https://github.com/mbdevpl/transpyle-flash

https://github.com/mbdevpl/transpyle-flash

Last synced: 11 days ago
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• Host: GitHub
• URL: https://github.com/mbdevpl/transpyle-flash
• Owner: mbdevpl
• Created: 2017-12-14T01:54:18.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2019-03-21T06:45:15.000Z (almost 7 years ago)
• Last Synced: 2025-02-08T04:26:03.595Z (12 months ago)
• Language: Jupyter Notebook
• Size: 117 KB
• Stars: 0
• Watchers: 4
• Forks: 1
• Open Issues: 9
• Metadata Files:
  • Readme: README.md

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README

          
# Docker container: Transpyle + FLASH

## Recommended knowledge

User must know how to use [FLASH](http://flash.uchicago.edu/site/flashcode/).

Familiarity at elementary level with the following will help:

* docker command-line interface

* Spack package manager

* `screen` linux command

* python

* jupyter notebook

## Using the Docker container

### Building the images

Rebuilding images is only necessary when:

* FLASH is updated (then, rebuild the main container image)

* dependencies are updated (then, rebuild the dependencies image and the main container image)

* transpyle framework is updated (changes in the [`Dockerfile`](dependencies/Dockerfile#L1)

  of the dependencies image plus rebuild of all of the above is required)

#### Rebuild the main container image

On the host, go to the root directory of this repository, and, first of all, update git submodules

with FLASH if necessary, as they will be copied into the image:

    git submodule update --init --remote

This requires access to FLASH repositories.

If you any modifications were made to submodules, you can revert them using:

    git submodule foreach git clean -f -d -x

    git submodule foreach git reset --hard HEAD

Then, build the image by running the following:

    sudo docker build --pull --no-cache -t mbdevpl/transpyle-flash:build-$(date +"%Y-%m-%d") .

    sudo docker push mbdevpl/transpyle-flash:build-$(date +"%Y-%m-%d")

    sudo docker tag mbdevpl/transpyle-flash:{build-$(date +"%Y-%m-%d"),latest}

    sudo docker push mbdevpl/transpyle-flash:latest

The, `--pull` option makes sure that image on which building this container depends, is also up to date.

#### Rebuilding the dependencies image

Normally you wouldn't need to do this, but if you want to update the dependencies image:

    cd dependencies

    sudo docker build --pull --no-cache -t mbdevpl/transpyle-flash:dependencies-$(date +"%Y-%m-%d") .

    sudo docker push mbdevpl/transpyle-flash:dependencies-$(date +"%Y-%m-%d")

And after that please update the 1st line of the main [`Dockerfile`](Dockerfile#L1) to mention

the latest dependencies image.

### Run the container

On the host, execute the following:

    sudo docker run -h transmachine -it mbdevpl/transpyle-flash:latest

## Using FLASH within the container

### Load Spack modules

We rely on Spack for FLASH dependencies. They have been already installed,

but necessary modules need to be loaded after starting the container.

For FLASH 4.4, 4.5 as well as FLASH subset:

    spack load mpich@3.2.1 hdf5@1.8.20 openblas@0.3.0 hypre@2.14.0

### Choose AMReX build

Additionally, FLASH subset depends on AMReX, which was also installed but outside of Spack due to

configuration issues with the version provided via Spack.

AMReX can be built:

- with or without MPI support,

- with or without OpenMP support,

- in debug or release mode, and

- for 2D or 3D grids.

The image comes with pre-built all 16 variants of AMReX. They are stored in `~/Software/` folder.

To choose a version to be used with FLASH, simply set the following environment variable before

running `setup` for FLASH.

    export AMREX_PATH=~/Software/AMReX_2d_noomp

### Run FLASH in the container

In the container, go to the directory containing FLASH, then set up and run the simulation.

Some examples of how to do this are in file [`flash_setup_examples.sh`](flash_setup_examples.sh).

You can, for example, run that file:

    ./flash_setup_examples.sh

Or, the following will pick up and test functions from [`test_flash.py`](test_flash.py):

    python3 -m unittest discover --verbose

    python3 -m unittest test_flash.Flash45Tests.test_eos_idealGamma

    python3 -m unittest test_flash.Flash45Tests.test_hy_8wv_sweep

    python3 -m unittest test_flash.FlashSubsetTests

### Transpile FLASH in the container

In the container, do the following:

    cd ~/Projects/transpyle-flash

    screen -S "TranspyleNotebook" python3 -m jupyter notebook --ip=$(hostname -i) --port=8080

Then, point your host browser to the address of the notebook which should be printed in the terminal.

After that, you can detach from the notebook's screen in the container (using `Ctrl+A+D`).

If at any time you want to return to the notebook console, type `screen -r TranspyleNotebook`.

In your host's browser, you should see jupyter notebook index page `http://container-ip:8080/tree`.

Open [`transpyle_flash.ipynb`](transpyle_flash.ipynb). To test default transpilation scenario,

execute all cells in the notebook.

After transpilation is finihsed, you can setup, build and run FLASH again to test it.

### Transpile host's FLASH from the container

You can also mount a directory with FLASH (or other Fortran code) into the container from your host,

via `--mount` comandline option of `docker run`. So instead of initial command, execute for example:

    sudo docker run -h transmachine --mount src=~/my-flash,target=/home/user/Projects/my-flash,type=bind -it transpyle-flash

That way the container is used only for transpilation, but building and execution of FLASH

can be done on pre-configured host.

Remark: when mounting, the mounted folder is owned by root within the container - and changing it's

ownership breaks ownership of files in the host system. Therefore it's best to mount files from

host with read-only intentions. See: https://github.com/moby/moby/issues/2259