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add dockerfile for docker image with dagmc, openmc, pyne and fusion-material-db #11

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add dockerfile for docker image with dagmc, openmc, pyne and fusion-material-db #11

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af7d182
add dockerfile for docker image with dagmc, openmc, pyne and fusion-m…
Edgar-21 Mar 26, 2025
cbfe3fd
majorly improved, plus apply pr comments
Edgar-21 Apr 18, 2025
91cad5c
capitilization
Edgar-21 Apr 18, 2025
a8849c4
change cores to be a build arg and set the default value to 1
Edgar-21 Apr 18, 2025
bd0ba25
add missing pyenv dependencies
Edgar-21 Apr 21, 2025
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197 changes: 197 additions & 0 deletions dockerfiles/pyne_dag_openmc
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FROM debian:bookworm-slim

# modified from OpenMC's dockerfile https://github.com/openmc-dev/openmc/blob/develop/Dockerfile
# Install and update dependencies from Debian package manager
RUN apt-get update -y && \
apt-get upgrade -y && \
apt-get install -y \
python3-pip \
python-is-python3 \
wget \
git \
build-essential \
cmake \
mpich \
libmpich-dev \
libpng-dev \
liblzma-dev \
make \
build-essential \
libssl-dev \
zlib1g-dev \
libbz2-dev \
libreadline-dev \
libsqlite3-dev \
wget \
ca-certificates \
curl \
llvm \
libncurses5-dev \
xz-utils \
tk-dev \
libxml2-dev \
libxmlsec1-dev \
libffi-dev \
liblzma-dev \
mecab-ipadic-utf8 \
git \
libeigen3-dev \
libnetcdf-dev \
libtbb-dev \
libglfw3-dev \
libblas-dev \
liblapack-dev \
wget \
nano

ENV HOME=/root

ENV PYTHON_VERSION 3.11.9

# Set-up necessary Env vars for PyEnv
ENV PYENV_ROOT /root/.pyenv
ENV PATH $PYENV_ROOT/shims:$PYENV_ROOT/bin:$PATH

# Install pyenv & python dependencies.
RUN set -ex \
&& curl https://pyenv.run | bash \
&& pyenv update \
&& pyenv install $PYTHON_VERSION \
&& pyenv global $PYTHON_VERSION \
&& pyenv rehash \
&& pip install --upgrade pip \
&& pip install packaging \
progress pyyaml pytest openmc-plasma-source vtk tables

ARG compile_cores=18

# HDF5 stuff
ENV HDF5_BUILD_DIR=/root/build/hdf5
ENV HDF5_INSTALL_DIR=/opt/hdf5
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@gonuke gonuke Apr 5, 2025

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Add an HDF5 version string as a variable as well?

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@Edgar-21 Edgar-21 Apr 18, 2025

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updated to use package manager install


# Embree variables
ENV EMBREE_TAG='v4.3.1'
ENV EMBREE_REPO='https://github.com/embree/embree'
ENV EMBREE_INSTALL_DIR=$HOME/EMBREE/

# MOAB variables
ENV MOAB_TAG='5.3.0'
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@gonuke gonuke Apr 5, 2025

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I'm pretty sure we should be using a newer MOAB, no?

ENV MOAB_REPO='https://bitbucket.org/fathomteam/moab/'

# Double-Down variables
ENV DD_TAG='v1.1.0'
ENV DD_REPO='https://github.com/pshriwise/double-down'
ENV DD_INSTALL_DIR=$HOME/Double_down

# DAGMC variables
ENV DAGMC_BRANCH='v3.2.3'
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@gonuke gonuke Apr 5, 2025

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Probably want a newer DAGMC 3.2.4

ENV DAGMC_REPO='https://github.com/svalinn/DAGMC'
ENV DAGMC_INSTALL_DIR=$HOME/DAGMC/

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@gonuke gonuke Apr 5, 2025

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Does it make sense to add a block for OpenMC and PyNE here with relevant version strings, etc?

# Setup environment variables for Docker image
ENV LD_LIBRARY_PATH=${DAGMC_INSTALL_DIR}/lib \
OPENMC_ENDF_DATA=/root/endf-b-vii.1 \
DEBIAN_FRONTEND=noninteractive

# HDF5
RUN mkdir -p ${HDF5_INSTALL_DIR}/temp \
&& wget https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_1_14_3/src/hdf5-1.14.3.tar.gz -O ${HDF5_INSTALL_DIR}/temp/hdf5-1.14.3.tar.gz \
&& cd ${HDF5_INSTALL_DIR}/temp \
&& tar -xvf hdf5-1.14.3.tar.gz \
&& cd hdf5-1.14.3 \
&& mkdir build \
&& cd build && \
../configure --prefix=${HDF5_INSTALL_DIR} \
--enable-optimization=high --enable-shared \
--enable-hl \
--enable-build-mode=production \
&& make -j${compile_cores} \
&& make install \
&& rm -rf ${HDF5_INSTALL_DIR}/temp
ENV HDF5_ROOT=${HDF5_INSTALL_DIR}

