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For Python3.12 mvapich build, pinned build tools to fix petsc4py, SymPy to avoid FFC/FIAT crash #4

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67 changes: 25 additions & 42 deletions tacc-mvapich2.3-ib-python3.12/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,10 +1,7 @@
# Builds a Docker image for running FEniCS on TACC machines
# The image is at:
#
# https://hub.docker.com/r/uvilla/fenics-2019.1-tacc-mvapich2.3-ib
#
# This is a modified version of
# https://bitbucket.org/fenics-project/docker/src/master/dockerfiles/dev-env/Dockerfile
# This is a modified version of
# https://bitbucket.org/fenics-project/docker/src/master/dockerfiles/dev-env/Dockerfile
#
# See License for further information
#
Expand All @@ -16,16 +13,12 @@

FROM tacc/tacc-ubuntu18-mvapich2.3-ib


RUN useradd -m -s /bin/bash -G sudo fenics && \
echo "fenics:docker" | chpasswd



USER root
WORKDIR /tmp

# Environment variables
ENV FENICS_HOME=/home/fenics
ENV PETSC_VERSION=3.20.2 \
SLEPC_VERSION=3.20.1 \
Expand All @@ -38,10 +31,8 @@ ENV PETSC_VERSION=3.20.2 \
OPENBLAS_VERBOSE=0 \
FENICS_PREFIX=$FENICS_HOME/local

# Non-Python utilities and libraries
RUN apt-get -qq update && \
apt-get -y --with-new-pkgs \
-o Dpkg::Options::="--force-confold" upgrade && \
apt-get -y --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
apt-get -y install curl && \
curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
apt-get -y install \
Expand Down Expand Up @@ -78,7 +69,7 @@ RUN apt-get -qq update && \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Build python 3.12 from source
# Build Python 3.12 from source
RUN apt-get -qq update && \
apt-get -y install build-essential libssl-dev zlib1g-dev libbz2-dev \
libreadline-dev libsqlite3-dev wget curl llvm \
Expand All @@ -96,8 +87,7 @@ RUN update-alternatives --install /usr/bin/python3 python3 /usr/local/bin/python

# Install Python3 based environment
RUN apt-get -qq update && \
apt-get -y --with-new-pkgs \
-o Dpkg::Options::="--force-confold" upgrade && \
apt-get -y --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
apt-get -y install \
python3-dev \
python3-flufl.lock \
Expand All @@ -110,16 +100,14 @@ RUN apt-get -qq update && \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install setuptools
# Install pip / setuptools for Python 3.12
RUN wget https://bootstrap.pypa.io/pip/get-pip.py && \
python3 get-pip.py && \
pip3 install --no-cache-dir setuptools && \
rm -rf /tmp/*

# Install PETSc from source
RUN apt-get -qq update && \
# apt-get -y install \
# python-minimal && \
wget -nc --quiet https://gitlab.com/petsc/petsc/-/archive/v${PETSC_VERSION}/petsc-v${PETSC_VERSION}.tar.gz -O petsc-${PETSC_VERSION}.tar.gz && \
mkdir -p petsc-src && tar -xf petsc-${PETSC_VERSION}.tar.gz -C petsc-src --strip-components 1 && \
cd petsc-src && \
Expand All @@ -138,7 +126,7 @@ RUN apt-get -qq update && \
--download-spai \
--download-suitesparse \
--download-superlu \
--download-hdf5\
--download-hdf5 \
--download-strumpack \
--download-ml \
--prefix=/usr/local/petsc-32 && \
Expand All @@ -150,11 +138,7 @@ ENV HDF5_ROOT=/usr/local/petsc-32
ENV SCOTCH_DIR=/usr/local/petsc-32

# Install SLEPc from source
# NOTE: Had issues building SLEPc from source tarball generated by bitbucket.
# Website tarballs work fine, however.
RUN apt-get -qq update && \
# apt-get -y install \
# python-minimal && \
wget -nc --quiet https://gitlab.com/slepc/slepc/-/archive/v${SLEPC_VERSION}/slepc-v${SLEPC_VERSION}.tar.gz -O slepc-${SLEPC_VERSION}.tar.gz && \
mkdir -p slepc-src && tar -xf slepc-${SLEPC_VERSION}.tar.gz -C slepc-src --strip-components 1 && \
export PETSC_DIR=/usr/local/petsc-32 && \
Expand All @@ -164,27 +148,26 @@ RUN apt-get -qq update && \
make install && \
rm -rf /tmp/*

# By default use the 32-bit build of SLEPc and PETSc.
# By default use the 32-bit build of SLEPc and PETSc
ENV SLEPC_DIR=/usr/local/slepc-32 \
PETSC_DIR=/usr/local/petsc-32

# Install jupyterlab, sympy, mpi4py, petsc4py, slepc4py and pybind11 from source.
RUN pip3 install --no-cache-dir jupyter jupyterlab matplotlib scipy sympy tqdm pkgconfig && \
pip3 install --no-cache-dir mpi4py==${MPI4PY_VERSION} && \
pip3 install --no-cache-dir petsc4py==${PETSC4PY_VERSION} && \
pip3 install --no-cache-dir slepc4py==${SLEPC4PY_VERSION} && \
pip3 install --no-cache-dir pybind11==${PYBIND11_VERSION} && \
wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz && \
tar -xf v${PYBIND11_VERSION}.tar.gz && \
cd pybind11-${PYBIND11_VERSION} && \
mkdir build && \
cd build && \
cmake -DPYBIND11_TEST=False ../ && \
make && \
make install && \
rm -rf /tmp/*
# Pin Cython to 3.0.x for petsc4py/slepc4py 3.20.x
# Pin SymPy to <1.14 to avoid FIAT/FFC crash during DOLFIN doc/demo generation
RUN pip3 install --no-cache-dir --upgrade pip setuptools wheel \
&& pip3 install --no-cache-dir "Cython>=3.0,<3.1" \
&& pip3 install --no-cache-dir jupyter jupyterlab matplotlib scipy "sympy>=1.12.1,<1.14" tqdm pkgconfig \
&& pip3 install --no-cache-dir mpi4py==${MPI4PY_VERSION} \
&& PETSC_DIR=/usr/local/petsc-32 pip3 install --no-cache-dir --no-build-isolation petsc4py==${PETSC4PY_VERSION} \
&& SLEPC_DIR=/usr/local/slepc-32 pip3 install --no-cache-dir --no-build-isolation slepc4py==${SLEPC4PY_VERSION} \
&& 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 && make install \
&& rm -rf /tmp/*

# Our helper scripts
WORKDIR $FENICS_HOME
COPY fenics.env.conf $FENICS_HOME/fenics.env.conf
COPY bin $FENICS_HOME/bin
Expand All @@ -211,6 +194,6 @@ RUN /home/fenics/bin/fenics-pull && \
/home/fenics/bin/fenics-build

# symbol link ufl to ufl_legacy
RUN ln -s /usr/local/lib/python3.12/site-packages/ufl_legacy /usr/local/lib/python3.12/site-packages/ufl
RUN ln -s /usr/local/lib/python3.12/site-packages/ufl_legacy /usr/local/lib/python3.12/site-packages/ufl || true

RUN ldconfig
RUN ldconfig