usr/src/dealii.

You should copy those examples to a directory where you have write access (your home directory), or mount a local directory and use the docker environment to build.

My suggestion is to do the following:

download the examples directory on your local machine (say under directory `pwd`/examples`), make it world writeable (chmod -R a+rw examples) and run

docker run -t -i --rm -v `pwd`/examples:/home/dealii/examples dealii/dealii:master-focal bash

-t: let docker know you’ll be using a terminal
-i: run interactively
—rm: remove the intermediate images once you exit
-v `pwd`/examples:/home/dealii/examples: mount the local directory “examples” to a directory inside the docker directory /home/dealii/examples

this will drop you in the directory dealii, where now you have also a directory examples, to which you have write access.

Now you can cd in any of the examples directory, and you should be able to run

cmake .
make run


Best,
Luca.