Dear all.
Already for some time, I installed Fenics and Mshr via Anaconda on Ubuntu. It work well.
Now, I tried to install Fenics on Ubuntu (20.04) from source. Then I followed the instruction for the Development version as mentioned (https://fenics.readthedocs.io/en/latest/installation.htm). I started by downloading the required packages by:
git cone https://github.com…
So far so good. Then I tried to install them manually by typing:
mkdir dolfin/build && cd dolfin/build && cmake … && make install && cd …/…
Here is a full step by step dockerfile for installing dolfin in ubuntu 20.04. One should simply be able to copy-paste each of the commands (stripping them of docker syntax), or build a corresponding dockerimage by saving this as Dockerfile and run docker build -t dolfinimage .
FROM ubuntu:20.04 as dolfinsrc
ARG PYBIND11_VERSION=2.5.0
ARG PETSC_VERSION=3.13.3
ARG SLEPC_VERSION=3.13.3
ARG PETSC4PY_VERSION=3.13.0
ARG SLEPC4PY_VERSION=3.13.0
# Flags to pass to ninja build system.
ARG MAKEFLAGS
# Compiler optimisation flags for SLEPc and PETSc, all languages.
ARG PETSC_SLEPC_OPTFLAGS="-O2 -march=sandybridge"
# Turn on PETSc and SLEPc debugging. "yes" or "no".
ARG PETSC_SLEPC_DEBUGGING="no"
# CMake build type for DOLFIN C++ build. See CMake documentation.
ARG DOLFIN_CMAKE_BUILD_TYPE="RelWithDebInfo"
# Extra CMake C++ compiler flags for DOLFIN C++ build.
ARG DOLFIN_CMAKE_CXX_FLAGS="-march=sandybridge"
# Ubuntu MPI variant. "mpich" or "openmpi".
ARG MPI="mpich"
WORKDIR /tmp
# Environment variables
ENV OPENBLAS_NUM_THREADS=1 \
OPENBLAS_VERBOSE=0
# Install dependencies available via apt-get.
# - First set of packages are required to build and run FEniCS.
# - Second set of packages are recommended and/or required to build
# documentation or tests.
RUN export DEBIAN_FRONTEND=noninteractive && \
apt-get -qq update && \
apt-get -yq --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
apt-get -y install \
clang-10 \
cmake \
g++ \
gfortran \
libboost-dev \
libboost-filesystem-dev \
libboost-iostreams-dev \
libboost-math-dev \
libboost-program-options-dev \
libboost-system-dev \
libboost-thread-dev \
libboost-timer-dev \
libeigen3-dev \
libhdf5-${MPI}-dev \
liblapack-dev \
lib${MPI}-dev \
libopenblas-dev \
ninja-build \
pkg-config \
python3-dev \
python3-matplotlib \
python3-numpy \
python3-pip \
python3-scipy \
python3-setuptools \
wget
# Install Python packages (via pip)
# - First set of packages are required to build and run FEniCS.
# - Second set of packages are recommended and/or required to build
# documentation or run tests.
RUN pip3 install --no-cache-dir mpi4py numba && \
pip3 install --no-cache-dir cffi cppimport flake8 pytest pytest-xdist sphinx sphinx_rtd_theme
# Install pybind11
RUN wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz && \
tar -xf v${PYBIND11_VERSION}.tar.gz && \
cd pybind11-${PYBIND11_VERSION} && \
mkdir build && \
cd build && \
cmake -DPYBIND11_TEST=False ../ && \
make install && \
rm -rf /tmp/*
# Install PETSc with real and complex types
ENV PETSC_DIR=/usr/local/petsc SLEPC_DIR=/usr/local/slepc
WORKDIR /tmp
RUN apt-get -qq update && \
apt-get -y install bison flex && \
wget -nc --quiet http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${PETSC_VERSION}.tar.gz -O petsc-${PETSC_VERSION}.tar.gz && \
mkdir -p ${PETSC_DIR} && tar -xf petsc-${PETSC_VERSION}.tar.gz -C ${PETSC_DIR} --strip-components 1 && \
