mpi4py Jupyter tutorial and frontend tutorial outline

.devcontainer/Dockerfile

@@ -16,6 +16,7 @@ RUN mkdir /opt/spack-environment \
 &&   echo '  - [email protected]+coinhsl~mumps+metis' \
 &&   echo '  - [email protected]+blas' \
 &&   echo '  - py-jupyterlab' \
+&&   echo '  - py-ipyparallel' \
 &&   echo '  concretizer:' \
 &&   echo '    unify: true' \
 &&   echo '    reuse: true' \
@@ -28,15 +29,32 @@ RUN mkdir /opt/spack-environment \
 &&   echo '        - openmpi' \
 &&   echo '        zlib-api:' \
 &&   echo '        - zlib' \
+&&   echo '    zlib-ng:' \
+&&   echo '      buildable: false' \
 &&   echo '  config:' \
 &&   echo '    install_tree: /opt/software' \
 &&   echo '  view: /opt/views/view') > /opt/spack-environment/spack.yaml
 
 # This is manual, and required to build Ipopt
 COPY coinhsl-archive-2019.05.21.tar.gz /opt/spack-environment/coinhsl-archive-2019.05.21.tar.gz
 
+# Find external packages
+RUN cd /opt/spack-environment && spack env activate . && spack external find --all --exclude python
+
 # Do this separate of install to cache keys...
-RUN spack mirror add develop https://binaries.spack.io/develop && spack buildcache keys --install --trust
+RUN cd /opt/spack-environment && spack env activate . && spack mirror add develop https://binaries.spack.io/develop && spack buildcache keys --install --trust && spack concretize -f && spack mirror create -a
+
+# Install Ipopt w/ CoinHSL (and other deps) in stages to cache builds
+RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast ipopt
+
+# Install PETSc 
+RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast petsc
+
+# Install py-jupyterlab
+RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast py-jupyterlab
+
+# Install py-ipyparallel
+RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast py-ipyparallel
 
 # Install the software, remove unnecessary deps
 RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
@@ -72,7 +90,7 @@ RUN { \
 
 
 RUN apt-get -yqq update && apt-get -yqq upgrade \
- && apt-get -yqq install gfortran \
+ && apt-get -yqq install gfortran npm postgresql \
  && rm -rf /var/lib/apt/lists/*
 ENTRYPOINT [ "/entrypoint.sh" ]
 CMD [ "/bin/bash" ]
@@ -83,6 +101,25 @@ RUN echo "source /entrypoint.sh" >> /home/vscode/.bashrc
 # Install the Jupyter kernel
 RUN . /entrypoint.sh && \
        python3 -m ipykernel install \
-        --name py311-exago\
-        --display-name ExaGO \
+        --name py311-exago \
+        --display-name "ExaGO" \
         --prefix=
+
+# Install the mpi4py Jupyter kernel
+RUN . /entrypoint.sh && \
+       python3 -m ipykernel install \
+        --name py311-mpi4py-exago \
+        --display-name "ExaGO w/ MPI" \
+        --prefix=
+
+# Make modifications that are necessary to run mpi4py in kernelspec
+RUN sed -i 's/\"\/opt\/views\/view\/bin\/python3\"/\"mpiexec\", \"-n\", \"1\", \"\/opt\/views\/view\/bin\/python3\"/g' /usr/local/share/jupyter/kernels/py311-mpi4py-exago/kernel.json
+
+# Configure user for container
+USER vscode
+
+# Install nvm
+RUN mkdir -p /home/vscode/nvm && cd /home/vscode/nvm && curl -O https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.1/install.sh
+RUN chown vscode /home/vscode/nvm/install.sh && chmod +x /home/vscode/nvm/install.sh
+
+# Install NodeJS version 16.13.0 with nvm

