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fortran Coarray Fortran Kernl on Backend.AI
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‎fortran/Dockerfile.caf

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FROM ubuntu:18.04
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MAINTAINER Mario Cho "[email protected]"
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ENV PATH=/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH \
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LANG=C.UTF-8
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# DEBIAN_FRONTEND=noninteractive
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ARG OPENCOARRAYS_VERSION=2.8.0
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ENV GCC_VERSION 8.2.0
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RUN DEBIAN_FRONTEND=noninteractive transientBuildDeps="file" && \
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set -v && \
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cat /etc/issue && \
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uname -a && \
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echo "${DEBIAN_FRONTEND}" && \
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apt-get update -y && \
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apt-get install -y \
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software-properties-common && \
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add-apt-repository ppa:ubuntu-toolchain-r/test -y && \
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apt-get update -y && \
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apt-get install -y \
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python3 python3-pip \
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gfortran \
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libssl-dev \
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make \
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curl \
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wget \
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gcc-8 \
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gfortran-8 \
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g++-8 \
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mpich \
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${transientBuildDeps} && \
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update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-8 60 --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-8 && \
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update-alternatives --set gcc "/usr/bin/gcc-8" && \
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gcc --version && \
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gfortran --version && \
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mpiexec --version && \
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mpifort --version && \
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mpicc --version && \
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apt-get clean && \
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apt-get purge -y --auto-remove ${transientBuildDeps} && \
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rm -rf /var/lib/apt/lists/* /var/log/* /tmp/*
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# Install commonly-used wheels
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RUN curl https://bootstrap.pypa.io/get-pip.py | python3 && \
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python3 -m pip install --no-cache-dir -U setuptools && \
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python3 -m pip install --no-cache-dir pyzmq && \
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python3 -m pip install --no-cache-dir ipython && \
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python3 -m pip install --no-cache-dir jupyter && \
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python3 -m pip install --no-cache-dir jupyterlab
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# Build-time metadata as defined at http://label-schema.org
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ARG BUILD_DATE
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ARG VCS_REF
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ARG VCS_URL
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ARG VCS_VERSION=latest
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LABEL org.label-schema.schema-version="1.0" \
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org.label-schema.build-date="${BUILD_DATE}" \
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org.label-schema.name="jupyter-CAF-kernel" \
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org.label-schema.description="Fortran Jupyter kernel with OpenCoarrays and MPICH backend on Basckend.AI" \
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org.label-schema.url="https://github.com/sourceryinstitute/jupyter-CAF-kernel/" \
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org.label-schema.vcs-ref="${VCS_REF}" \
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org.label-schema.vcs-url="${VCS_URL}" \
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org.label-schema.version="${VCS_VERSION}" \
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org.label-schema.vendor="SourceryInstitute" \
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org.label-schema.license="MIT"
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COPY ./jupyter-caf-kernel /opt/jupyter/jupyter-caf-kernel
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RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 2
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WORKDIR /tmp
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RUN DEBIAN_FRONTEND=noninteractive transientBuildDeps="cmake git" && \
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set -v && \
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echo "${DEBIAN_FRONTEND}" && \
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apt-get update && \
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apt-get install -y ${transientBuildDeps} && \
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cmake --version && \
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wget -nv -t 3 https://github.com/sourceryinstitute/opencoarrays/releases/download/${OPENCOARRAYS_VERSION}/OpenCoarrays-${OPENCOARRAYS_VERSION}.tar.gz && \
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wget -nv -t 3 https://github.com/sourceryinstitute/opencoarrays/releases/download/${OPENCOARRAYS_VERSION}/opencoarrays-${OPENCOARRAYS_VERSION}-SHA256.txt && \
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sha256sum -c opencoarrays-${OPENCOARRAYS_VERSION}-SHA256.txt && \
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echo "sha" && \
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tar xzf OpenCoarrays-${OPENCOARRAYS_VERSION}.tar.gz && \
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cd OpenCoarrays-${OPENCOARRAYS_VERSION} && \
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echo "Installing OpenCoarrays using CMake in $(pwd)" && \
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mkdir build && \
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cd build && \
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gcc --version && \
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gfortran --version && \
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FC="`which gfortran`" CC="`which gcc`" cmake .. && \
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make -j "$(nproc)" install && \
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if [ "${RUN_TESTS}" = "true" ] ; then ctest --output-on-failure; fi && \
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cd && \
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rm -rf OpenCoarrays* opencoarrays* && \
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caf --version && \
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python3 -m pip install --no-cache-dir notebook==5.* && \
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python3 -m pip install -e /opt/jupyter/jupyter-caf-kernel && \
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jupyter-kernelspec install /opt/jupyter/jupyter-caf-kernel/Coarray-Fortran/ && \
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jupyter-kernelspec list && \
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rm -rf jupyter-caf-kernel && \
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apt-get clean && \
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apt-get purge -y --auto-remove ${transientBuildDeps} && \
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rm -rf /var/lib/apt/lists/* /var/log/* /tmp/*
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# chown -R ${NB_USER} /home/${NB_USER&& }
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# Install ipython kernelspec
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RUN python3 -m ipykernel install --display-name "gFrotran 8.3 on Backend.AI" && \
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cat /usr/local/share/jupyter/kernels/python3/kernel.json
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LABEL ai.backend.kernelspec="1" \
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ai.backend.envs.corecount="OPENBLAS_NUM_THREADS,OMP_NUM_THREADS,NPROC" \
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ai.backend.features="batch query uid-match user-input" \
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ai.backend.resource.min.cpu="1" \
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ai.backend.resource.min.mem="256m" \
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ai.backend.base-distro="ubuntu16.04" \
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ai.backend.runtime-type="python" \
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ai.backend.runtime-path="/usr/bin/python3" \
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ai.backend.service-ports="jupyter:http:8080,jupyterlab:http:8090"
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COPY policy.yml /etc/backend.ai/jail/policy.yml
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# vim: ft=dockerfile
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# build-essential \
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‎fortran/jupyter-caf-kernel/Coarray-Fortran/kernel.json