cd ${PETSC_DIR} && \
# Real, 32-bit int
python3 ./configure \
PETSC_ARCH=linux-gnu-real-32 \
--COPTFLAGS=${PETSC_SLEPC_OPTFLAGS} \
--CXXOPTFLAGS=${PETSC_SLEPC_OPTFLAGS} \
--FOPTFLAGS=${PETSC_SLEPC_OPTFLAGS} \
--with-64-bit-indices=no \
--with-debugging=${PETSC_SLEPC_DEBUGGING} \
--with-fortran-bindings=no \
--with-shared-libraries \
--download-blacs \
--download-hypre \
--download-metis \
--download-mumps \
--download-ptscotch \
--download-scalapack \
--download-spai \
--download-suitesparse \
--download-superlu \
--download-superlu_dist \
--with-scalar-type=real && \
make PETSC_DIR=/usr/local/petsc PETSC_ARCH=linux-gnu-real-32 ${MAKEFLAGS} all && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Install SLEPc
WORKDIR /tmp
RUN wget -nc --quiet https://slepc.upv.es/download/distrib/slepc-${SLEPC_VERSION}.tar.gz -O slepc-${SLEPC_VERSION}.tar.gz && \
mkdir -p ${SLEPC_DIR} && tar -xf slepc-${SLEPC_VERSION}.tar.gz -C ${SLEPC_DIR} --strip-components 1 && \
cd ${SLEPC_DIR} && \
export PETSC_ARCH=linux-gnu-real-32 && \
python3 ./configure && \
make && \
rm -rf ${SLEPC_DIR}/CTAGS ${SLEPC_DIR}/TAGS ${SLEPC_DIR}/docs ${SLEPC_DIR}/src/ ${SLEPC_DIR}/**/obj/ ${SLEPC_DIR}/**/test/ && \
rm -rf /tmp/*
# Install petsc4py and slepc4py with real and complex types
RUN PETSC_ARCH=linux-gnu-real-32 pip3 install --no-cache-dir petsc4py==${PETSC4PY_VERSION} slepc4py==${SLEPC4PY_VERSION}
WORKDIR /src
RUN apt-get -qq update && \
apt-get -y install git
# This leaves the sources inside the container. This is a limitation of Docker.
# There is some trickery in the intermediate and dolfin containers that can be
# used to remove this source if needed, see below.
RUN git clone https://github.com/FEniCS/fiat.git && \
git clone https://bitbucket.com/fenics-project/ffc.git && \
git clone https://github.com/FEniCS/ufl.git && \
git clone https://bitbucket.com/fenics-project/dolfin.git && \
git clone https://bitbucket.com/fenics-project/dijitso.git
# The dolfin-onbuild container expects to have folders fiat/ ufl/ ffc/ and
# dolfin/ mounted/shared at /src.
RUN cd fiat && pip3 install --no-cache-dir . && \
cd ../ufl && pip3 install --no-cache-dir . && \
cd ../dijitso && pip3 install --no-cache-dir . && \
cd ../ffc && pip3 install --no-cache-dir . && \
cd ../ && pip3 install --no-cache-dir ipython
RUN cd dolfin && \
mkdir build && \
cd build && \
PETSC_ARCH=linux-gnu-real-32 cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfin -DCMAKE_BUILD_TYPE=${DOLFIN_CMAKE_BUILD_TYPE} -DCMAKE_CXX_FLAGS=${DOLFIN_CMAKE_CXX_FLAGS} .. && \
ninja ${MAKEFLAGS} install && \
cd ../python && \
PETSC_ARCH=linux-gnu-real-32 pip3 install --target /usr/local/dolfin/lib/python3.8/dist-packages --no-dependencies .
# Real by default.
ENV PKG_CONFIG_PATH=/usr/local/dolfin/lib/pkgconfig:$PKG_CONFIG_PATH \
PETSC_ARCH=linux-gnu-real-32 \
PYTHONPATH=/usr/local/dolfin/lib/python3.8/dist-packages:$PYTHONPATH \
LD_LIBRARY_PATH=/usr/local/dolfin/lib:$LD_LIBRARY_PATH
WORKDIR /src
RUN apt-get -qq update && \
apt-get -y install pkg-config && \
pip3 install pkgconfig
WORKDIR /root
# Note that because we inherit from dev-env we do not inherit these ENV from
# dolfin-onbuild.
ENV PKG_CONFIG_PATH=/usr/local/dolfin/lib/pkgconfig:$PKG_CONFIG_PATH \
PETSC_ARCH=linux-gnu-real-32 \
PYTHONPATH=/usr/local/dolfin/lib/python3.8/dist-packages:$PYTHONPATH \
LD_LIBRARY_PATH=/usr/local/dolfin/lib:$LD_LIBRARY_PATH
