Create Docker Image for Titanic

Idea

I would like to have a docker_image that is able to run dnadna and compatible with the work already done on Titanic (sjupyter, srun, sbatch, slurm and other stuff that I don't know about).
The idea could be, in order to be helpful for everyone, to have a minimalist image upon which we can build other personalized images.

Issue

Actually, based on theophile's advice, I took his image thesanc/dlgene:0.993 (find link below) and made a Dockerfile to build another image.

Here is the docker file:

FROM thesanc/dlgene:0.993

WORKDIR /dnadna

COPY ./dnadna .

# Install DNADNA and dependencies
RUN conda env update -f environment-cuda.yml
RUN pip install -e .

# Make RUN commands use the new environment:
# SHELL ["conda", "run", "-n", "dnadna", "/bin/bash", "-c"]

# Make sure the environment is activated:
RUN echo "Make sure numpy is installed:"
RUN python -c "import numpy"

RUN conda env list

# Make RUN commands use the new environment:
SHELL ["conda", "run", "-n", "myenv", "/bin/bash", "-c"]

RUN dnadna simulation init my_model one_event

And that was the kind of error we got (it is not exactly the same Dockerfile for this log):

Ran pip subprocess with arguments:
['/opt/conda/envs/dnadna/bin/python', '-m', 'pip', 'install', '-U', '-r', '/dnadna/condaenv.9xaucu34.requirements.txt']
Pip subprocess output:
Collecting mistletoe
  Downloading mistletoe-0.7.2-py3-none-any.whl (28 kB)
Collecting m2r
  Downloading m2r-0.2.1.tar.gz (16 kB)
Collecting pygments-csv-lexer
  Downloading pygments-csv-lexer-0.1.3.tar.gz (7.4 kB)
Collecting sphinxcontrib-napoleon
  Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB)
Collecting mistune
  Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Requirement already satisfied, skipping upgrade: docutils in /opt/conda/envs/dnadna/lib/python3.7/site-packages (from m2r->-r /dnadna/condaenv.9xaucu34.requirements.txt (line 2)) (0.16)
Requirement already satisfied, skipping upgrade: Pygments>=2.1.0 in /opt/conda/envs/dnadna/lib/python3.7/site-packages (from pygments-csv-lexer->-r /dnadna/condaenv.9xaucu34.requirements.txt (line 3)) (2.6.1)
Requirement already satisfied, skipping upgrade: six>=1.5.2 in /opt/conda/envs/dnadna/lib/python3.7/site-packages (from sphinxcontrib-napoleon->-r /dnadna/condaenv.9xaucu34.requirements.txt (line 4)) (1.15.0)
Collecting pockets>=0.3
  Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB)
Building wheels for collected packages: m2r, pygments-csv-lexer
  Building wheel for m2r (setup.py): started
  Building wheel for m2r (setup.py): finished with status 'done'
  Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10466 sha256=cb8956f04cadfdc608e34028d89e413b952c934511fb1e14c11a5e7a9037fef2
  Stored in directory: /root/.cache/pip/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f
  Building wheel for pygments-csv-lexer (setup.py): started
  Building wheel for pygments-csv-lexer (setup.py): finished with status 'done'
  Created wheel for pygments-csv-lexer: filename=pygments_csv_lexer-0.1.3-py3-none-any.whl size=4867 sha256=8abda8352d6c31f67a1908248e8f5e39534420d6cc53505a520e239f625c1c4e
  Stored in directory: /root/.cache/pip/wheels/e9/5f/00/f1d98db0ff66c88bc3a6346e66b9fe183922c652478c879f17
Successfully built m2r pygments-csv-lexer
Installing collected packages: mistletoe, mistune, m2r, pygments-csv-lexer, pockets, sphinxcontrib-napoleon
Successfully installed m2r-0.2.1 mistletoe-0.7.2 mistune-0.8.4 pockets-0.9.1 pygments-csv-lexer-0.1.3 sphinxcontrib-napoleon-0.7

#
# To activate this environment, use
#
#     $ conda activate dnadna
#
# To deactivate an active environment, use
#
#     $ conda deactivate


Removing intermediate container ab6229abfdff
 ---> ffa0e9182a04
Step 6/6 : RUN conda activate dnadna
 ---> Running in 2c6d9d450192

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

Resulting in issues I have with Torch and Torchvision dependencies or Docker specialties:

1. thesanc.torch.__version__ == 1.5 / thesanc.torchvision.__version__ == 0.6
2. dnadna.torch.__version__ == 1.2 / dnadna.torch.__version__ == DONT_KNOW
3. Either conda activate is not running as expected (we can't switch to dnadna env)
4. Either the <Shell> is not running as expected (forcing to switch to dnadna env with shell commands)

Solution ?

• Link to Titanic doc, to pay attention to build-in package under Titanic
• there are already 'base' docker images on Titanic
• there is also Theophile's image
• there is also embray's miniconda image to run tests

To be honest, I don't really know what are inside these images, and what is the best solutions that is compatible with Titanic built-in functionalities and that would be helpful for everybody that wants to run dnadna on Titanic (or any cluster)