# Install addition packages required for DAGMC
RUN pip install --upgrade "numpy<2.0" "cython<3.0" \
# Clone and install EMBREE
&& mkdir -p $HOME/EMBREE && cd $HOME/EMBREE \
&& git clone --single-branch -b ${EMBREE_TAG} --depth 1 ${EMBREE_REPO} \
&& mkdir build && cd build \
&& cmake ../embree \
-DCMAKE_INSTALL_PREFIX=${EMBREE_INSTALL_DIR} \
-DEMBREE_MAX_ISA=NONE \
-DEMBREE_ISA_SSE42=ON \
-DEMBREE_ISPC_SUPPORT=OFF \
&& make 2>/dev/null -j${compile_cores} install \
&& rm -rf ${EMBREE_INSTALL_DIR}/build ${EMBREE_INSTALL_DIR}/embree
# Clone and install MOAB
RUN mkdir -p $HOME/MOAB && cd $HOME/MOAB \
&& git clone --single-branch -b ${MOAB_TAG} --depth 1 ${MOAB_REPO} \
&& mkdir build && cd build \
&& cmake ../moab -DCMAKE_BUILD_TYPE=Release \
-DENABLE_HDF5=ON \
-DHDF5_ROOT=${HDF5_INSTALL_DIR} \
-DBUILD_SHARED_LIBS=OFF \
-DENABLE_FORTRAN=OFF \
-DENABLE_BLASLAPACK=OFF \
&& make 2>/dev/null -j${compile_cores} install \
&& cmake ../moab \
-DENABLE_PYMOAB=ON \
-DBUILD_SHARED_LIBS=ON \
&& make 2>/dev/null -j${compile_cores} install \
&& cd pymoab && bash install.sh \
&& python setup.py install \
&& python -c "import pymoab" \
&& rm -rf $HOME/MOAB

# Clone and install Double-Down
RUN mkdir -p $HOME/Double_down && cd $HOME/Double_down \
&& git clone --single-branch -b ${DD_TAG} --depth 1 ${DD_REPO} \
&& mkdir build && cd build \
&& cmake ../double-down -DCMAKE_INSTALL_PREFIX=${DD_INSTALL_DIR} \
-DMOAB_DIR=/usr/local \
-DEMBREE_DIR=${EMBREE_INSTALL_DIR} \
&& make 2>/dev/null -j${compile_cores} install \
&& rm -rf ${DD_INSTALL_DIR}/build ${DD_INSTALL_DIR}/double-down
# Clone and install DAGMC
RUN mkdir -p $HOME/DAGMC && cd $HOME/DAGMC \
&& git clone --single-branch -b ${DAGMC_BRANCH} --depth 1 ${DAGMC_REPO} \
&& mkdir build && cd build \
&& cmake ../DAGMC -DBUILD_TALLY=ON \
-DCMAKE_INSTALL_PREFIX=${DAGMC_INSTALL_DIR} \
-DMOAB_DIR=/usr/local \
-DDOUBLE_DOWN=ON \
-DDOUBLE_DOWN_DIR=${DD_INSTALL_DIR} \
-DCMAKE_PREFIX_PATH=${DD_INSTALL_DIR}/lib \
-DBUILD_STATIC_LIBS=OFF \
&& make 2>/dev/null -j${compile_cores} install \
&& rm -rf ${DAGMC_INSTALL_DIR}/DAGMC ${DAGMC_INSTALL_DIR}/build

ARG openmc_branch=develop
ENV OPENMC_REPO='https://github.com/openmc-dev/openmc'

ENV DAGMC_INSTALL_DIR=$HOME/DAGMC/
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@gonuke gonuke Apr 5, 2025

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This is already defined above


# clone and install openmc
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@dean-krueger dean-krueger Apr 18, 2025

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Incredibly pedantic point: All the other comments are "Clone", but this one is "clone"

RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
&& git clone --shallow-submodules --recurse-submodules --single-branch -b ${openmc_branch} --depth=1 ${OPENMC_REPO} \
&& mkdir build && cd build &&\
cmake ../openmc \
-DCMAKE_CXX_COMPILER=mpicxx \
-DOPENMC_USE_MPI=on \
-DHDF5_PREFER_PARALLEL=on \
-DOPENMC_USE_DAGMC=ON \
-DCMAKE_PREFIX_PATH=${DAGMC_INSTALL_DIR} \
&& make 2>/dev/null -j${compile_cores} install \
&& cd ../openmc && pip install .[test,depletion-mpi] \
&& python -c "import openmc"

WORKDIR $HOME/opt
RUN git clone -b 0.7.8 https://github.com/pyne/pyne.git
RUN cd $HOME/opt/pyne \
&& python setup.py install --user \
--clean -j${compile_cores}
RUN ./pyne/scripts/nuc_data_make

RUN git clone https://github.com/svalinn/fusion-material-db.git
ENV PYTHONPATH=$PYTHONPATH:$HOME/opt/fusion-material-db/material-db-tools
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@FusionSandwich FusionSandwich Apr 22, 2025

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Suggested change
ENV PYTHONPATH=$PYTHONPATH:$HOME/opt/fusion-material-db/material-db-tools
ENV PYTHONPATH=""
ENV PYTHONPATH=$PYTHONPATH:$HOME/opt/fusion-material-db/material-db-tools

Either define the variable before or get rid of the line

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@gonuke gonuke Apr 22, 2025

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Yikes! Won't this remove default values of PYTHONPATH?

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@Edgar-21 Edgar-21 Apr 22, 2025

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The PYTHONPATH is empty by default, docker gives a build warning about using an undefined variable as written, this suggestion is to resolve the warning. Another alternative would be to just do

ENV PYTHONPATH=$HOME/opt/fusion-material-db/material-db-tools

But I think I like defining PYTHONPATH as an empty string elsewhere so we can maintain the convention of appending all additions to PYTHONPATH to itself. Not a big deal since we only add one thing to it in this dockerfile, but if more things needed to be added it would be convenient to not worry about whether you are changing the first place it is declared.

Or we could just ignore the warning.