Merge pull request aurora-multiphysics#5 from aurora-multiphysics/Edw…

…ardPalmer99/remove-hephaestus-dependency

Remove Hephaestus Dependency

.clang-tidy

@@ -1,4 +1,4 @@
-HeaderFilterRegex: 'hephaestus/[ste]'
+HeaderFilterRegex: 'platypus/[is]'
 Checks:              '-*,readability-identifier-naming,readability-redundant-member-init,modernize-*,-modernize-use-trailing-return-type,-modernize-avoid-c-arrays'
 CheckOptions:
   - key:             readability-identifier-naming.AggressiveDependentMemberLookup

.gitmodules

@@ -1,6 +1,3 @@
 [submodule "python/pybind11"]
 	path = python/pybind11
 	url = https://github.com/pybind/pybind11.git
-[submodule "contrib/hephaestus"]
-	path = contrib/hephaestus
-	url = https://github.com/aurora-multiphysics/hephaestus

Makefile

@@ -28,20 +28,29 @@ ALL_MODULES                 := no
 
 CHEMICAL_REACTIONS          := no
 CONTACT                     := no
+ELECTROMAGNETICS            := no
 EXTERNAL_PETSC_SOLVER       := no
 FLUID_PROPERTIES            := no
+FSI                         := no
 FUNCTIONAL_EXPANSION_TOOLS  := no
-HEAT_TRANSFER             	:= yes
+GEOCHEMISTRY                := no
+HEAT_TRANSFER               := yes
 LEVEL_SET                   := no
 MISC                        := no
+OPTIMIZATION                := no
 NAVIER_STOKES               := no
+PERIDYNAMICS                := no
 PHASE_FIELD                 := no
 POROUS_FLOW                 := no
+RAY_TRACING                 := no
 RDG                         := no
+REACTOR                     := no
 RICHARDS                    := no
+SCALAR_TRANSPORT            := no
 SOLID_MECHANICS             := yes
+SOLID_PROPERTIES            := no
 STOCHASTIC_TOOLS            := no
-TENSOR_MECHANICS            := no
+THERMAL_HYDRAULICS          := no
 XFEM                        := no
 
 include $(MOOSE_DIR)/modules/modules.mk
@@ -55,7 +64,7 @@ printer:
 
 # dep apps
 APPLICATION_DIR    := $(CURDIR)
-PLATYPUS_DIR         := $(CURDIR)
+PLATYPUS_DIR       := $(CURDIR)
 APPLICATION_NAME   := platypus
 BUILD_EXEC         := yes
 GEN_REVISION       := no

docker/platypus-deps/Dockerfile

@@ -1,20 +1,153 @@
-# Build Platypus dependencies
+# Ignore warnings for not pinning versions in pip, apt-get install.
+# hadolint global ignore=DL3008,DL3013
+
 # Get base image
-FROM alexanderianblair/hephaestus-deps:master
+FROM ubuntu:22.04
+
+# This is needed or it mpiexec complains because docker runs as root
+# Discussion on this issue https://github.com/open-mpi/ompi/issues/4451
+ENV OMPI_ALLOW_RUN_AS_ROOT=1
+ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
 # By default four cores are used to compile
 ARG compile_cores=4
 