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{
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"argv": [
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"python3",
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"-m",
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"jupyter_caf_kernel",
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"-f",
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"{connection_file}"
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],
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"display_name": "Coarray Fortran",
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"language": "Fortran"
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}

‎fortran/jupyter-caf-kernel/LICENSE.txt

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MIT License
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Copyright (c) 2017 Sourcery Institute
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎fortran/jupyter-caf-kernel/MANIFEST.in

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include LICENSE.txt

‎fortran/jupyter-caf-kernel/README.md

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<div align="center">
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# Fortran kernel for Jupyter with Coarray support
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[![Binder](http://mybinder.org/badge.svg)](https://beta.mybinder.org/v2/gh/sourceryinstitute/jupyter-CAF-kernel/master)
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[![](https://images.microbadger.com/badges/image/sourceryinstitute/jupyter-caf-kernel.svg)](https://microbadger.com/images/sourceryinstitute/jupyter-caf-kernel)
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[![](https://images.microbadger.com/badges/version/sourceryinstitute/jupyter-caf-kernel.svg)](https://hub.docker.com/r/sourceryinstitute/jupyter-caf-kernel/)
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[![](https://images.microbadger.com/badges/commit/sourceryinstitute/jupyter-caf-kernel.svg)](https://github.com/sourceryinstitute/jupyter-CAF-kernel#readme)
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[![](https://images.microbadger.com/badges/license/sourceryinstitute/jupyter-caf-kernel.svg)][license]
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</div>
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----
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## Quick start
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* [Try][try CAF] Coarray Fortran in the cloud with [GFortran] and [OpenCoarrays]
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using [Binder]: __http://bit.ly/TryCoarrays__
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This will open the [`index.ipynb`] file in an interactive
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environment using [Binder].
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* Launch a full JupyterHub [Binder] Fortran environment in the cloud with [OpenCoarrays]: __http://bit.ly/CAF-Binder__
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## Run locally
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```bash
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docker pull sourceryinstitute/jupyter-caf-kernel:latest
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docker run -i -t -p 8888:8888 sourceryinstitute/jupyter-caf-kernel:latest
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```
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You should see output similar to the following which will instruct you
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to point your web browser to `http://localhost:8888/?token=...`
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```
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[I 19:29:08.089 NotebookApp] Writing notebook server cookie secret to /home/jovyan/.local/share/jupyter/runtime/notebook_cookie_secret
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[W 19:29:08.188 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
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[I 19:29:08.221 NotebookApp] JupyterLab alpha preview extension loaded from /opt/conda/lib/python3.5/site-packages/jupyterlab
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[I 19:29:08.233 NotebookApp] Serving notebooks from local directory: /home/jovyan
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[I 19:29:08.233 NotebookApp] 0 active kernels
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[I 19:29:08.233 NotebookApp] The Jupyter Notebook is running at: http://[all ip addresses on your system]:8888/?token=67e0bf26a40f863c8af93c030de57b4802cd7b3d9f10ae17
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[I 19:29:08.233 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
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[C 19:29:08.234 NotebookApp]
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Copy/paste this URL into your browser when you connect for the first time,
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to login with a token:
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http://localhost:8888/?token=67e0bf26a40f863c8af93c030de57b4802cd7b3d9f10ae17
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```
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When running locally (this way) you won't have access to the examples
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folder or [`index.ipynb`].
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## About
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This Coarray Fortran kernel is still a bit rough around the edges. It
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is a shameless fork of the [jupyter-c-kernel], quickly thrown
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together. This is [licensed under the MIT license][license], as is
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[jupyter-c-kernel]. I also drew inspiration from the
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[jupyter-fortran-kernel].
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### Whats up with the `prebuild` directory?
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The `prebuild` directory is there so that the docker image used to
