Skip to content

README.md

Latest commit

 

History

History
72 lines (65 loc) · 3.65 KB

README.md

File metadata and controls

72 lines (65 loc) · 3.65 KB
Raw

The Docker way (only for Linux)

In order to run the present work in a Docker container, you can directly pull the built image as:

docker pull jimjdocker/seatos:v1

Or you can build the Docker image (say ImageName) using this Dockerfile as:

# Note that <Dockerfile-directory> must be the absolute path 
# to the directory where the Dockerfile is placed (not the path
# to the Dockerfile itself)
docker build --rm -t <ImageName> <Dockerfile-directory>
# this might take ~20min the first time

Now you are ready to run Python inside a Docker container:

HOME_GUST=/home/docker
XCONFIG_HOST=<this-repository>/docker-x
XCONFIG_GUST=${HOME_GUST}/src
EXEC=/condadir/bin/ipython # (can be replaced by any executable file)
docker run -it --rm --name ubuntuX2 --volume=${XCONFIG_HOST}:${XCONFIG_GUST} --user=$UID:${GID} -w ${HOME_GUST} <ImageName> $EXEC

But if you need to run a script that needs a valid DISPLAY environment variable:

docker run -it --name ubuntuX2 --volume=${XCONFIG_HOST}:${XCONFIG_GUST} --user=1000:1000 -w ${HOME_GUST} <ImageNameN> /bin/bash
#--- and inside the container (start a DISPLAY in :10):
$HOME/src/config/docker-desktop -s 800x600 -d 10
DISPLAY=:10 ipython
#--- and inside IPython:
In [1]: run ./script.py  ## IT WORKS GREAT!!

Reproduction of A&A figures

The bash script rundocker.sh uses a Docker container (associated to the Docker image above) as a "friendly" environment to run python scripts that generate some figures of the A&A paper "Superposed epoch study of ICME sub-structures near Earth and their effects on Galactic cosmic rays". Execute it by passing as argument an empty directory <absolute-output-directory> (an absolute path) for the output files:

cd docker-x
./rundocker.sh <absolute-output-directory>

Technical remarks:

  • the above script (rundocker.sh) needs a valid REPO_HOST environment variable, which has to be the path to this Git repository (in this commit).
  • all variables with suffixes _HOST and _GUST refers to paths in the host ("real") and guest (i.e. inside the Docker container) systems.
  • the DOCKER_IMAGE env variable refers to the Docker image you'll execute.
  • the section "List of data sources" (inside rundocker.sh) defines paths to input filenames (which have prefix fnm_) that exist in the host system. Make sure to correct those if necessary.
  • this script takes as 1st argument a path where output files will be placed. In case such path already exists and is not empty, a backup will be made using the current date and time as suffix for the backup directory (see _dirbckp variable).
  • If the variable ProvideExtractedData equals 1, the script won't perform data extraction. Instead, the paths given by LEFT_HOST and RIGHT_HOST will be used by the script docker_test.sh to build mixed profiles. If the variable ProvideExtractedData equals 0, the script will perform data extraction from the ACE and CR-detector datasets, and later the mixed profiles will be built. Note that for the later option, you'll have to modify the LEFT and RIGHT variable by hand in docker_test.sh.
  • you can use these LEFT and RIGHT directories as input for this script (which is called by the chain script1 --> script2 --> script3) They are set with the variables LEFT_HOST and RIGHT_HOST.