 # By default we install everything under /opt
 ARG WORKDIR=opt
 
+# Install apt dependencies
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get install -y --no-install-recommends \
+    build-essential \
+    bison \
+    flex \
+    clang-format \
+    clang-tidy \
+    curl \
+    doxygen \
+    git \
+    ninja-build \
+    pre-commit \
+    python3 \
+    python3-dev \
+    python3-distutils \
+    python-is-python3 \
+    python3-pip \
+    libboost-all-dev \
+    libfontconfig1-dev \
+    libfreetype6-dev \
+    libglew-dev \
+    libglm-dev \
+    libhdf5-mpich-dev \
+    libnetcdf-dev \
+    libomp-14-dev \
+    libpng-dev \
+    libsdl2-dev \
+    libssl-dev \
+    rsync \
+    xxd && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install pip packages
+RUN pip install --no-cache-dir packaging && \
+    pip install --no-cache-dir pyyaml && \
+    pip install --no-cache-dir setuptools && \
+    pip install --no-cache-dir jinja2
+
+# Install CMake
+WORKDIR /$WORKDIR
+RUN git clone https://github.com/Kitware/CMake.git
+WORKDIR /$WORKDIR/CMake
+RUN git checkout 78ae759 && \
+    ./bootstrap --parallel=$compile_cores && \
+    make -j$compile_cores && \
+    make install && \
+    alias cmake='/$WORKDIR/CMake/bin/cmake'
+
+# Download SuperLU
+WORKDIR /$WORKDIR
+RUN curl -LJO https://github.com/xiaoyeli/superlu_dist/archive/refs/tags/v8.1.0.tar.gz
+
+# Download PETSc
+WORKDIR /$WORKDIR
+RUN mkdir petsc
+WORKDIR /$WORKDIR/petsc
+RUN curl -L -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.19.3.tar.gz && \
+    tar -xf petsc-3.19.3.tar.gz -C .
+
+# Build PETSc
+WORKDIR /$WORKDIR/petsc/petsc-3.19.3
+RUN ./configure \
+    --prefix=/$WORKDIR/petsc \
+    CXXOPTFLAGS='-O3 -funroll-loops' COPTFLAGS='-O3 -funroll-loops' FOPTFLAGS='-O3' \
+    --with-debugging=0 \
+    --with-ssl=0 \
+    --with-pic=1 \
+    --with-openmp=1 \
+    --with-mpi=1 \
+    --with-shared-libraries=1 \
+    --with-fortran-bindings=0 \
+    --with-sowing=0 \
+    --download-hypre=1 \
+    --download-fblaslapack=1 \
+    --download-metis=1 \
+    --download-ptscotch=1 \
+    --download-parmetis=1 \
+    --download-superlu_dist=/$WORKDIR/superlu_dist-8.1.0.tar.gz \
+    --download-scalapack=1 \
+    --download-mumps=1 \
+    --download-slepc=1 \
+    --with-64-bit-indices=1 \
+    PETSC_DIR="$(pwd)" PETSC_ARCH=arch-linux-c-opt && \
+    make
+
+# Install PETSc
+WORKDIR /$WORKDIR/petsc/petsc-3.19.3
+RUN make PETSC_DIR=/$WORKDIR/petsc/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install && \
+    make PETSC_DIR=/$WORKDIR/petsc/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt check
+WORKDIR /$WORKDIR
+RUN export PETSC_DIR=/$WORKDIR/petsc
+
+# Build MFEM and common miniapp
+WORKDIR /$WORKDIR
+RUN git clone https://github.com/Heinrich-BR/mfem.git
+WORKDIR /$WORKDIR/mfem 
+RUN git checkout SubmeshBoundary && mkdir build
+WORKDIR /$WORKDIR/mfem/build
+RUN cmake .. \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_POSITION_INDEPENDENT_CODE=YES \
+    -DMFEM_USE_OPENMP=NO \
+    -DMFEM_THREAD_SAFE=NO \
+    -DHYPRE_DIR=/$WORKDIR/petsc/ \
+    -DBLAS_LIBRARIES=/$WORKDIR/petsc/lib/libfblas.a \
+    -DLAPACK_LIBRARIES=/$WORKDIR/petsc/lib/libflapack.a \
+    -DMFEM_USE_MPI=YES \
+    -DMFEM_USE_METIS_5=YES \
+    -DMETIS_DIR=/$WORKDIR/petsc/ \
+    -DParMETIS_DIR=/$WORKDIR/petsc/ \
+    -DMFEM_USE_SUPERLU=YES \
+    -DSuperLUDist_DIR=/$WORKDIR/petsc/ \
+    -DMFEM_USE_NETCDF=YES \
+    -DHDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/mpich/ && \
+    make -j$compile_cores
+WORKDIR /$WORKDIR/mfem/build/miniapps/common
+RUN make -j$compile_cores
+
+# Build GLVis
+WORKDIR /$WORKDIR
+RUN git clone https://github.com/GLVis/glvis.git 
+WORKDIR /$WORKDIR/glvis
+RUN mkdir build
+WORKDIR /$WORKDIR/glvis/build/
+RUN cmake -G Ninja -DMFEM_DIR=/$WORKDIR/mfem/build .. && \
+    ninja
+
 # Configure MOOSE
 WORKDIR /$WORKDIR
-# hadolint ignore=DL3003
 RUN export MOOSE_JOBS=$compile_cores && \
-    git clone https://github.com/idaholab/moose && \
-    cd moose && \
-    git checkout master && \
+    git clone https://github.com/idaholab/moose
+WORKDIR /$WORKDIR/moose
+RUN git checkout master && \
     export PETSC_DIR=/$WORKDIR/petsc && \
     export PETSC_ARCH=arch-linux-c-opt && \
     export CC=mpicc && \
@@ -34,15 +167,4 @@ WORKDIR /$WORKDIR/moose/framework
 RUN METHOD=opt make -j$compile_cores
 
 WORKDIR /$WORKDIR/moose/test
-RUN METHOD=opt make -j$compile_cores
-
-# This is needed or it mpiexec complains because docker runs as root
-# Discussion on this issue https://github.com/open-mpi/ompi/issues/4451
-ENV OMPI_ALLOW_RUN_AS_ROOT=1
-ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-
-# WORKDIR /$WORKDIR/moose/test
-# RUN ./run_tests -j"$compile_cores" --re='(?!initial_condition.newton_with_exact_initialization)'
-
-# ENV OMPI_ALLOW_RUN_AS_ROOT=
-# ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=
+RUN METHOD=opt make -j$compile_cores

docker/platypus/Dockerfile

@@ -15,25 +15,11 @@ ARG WORKDIR=opt
 # By default, build without code coverage flags
 ARG coverage=false
 
-# Get Platypus with Hephaestus
-WORKDIR /$WORKDIR 
-# hadolint ignore=DL3003
-RUN git clone https://github.com/$build_git_repo && \
-    cd platypus && \
-    git checkout $build_git_sha && \
-    git submodule update --init --recursive
-
-# Build Hephaestus
-WORKDIR /$WORKDIR/platypus/contrib/hephaestus/
-# hadolint ignore=DL3003
-RUN mkdir build && \
-    cd build && \
-    cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DMFEM_DIR=/$WORKDIR/mfem/build .. && \
-    ninja
-
-# Test Hephaestus
-WORKDIR /$WORKDIR/platypus/contrib/hephaestus/build
-RUN ninja test
+# Get Platypus
+WORKDIR /$WORKDIR
+RUN git clone https://github.com/$build_git_repo
+WORKDIR /$WORKDIR/platypus
+RUN git checkout $build_git_sha
 
 # Build Platypus
 WORKDIR /$WORKDIR/platypus