Initial commit

Dockerfile.ubuntu

@@ -0,0 +1,100 @@
+# First stage
+# ===================================
+FROM --platform=linux/amd64 ubuntu:22.04 as intermediate
+
+RUN apt update && \
+    DEBIAN_FRONTEND=noninteractive  apt-get install -y  build-essential gfortran git m4 wget cmake ninja-build \
+    libopenblas-dev libfftw3-dev libhdf5-dev libhdf5-serial-dev libnetcdf-dev libnetcdff-dev libgl1-mesa-dev \
+    python3-dev python3-pip python3-venv
+
+# Install mpich manually
+WORKDIR /src
+ARG mpich=4.0.3
+ARG mpich_prefix=mpich-$mpich
+
+RUN \
+    wget https://www.mpich.org/static/downloads/$mpich/$mpich_prefix.tar.gz && \
+    tar xvzf $mpich_prefix.tar.gz   && \
+    cd $mpich_prefix                && \
+    FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch ./configure                     && \
+    make -j 4                       && \
+    make install                    && \
+    make clean                      && \
+    cd ..                           && \
+    rm -rf $mpich_prefix
+
+
+RUN /sbin/ldconfig
+
+RUN \
+    git clone --depth 1 https://github.com/Reference-ScaLAPACK/scalapack.git scalapack && \
+    mkdir scalapack/build && \
+    cd scalapack/build && \
+    CC=mpicc F77=mpif77 FC=mpif90 CXX=mpicxx cmake -DBUILD_SHARED_LIBS=ON -GNinja .. && \
+    cmake --build .  2>&1 | tee scalapack_build.log && \
+    cmake --install . 2>&1 | tee scalapack_install.log
+
+RUN /sbin/ldconfig
+
+RUN python3 -m pip install wheel
+RUN python3 -m venv /venv/
+
+RUN /venv/bin/pip install -U pip
+RUN /venv/bin/python -m pip install numpy scipy jax jaxlib f90nml mpi4py jupyter notebook jupyterlab ipython qsc sympy scikit-build ninja "pybind11[global]" cmake
+RUN /venv/bin/pip install git+https://github.com/zhucaoxiang/f90wrap
+ENV PATH="/venv/bin:${PATH}"
+
+RUN git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git /src/SPEC && \
+    cd /src/SPEC   &&  \
+    /venv/bin/pip install -v . 2>&1 | tee spec_build.log
+
+RUN git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git /src/VMEC && \
+    cd /src/VMEC && \
+    cp cmake/machines/ubuntu.json cmake_config_file.json && \
+    /venv/bin/pip install -v . 2>&1 | tee vmec_build.log
+
+RUN /venv/bin/pip install h5py pyoculus py_spec
+RUN /venv/bin/pip install vtk==9.2.6 pyqt5 matplotlib pyevtk plotly
+RUN /venv/bin/pip install mayavi
+RUN /venv/bin/pip install  git+https://github.com/hiddenSymmetries/booz_xform
+RUN /venv/bin/pip install  git+https://github.com/hiddenSymmetries/virtual-casing
+RUN /venv/bin/pip install  git+https://github.com/rogeriojorge/pyQIC
+RUN /venv/bin/pip install  git+https://github.com/landreman/pyQSC
+
+# ENV CI=True
+# RUN git clone --recurse-submodules https://github.com/hiddenSymmetries/simsopt.git /src/simsopt && \
+#     cd /src/simsopt && \
+#     git fetch --tags --all && \
+#     /venv/bin/pip install  -v .
+
+# Get the failure logs by uncommenting the two lines following # === and running
+# DOCKER_BUILDKIT=1 docker build -t test -f Dockerfile.ubuntu . --target=fail-logs --output type=local,dest=./output/
+# For Mac, don't forget sudo before docker command
+# ========================================
+#FROM scratch AS fail-logs
+#COPY --from=intermediate /src /output
+
+# Second stage
+# ===================================
+FROM --platform=linux/amd64 ubuntu:22.04
+
+LABEL maintainer.name="Bharat Medasani" \
+      maintainer.email="mbkumar.at.gmail" \
+      developers="Hidden Symmetries Team" \
+      version="0.07" \
+      description="Docker file for simsopt container based on ubuntu image" 
+
+RUN apt update && \
+    DEBIAN_FRONTEND=noninteractive  apt-get install -y m4 vim emacs nano git wget \
+    libfftw3-dev  libopenblas-dev libhdf5-serial-dev libnetcdf-dev libnetcdff-dev libgl1-mesa-dev \
+    python3-dev python3-venv
+
+COPY --from=intermediate /venv /venv
+COPY --from=intermediate /usr/local /usr/local
+RUN /sbin/ldconfig
+COPY entrypoint.sh /venv/bin
+
+#env PATH=$PATH:/venv/bin
+# ENV OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ENTRYPOINT ["bash", "/venv/bin/entrypoint.sh"]
+CMD ["bash"]

README.md

@@ -1,2 +1,52 @@
-# dev_container
-Builds development container with all the dependencies built
+# Simsopt and Docker Containers
+
+
+This document explains how to build docker container for simsopt. It also provides
+instructions on how to run simsopt docker container
+
+
+## Build the container
+
+0. Install docker
+1. Build the docker image by running the `docker build` command:
+
+   ```bash
+   docker build -t <[user_name/]image_name:[tag]> -f Dockerfile.ubuntu .
+   # In the above command, user_name is typically used for uploading the image to docker hub
+   # For local builds, you can omit the user_name/ and just use your choice of image_name
+   # Tag is optional. If not given, default is latest
+   ```
+2. Upload the image to docker hub if you want to distribute it
+   ```bash
+   docker push <image_name:tag>
+   ```
+
+
+## Run the container
+There are two cases here: 1) docker image is built locally and 2) docker image downloaded from a repo
+
+### For local builds:
+0. Identify the local image using the command
+   ```bash
+    docker image ls
+    ```
+    After identifying the image built locally, you can use either <image_name:tag> or the image id, which 
+    is an hexadecimal number, to run the docker image in the next command
+
+### Remote repo
+0. Assuming image is uploaded to docker hub, use the <user_name/image_name:tag> to automatically download
+   the image in the next command
+
+1. For interactive runs, run the docker container with the command:
+   ```bash
+   docker run -it --rm  <image>
+   ```
+
+2. To execute a python script
+   ```bash
+   docker run -v$PWD:$PWD <image> python3 $PWD/<python_script>
+   ```
+   **This command works only if no additional files are needed to run the script**
+
+
+

entrypoint.sh

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+#!/bin/bash
+# Read in the file of environment settings
+source /venv/bin/activate
+# Then run the CMD
+exec "$@"