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Reduce number of packages installed in docker images #193

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May 10, 2023
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Reduce number of packages installed in docker images #193

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2aedf3c
replace np.object with object
mscroggs May 5, 2023
0f17e7a
Use intel OpenCL and tidy dependencies in dev-env image
mscroggs May 5, 2023
61376d0
tidy up Dockerfile
mscroggs May 10, 2023
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249 changes: 48 additions & 201 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -35,141 +35,31 @@ ARG EXAFMM_VERSION

WORKDIR /tmp

# Install dependencies available via apt-get.
# - First set of packages are required to build and run Bempp-cl.
# - Second set of packages are recommended and/or required to build
# documentation or tests.
# - Third set of packages are optional, but required to run gmsh
# pre-built binaries.
# - Fourth set of packages are optional, required for meshio.
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 \
cmake \
git \
ipython3 \
pkg-config \
python-is-python3 \
python3-dev \
python3-matplotlib \
python3-mpi4py \
python3-pip \
python3-pyopencl \
python3-scipy \
python3-setuptools \
jupyter \
wget && \
apt-get -y install \
libfftw3-dev \
libfltk-gl1.3 \
libfltk-images1.3 \
libfltk1.3 \
libfreeimage3 \
libgl2ps1.4 \
libglu1-mesa \
libilmbase25 \
libjxr0 \
libocct-data-exchange-7.5 \
libocct-foundation-7.5 \
libocct-modeling-algorithms-7.5 \
libocct-modeling-data-7.5 \
libocct-ocaf-7.5 \
libocct-visualization-7.5 \
libopenblas-dev \
libopenexr25 \
libopenjp2-7 \
libraw-dev \
libtbb2 \
libxcursor1 \
libxinerama1 && \
apt-get -y install \
python3-lxml && \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install Python packages (via pip)
RUN pip3 install --no-cache-dir "numpy>=1.21,<1.23" numba>=0.55.2 meshio>=4.0.16 && \
pip3 install --no-cache-dir flake8 pytest pydocstyle pytest-xdist

# Download Install Gmsh SDK
RUN cd /usr/local && \
wget -nc --quiet http://gmsh.info/bin/Linux/gmsh-${GMSH_VERSION}-Linux64-sdk.tgz && \
tar -xf gmsh-${GMSH_VERSION}-Linux64-sdk.tgz && \
rm gmsh-${GMSH_VERSION}-Linux64-sdk.tgz

ENV PATH=/usr/local/gmsh-${GMSH_VERSION}-Linux64-sdk/bin:$PATH

RUN git clone -b v${EXAFMM_VERSION} https://github.com/exafmm/exafmm-t.git
RUN cd exafmm-t && sed -i 's/march=native/march=ivybridge/g' ./setup.py && python3 setup.py install

# Clear /tmp
RUN rm -rf /tmp/*

WORKDIR /root

########################################

FROM ubuntu:22.04 as bempp-dev-env-with-dolfin
LABEL maintainer="Matthew Scroggs <[email protected]>"
LABEL description="Bempp-cl development environment with FEniCS"

ARG GMSH_VERSION
ARG MAKEFLAGS
ARG EXAFMM_VERSION

WORKDIR /tmp

# Install dependencies
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 \
cmake \
git \
ipython3 \
pkg-config \
python-is-python3 \
python3-dev \
python3-mpi4py \
python3-pip \
python3-pyopencl \
python3-setuptools \
jupyter \
wget && \
apt-get -y install \
libfftw3-dev \
libfltk-gl1.3 \
libfltk-images1.3 \
libfltk1.3 \
libfreeimage3 \
libgl2ps1.4 \
libglu1-mesa \
libilmbase25 \
libjxr0 \
libocct-data-exchange-7.5 \
libocct-foundation-7.5 \
libocct-modeling-algorithms-7.5 \
libocct-modeling-data-7.5 \
libocct-ocaf-7.5 \
libocct-visualization-7.5 \
libopenblas-dev \
libopenexr25 \
libopenjp2-7 \
libraw-dev \
libtbb2 \
libxcursor1 \
libxinerama1
RUN pip3 install --no-cache-dir meshio>=4.0.16 \
numba numpy==1.20 scipy matplotlib && \
pip3 install --no-cache-dir flake8 pytest pydocstyle pytest-xdist
RUN apt-get -y install \
python3-dolfin \
python3-lxml && \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install Python packages (via pip)
wget \
git \
pkg-config \
build-essential \
# ExaFMM dependencies
libfftw3-dev \
libopenblas-dev \
# Gmsh dependencies
libfltk-gl1.3 \
libfltk-images1.3 \
libfltk1.3 \
libglu1-mesa \
# OpenCL
libpocl-dev \
# Python
python3-dev \
python3-pip \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN python3 -m pip install --no-cache-dir matplotlib pyopencl numpy scipy numba meshio && \
python3 -m pip install --no-cache-dir flake8 pytest pydocstyle pytest-xdist