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launch the Coarray Fortran kernel on [Binder] can be built
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automatically on Docker Hub. The `Dockerfile` at the project root then
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wraps the one located in `prebuild`. This is because we must compile
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GCC from source to get a new enough version and this takes a very long
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time. We don't want users to have to wait forever to spawn a new
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notebook on [Binder], so we ensure that the base image is built ahead
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of time, locally, or through the Docker Hub automated build process.
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## Manual local installation
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The recommended usage of this kernel is through [Binder] in the cloud,
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or [via Docker, as described above](#Run-locally). If you decide to
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install this kernel locally on your system you will need the following
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software packages installed:
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* GCC and [GFortran] >= 8.2
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* [MPICH] >= 3.2
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* [OpenCoarrays]
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* [Jupyter]
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* Python 3
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* pip
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### Step-by-step
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1. `git clone https://github.com/sourceryinstitute/jupyter-CAF-kernel`
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1. `cd jupyter-CAF-kernel`
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1. `pip install -e prebuild/jupyter-caf-kernel`
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1. `jupyter-kernelspec install prebuild/jupyter-caf-kernel/Coarray-Fortran/`
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1. `jupyter-notebook .`
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## Contributing
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Contributions are most welcome!
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### ToDo
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* [ ] Use proper Python OOP class extension & better understand base class
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* [ ] Improve I/O
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* [ ] Improve exception handling and error reporting
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* [x] Improve magics
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* [ ] Use [MetaKernel] to build the kernel and magics
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* [ ] Allow use of all aplicable [MetaKernel magics]
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* [ ] Don't attempt to compile code when only magics are present
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* [ ] Different flavors of Docker images (so that less space is
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used). See [jupyter/docker-stacks][jupyter-stacks]
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### Version control
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1. [Fork]
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1. Create branches named `issue-X` where `X` is the number of the
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issue.
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1. Commit changes
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1. [Pull Request]
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## License
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[MIT][license]
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[Binder]: https://beta.mybinder.org
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[try CAF]: http://bit.ly/TryCoarrays
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[GFortran]: https://gcc.gnu.org/wiki/GFortran
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[OpenCoarrays]: https://github.com/sourceryinstitute/OpenCoarrays#readme
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[`index.ipynb`]: https://nbviewer.jupyter.org/github/sourceryinstitute/jupyter-CAF-kernel/blob/master/index.ipynb
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[jupyter-c-kernel]: https://github.com/brendan-rius/jupyter-c-kernel#readme
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[jupyter-fortran-kernel]: https://github.com/ZedThree/jupyter-fortran-kernel
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[MPICH]: https://www.mpich.org
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[license]: https://github.com/sourceryinstitute/jupyter-CAF-kernel/blob/master/LICENSE
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[Fork]: https://github.com/sourceryinstitute/jupyter-CAF-kernel/fork
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[Pull Request]: https://github.com/sourceryinstitute/jupyter-CAF-kernel/compare?expand=1
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[MetaKernel]: https://github.com/Calysto/metakernel#readme
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[MetaKernel magics]: https://github.com/Calysto/metakernel/blob/master/metakernel/magics/README.md
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[jupyter-stacks]: https://github.com/jupyter/docker-stacks#readme
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[Jupyter]: https://jupyter.org

‎fortran/jupyter-caf-kernel/jupyter_caf_kernel/__init__.py

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‎fortran/jupyter-caf-kernel/jupyter_caf_kernel/__main__.py

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from ipykernel.kernelapp import IPKernelApp
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from .kernel import CafKernel
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IPKernelApp.launch_instance(kernel_class=CafKernel)

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