.devcontainer/create_dockerfile_devcontainer.sh

@@ -0,0 +1,137 @@
+#!/bin/bash
+# Generates Dockerfile for use as Devcontainer...
+
+# Only necessary for HTTPS operations on PNNL VPN
+# export HTTPS_PROXY=http://proxy01.pnl.gov:3128 &&
+# export https_proxy=http://proxy01.pnl.gov:3128 &&
+
+# Get CoinHSL tarball if not present
+if [ ! -f "./coinhsl-archive-2019.05.21.tar.gz" ]; then
+    echo "No coinhsl-archive-2019.05.21.tar.gz found - make sure to get your own license and copy it to this directory"
+    echo "Note that the tarball must be named coinhsl-archive-2019.05.21.tar.gz"
+    exit 1
+fi
+
+# Add read/execute permissions to CoinHSL tarball
+chmod +rx ./coinhsl-archive-2019.05.21.tar.gz &&
+
+# If "-f" flag passed, force rebuild
+if [ "$1" == "-f" ]; then
+    echo "Forcing rebuild" &&
+    rm -rf ~/.spack &&
+    rm -rf ./spack &&
+    rm -rf ./spack-env
+fi
+
+#  or no ./spack dir, force a rebuild
+if [ ! -d "./tpl/spack/share" ]; then
+    echo "No spack submodule directory found, downloading spack"
+    git submodule update --init --recursive
+fi
+
+export SPACK_PYTHON=$(which python3) &&
+# Setup spack
+source ./tpl/spack/share/spack/setup-env.sh &&
+
+# Create heredoc for spack.yaml with environment
+cat > $(pwd)/spack.yaml <<EOF
+spack:
+  specs:
+    - [email protected]+ipopt+python+mpi
+    - petsc~fortran~hdf5~hypre+metis
+    - [email protected]+coinhsl~mumps+metis
+    - [email protected]+blas
+    - py-jupyterlab
+    - py-ipyparallel
+  concretizer:
+    unify: true
+    reuse: true
+  mirrors:
+    spack: https://binaries.spack.io/develop
+  container:
+    format: docker
+    images:
+      build: spack/ubuntu-jammy
+      final: mcr.microsoft.com/devcontainers/python:3.11-bookworm
+    os_packages:
+      command: apt
+      build:
+      - autoconf
+      final:
+      - gfortran
+      - npm
+      - postgresql
+  packages:
+    all:
+      providers:
+        mpi:
+        - openmpi
+        zlib-api:
+        - zlib
+    zlib-ng:
+      buildable: false
+EOF
+
+# Containerize into a Dockerfile
+# Eventually put this straight into ExaGO repo...
+spack containerize > ./.devcontainer/Dockerfile
+
+# THIS ONLY WORKS ON MAC!!! - maybe get gsed wit brew working...
+# Add Docker command before "# Install" that copies CoinHSL into image
+sed -i "" "s|# Install the software|# This is manual, and required to build Ipopt\nCOPY coinhsl-archive-2019.05.21.tar.gz /opt/spack-environment/coinhsl-archive-2019.05.21.tar.gz\n\n# Install the software|" ./.devcontainer/Dockerfile
+
+# Find external packages
+sed -i "" "s|# Install the software|# Find external packages\nRUN cd /opt/spack-environment \&\& spack env activate . \&\& spack external find --all --exclude python\n\n# Install the software|" ./.devcontainer/Dockerfile
+
+# Also trusts the build cache and create source mirror
+sed -i "" "s|# Install the software|# Do this separate of install to cache keys...\nRUN cd /opt/spack-environment \&\& spack env activate . \&\& spack mirror add develop https://binaries.spack.io/develop \&\& spack buildcache keys --install --trust \&\& spack concretize -f \&\& spack mirror create -a\n\n# Install the software|" ./.devcontainer/Dockerfile
+
+# Install Ipopt and packages in separate stages to cache builds
+sed -i "" "s|# Install the software|# Install Ipopt w/ CoinHSL (and other deps) in stages to cache builds\nRUN cd /opt/spack-environment \&\& spack env activate . \&\& spack install --fail-fast ipopt\n\n# Install the software|" ./.devcontainer/Dockerfile
+sed -i "" "s|# Install the software|# Install PETSc \nRUN cd /opt/spack-environment \&\& spack env activate . \&\& spack install --fail-fast petsc\n\n# Install the software|" ./.devcontainer/Dockerfile
+sed -i "" "s|# Install the software|# Install py-jupyterlab\nRUN cd /opt/spack-environment \&\& spack env activate . \&\& spack install --fail-fast py-jupyterlab\n\n# Install the software|" ./.devcontainer/Dockerfile
+sed -i "" "s|# Install the software|# Install py-ipyparallel\nRUN cd /opt/spack-environment \&\& spack env activate . \&\& spack install --fail-fast py-ipyparallel\n\n# Install the software|" ./.devcontainer/Dockerfile
+
+# Configure environment for VSCode User in devcontainer
+echo "# Make sure devcontainer user gets spack packages" >> ./.devcontainer/Dockerfile
+echo "RUN echo \"source /entrypoint.sh\" >> /home/vscode/.bashrc" >> ./.devcontainer/Dockerfile
+
+# Finally install the Jupyter kernel
+echo "" >> ./.devcontainer/Dockerfile
+echo "# Install the Jupyter kernel" >> ./.devcontainer/Dockerfile
+echo "RUN . /entrypoint.sh && \\" >> ./.devcontainer/Dockerfile
+echo "       python3 -m ipykernel install \\" >> ./.devcontainer/Dockerfile
+echo "        --name py311-exago \\" >> ./.devcontainer/Dockerfile
+echo "        --display-name \"ExaGO\" \\" >> ./.devcontainer/Dockerfile
+echo "        --prefix=$(which jupyter)" >> ./.devcontainer/Dockerfile
+
+# Install the mpi4py Jupyter kernel
+echo "" >> ./.devcontainer/Dockerfile
+echo "# Install the mpi4py Jupyter kernel" >> ./.devcontainer/Dockerfile
+echo "RUN . /entrypoint.sh && \\" >> ./.devcontainer/Dockerfile
+echo "       python3 -m ipykernel install \\" >> ./.devcontainer/Dockerfile
+echo "        --name py311-mpi4py-exago \\" >> ./.devcontainer/Dockerfile
+echo "        --display-name \"ExaGO w/ MPI\" \\" >> ./.devcontainer/Dockerfile
+echo "        --prefix=$(which jupyter)" >> ./.devcontainer/Dockerfile
+
+# Modify mpi4py kernel to actually launch process with mpiexec
+echo "" >> ./.devcontainer/Dockerfile
+echo "# Make modifications that are necessary to run mpi4py in kernelspec" >> ./.devcontainer/Dockerfile
+echo "RUN sed -i 's/\\\"\/opt\/views\/view\/bin\/python3\\\"/\\\"mpiexec\\\", \\\"-n\\\", \\\"1\\\", \\\"\/opt\/views\/view\/bin\/python3\\\"/g' /usr/local/share/jupyter/kernels/py311-mpi4py-exago/kernel.json" >> ./.devcontainer/Dockerfile
+
+# Make sure vscode user is correct
+echo "" >> ./.devcontainer/Dockerfile
+echo "# Configure user for container" >> ./.devcontainer/Dockerfile
+echo "USER vscode" >> ./.devcontainer/Dockerfile
+
+# Install nvm for VSCode user
+echo "" >> ./.devcontainer/Dockerfile
+echo "# Install nvm" >> ./.devcontainer/Dockerfile
+echo "RUN mkdir -p /home/vscode/nvm && cd /home/vscode/nvm && curl -O https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.1/install.sh" >> ./.devcontainer/Dockerfile
+echo "RUN chown vscode /home/vscode/nvm/install.sh && chmod +x /home/vscode/nvm/install.sh" >> ./.devcontainer/Dockerfile
+
+# Install NodeJS version 16.13.0 with nvm
+echo "" >> ./.devcontainer/Dockerfile
+echo "# Install NodeJS version 16.13.0 with nvm" >> ./.devcontainer/Dockerfile
+#echo "RUN . /opt/nvm/nvm.sh && \\" >> ./.devcontainer/Dockerfile
+#echo "       nvm install v16.13.0" >> ./.devcontainer/Dockerfile