# Download Install Gmsh SDK
RUN cd /usr/local && \
Expand All @@ -180,7 +70,7 @@ RUN cd /usr/local && \
ENV PATH=/usr/local/gmsh-${GMSH_VERSION}-Linux64-sdk/bin:$PATH

RUN git clone -b v${EXAFMM_VERSION} https://github.com/exafmm/exafmm-t.git
RUN cd exafmm-t && sed -i 's/march=native/march=ivybridge/g' ./setup.py && python3 setup.py install
RUN cd exafmm-t && sed -i 's/march=native/march=ivybridge/g' ./setup.py && python3 -m pip install .

# Clear /tmp
RUN rm -rf /tmp/*
Expand All @@ -207,32 +97,32 @@ 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 \
libpugixml-dev \
python3-pyopencl \
python3-pybind11 \
libfftw3-dev \
pkg-config \
python-is-python3 \
# OpenCL
libpocl-dev \
# ExaFMM dependencies
libfftw3-dev \
&& \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN python3 -m pip install --no-cache-dir matplotlib pyopencl numpy scipy numba meshio && \
python3 -m pip install --no-cache-dir flake8 pytest pydocstyle pytest-xdist

# Install Python packages (via pip)
RUN pip3 install --no-cache-dir meshio>=4.0.16 numpy matplotlib && \
pip3 install --upgrade six
RUN python3 -m pip install --no-cache-dir meshio numpy matplotlib pyopencl

# Install Basix
RUN git clone --depth 1 --branch ${FENICSX_BASIX_TAG} https://github.com/FEniCS/basix.git basix-src && \
cd basix-src && \
cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -B build-dir -S . && \
cmake --build build-dir && \
cmake --install build-dir && \
pip3 install ./python
python3 -m pip install ./python

# Install FEniCSx components
RUN pip3 install --no-cache-dir ipython && \
pip3 install --no-cache-dir git+https://github.com/FEniCS/ufl.git@${FENICSX_UFL_TAG} && \
pip3 install --no-cache-dir git+https://github.com/FEniCS/ffcx.git@${FENICSX_FFCX_TAG}
RUN python3 -m pip install --no-cache-dir ipython && \
python3 -m pip install --no-cache-dir git+https://github.com/FEniCS/ufl.git@${FENICSX_UFL_TAG} && \
python3 -m pip install --no-cache-dir git+https://github.com/FEniCS/ffcx.git@${FENICSX_FFCX_TAG}

# Install FEniCSx
RUN git clone --depth 1 --branch ${FENICSX_DOLFINX_TAG} https://github.com/fenics/dolfinx.git && \
Expand All @@ -243,7 +133,7 @@ RUN git clone --depth 1 --branch ${FENICSX_DOLFINX_TAG} https://github.com/fenic
ninja ${DOLFINX_MAKEFLAGS} install && \
. /usr/local/dolfinx-complex/lib/dolfinx/dolfinx.conf && \
cd ../python && \
PETSC_ARCH=linux-gnu-complex-32 pip3 install --target /usr/local/dolfinx-complex/lib/python3.8/dist-packages --no-dependencies --ignore-installed .
PETSC_ARCH=linux-gnu-complex-32 python3 -m pip install --target /usr/local/dolfinx-complex/lib/python3.8/dist-packages --no-dependencies --ignore-installed .

# complex by default.
ENV LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH \
Expand All @@ -256,7 +146,7 @@ ENV LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH \
RUN wget -nc --quiet https://github.com/exafmm/exafmm-t/archive/v${EXAFMM_VERSION}.tar.gz && \
tar -xf v${EXAFMM_VERSION}.tar.gz && \
cd exafmm-t-${EXAFMM_VERSION} && \
sed -i 's/march=native/march=ivybridge/g' ./setup.py && python3 setup.py install
sed -i 's/march=native/march=ivybridge/g' ./setup.py && python3 -m pip install .

