Docker with examples

Docker/simex/Dockerfile

@@ -1,19 +1,21 @@
 # [email protected] - Daniel Webster
 FROM chuckie82/centos_env
-LABEL maintainer="Chunhong Yoon <[email protected]>"
+LABEL maintainer="Carsten Fortmann-Grote [email protected] github:CFGrote dockerhub:cfgrote"
 
 ADD requirements.txt /opt/requirements.txt
 ADD python_install.sh /opt/python_install.sh
-RUN yum remove -y cmake && yum install -y cmake3 hdf5-devel flex bison   && \
+RUN yum remove -y cmake && yum install -y cmake3 hdf5-devel flex sudo  bison git   && \
     yum clean all && rm -rf /var/cache/yum                               && \
-    update-alternatives --install /usr/bin/cmake cmake /usr/bin/cmake3 3 && \
-    /opt/python_install.sh
+    update-alternatives --install /usr/bin/cmake cmake /usr/bin/cmake3 3
+
+RUN ["chmod", "a+x", "/opt/python_install.sh"]
+RUN "/opt/python_install.sh"
 ENV PATH /opt/miniconda/bin:$PATH
 
 ARG simex_script=simex_install.sh
 ADD $simex_script /opt/simex_install.sh
 
-RUN ["bash", "/opt/simex_install.sh"]
+RUN ["sudo", "bash", "/opt/simex_install.sh"]
 
 ENV MKLROOT=/opt/miniconda
 ENV MKL_ROOT=/opt/miniconda
@@ -25,4 +27,14 @@ ENV PYTHONPATH=$SIMEX_ROOT/Sources/python:$SIMEX_ROOT/lib/python3.7:$PYTHONPATH:
 ENV SIMEX_TESTS=$SIMEX_ROOT/Tests
 ENV PYFAI_TESTIMAGES=/tmp
 
+RUN ["pip3", "install", "jupyter"]
+
 RUN useradd -m jovyan
+
+RUN ["git", "clone", "--depth", "1", "https://github.com/PaNOSC-ViNYL/SimEx-notebooks.git", "/home/jovyan/simex_notebooks"]
+
+WORKDIR /home/jovyan/simex_notebooks
+
+CMD ["jupyter", "notebook", "--port=24306", "--no-browser", "--ip=0.0.0.0", "--allow-root"]
+
+

Docker/simex/README.md

@@ -0,0 +1,22 @@
+# Instructions for building, tagging, pushing, and running the simex docker container
+## Building
+```
+./build_image.sh
+```
+
+## Tag
+```
+docker tag simex cfgrote/simex
+```
+
+## Push
+```
+docker push cfgrote/simex
+```
+
+## Run container and start jupyter to be accessed from host or remote client on port `HOSTPORT`.
+```
+docker run -p HOSTPORT:24306 cfgrote/simex 
+```
+
+

Docker/simex/build_image

@@ -1,4 +1,4 @@
 cp ../../requirements.txt .
 
-buildah bud -t cloudbusting/simex -f Dockerfile .
+docker build -t cfgrote/simex .
 

README.md

@@ -76,6 +76,22 @@ git clone --depth 1 -b develop https://github.com/PaNOSC-ViNYL/SimEx.git
 Now the TestFiles are hosted at [Zenodo](https://zenodo.org/record/3750541#.X2R9DZMzZE5).
 The files can be downloaded with [this script](get_testdata.sh).
 
+## Docker
+Our docker image `cfgrote/simex` provides a complete runtime environment including
+* The SimEx python library
+* All dependencies and backengines
+* jupyter lab
+* Example jupyter notebooks from [simex_notebooks](https://github.com/PaNOSC-ViNYL/SimEx-notebooks). 
+
+### Running the container
+In the terminal, run
+```
+docker run --port HOSTPORT:24306 cfgrote/simex 
+```
+If the docker image is not found on the host system, it will first be `pull`ed from dockerhub.
+
+Then, navigate to http://host:HOSTPORT and find yourself in a running jupyter notebook environment.
+
 
 ## Acknowledgements
 This project has received funding from the European Union’s Horizon 2020 research