.devcontainer/devcontainer.json

@@ -9,7 +9,8 @@
 				"ms-azuretools.vscode-docker",
 				"github.vscode-github-actions",
 				"ms-toolsai.jupyter",
-				"GitHub.copilot"
+				"GitHub.copilot",
+				"ms-vsliveshare.vsliveshare"
 			]
 		}
 	},

.gitignore

@@ -5,7 +5,7 @@ install/*
 .ubuild.json
 *__pycache__*
 *nvblas.conf
-spack-*
+spack*
 .vscode/
 coinhsl-*
 node_modules
@@ -14,3 +14,4 @@ package-lock.json
 config.py
 spack_*
 hiop/
+solution

docs/devcontainer/README.md

@@ -7,6 +7,10 @@
 1. open your local clone of exago in VSCode
 1. copy the CoinHSL 2019 tarball to the top level of your exago directory
 
+## Generate the container
+
+Spack is used to generate the base image, with some sed/echo commands used to fine-tune Dockerfile for use case within a Dev Container. Run `.devcontainer/create_dockerfile.sh` in order to re-generate the Dockerfile. This should be done semi-frequently whenever a spack version or exago version needs updating.
+
 ## Build Container
 
 The build info for this container is in `.devcontainer/`. There is a Dockerfile and json file associated with the configuration.