# Clear /tmp
RUN rm -rf /tmp/*
Expand All @@ -283,31 +173,26 @@ 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 \
python3-pybind11 \
python3-matplotlib \
# ExaFMM dependencies
libfftw3-dev \
pkg-config \
python-is-python3 \
&& \
apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install Python packages (via pip)
RUN pip3 install --no-cache-dir meshio>=4.0.16 "numpy>=1.21,<1.23" && \
pip3 install --upgrade six
RUN python3 -m pip install --no-cache-dir meshio numpy matplotlib

# Install Basix
RUN git clone --depth 1 --branch ${FENICSX_BASIX_TAG} https://github.com/FEniCS/basix.git basix-src && \
cd basix-src && \
cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -B build-dir -S . && \
cmake --build build-dir && \
cmake --install build-dir && \
pip3 install ./python
python3 -m pip install ./python

# Install FEniCSx components
RUN pip3 install --no-cache-dir ipython && \
pip3 install --no-cache-dir git+https://github.com/FEniCS/ufl.git@${FENICSX_UFL_TAG} && \
pip3 install --no-cache-dir git+https://github.com/FEniCS/ffcx.git@${FENICSX_FFCX_TAG}
RUN python3 -m pip install --no-cache-dir git+https://github.com/FEniCS/ufl.git@${FENICSX_UFL_TAG} && \
python3 -m pip install --no-cache-dir git+https://github.com/FEniCS/ffcx.git@${FENICSX_FFCX_TAG}

# Install FEniCSx
RUN git clone --depth 1 --branch ${FENICSX_DOLFINX_TAG} https://github.com/fenics/dolfinx.git && \
Expand All @@ -318,7 +203,7 @@ RUN git clone --depth 1 --branch ${FENICSX_DOLFINX_TAG} https://github.com/fenic
ninja ${DOLFINX_MAKEFLAGS} install && \
. /usr/local/dolfinx-complex/lib/dolfinx/dolfinx.conf && \
cd ../python && \
PETSC_ARCH=linux-gnu-complex-32 pip3 install --target /usr/local/dolfinx-complex/lib/python3.8/dist-packages --no-dependencies --ignore-installed .
PETSC_ARCH=linux-gnu-complex-32 python3 -m pip install --target /usr/local/dolfinx-complex/lib/python3.8/dist-packages --no-dependencies --ignore-installed .

# complex by default.
ENV LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH \
Expand All @@ -331,7 +216,7 @@ ENV LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH \
RUN wget -nc --quiet https://github.com/exafmm/exafmm-t/archive/v${EXAFMM_VERSION}.tar.gz && \
tar -xf v${EXAFMM_VERSION}.tar.gz && \
cd exafmm-t-${EXAFMM_VERSION} && \
sed -i 's/march=native/march=ivybridge/g' ./setup.py && python3 setup.py install
sed -i 's/march=native/march=ivybridge/g' ./setup.py && python3 -m pip install .

# Clear /tmp
RUN rm -rf /tmp/*
Expand All @@ -345,21 +230,7 @@ LABEL description="Bempp-cl environment with FEniCSx"

WORKDIR /tmp
RUN git clone https://github.com/bempp/bempp-cl
RUN cd bempp-cl && python3 setup.py install

# Clear /tmp
RUN rm -rf /tmp/*

WORKDIR /root

########################################

FROM bempp-dev-env-with-dolfin as with-dolfin
LABEL description="Bempp-cl environment with FEniCS"

WORKDIR /tmp
RUN git clone https://github.com/bempp/bempp-cl
RUN cd bempp-cl && python3 setup.py install
RUN cd bempp-cl && python3 -m pip install .

# Clear /tmp
RUN rm -rf /tmp/*
Expand All @@ -373,7 +244,7 @@ LABEL description="Bempp Jupyter Lab"

WORKDIR /tmp
RUN git clone https://github.com/bempp/bempp-cl
RUN cd bempp-cl && python3 setup.py install
RUN cd bempp-cl && python3 -m pip install .
RUN cp -r bempp-cl/notebooks /root/example_notebooks
RUN rm /root/example_notebooks/conftest.py /root/example_notebooks/test_notebooks.py

Expand All @@ -385,7 +256,7 @@ WORKDIR /root
ARG TINI_VERSION
ADD https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini /tini
RUN chmod +x /tini && \
pip3 install --no-cache-dir jupyter jupyterlab plotly
python3 -m pip install --no-cache-dir jupyter jupyterlab plotly
EXPOSE 8888/tcp

ENTRYPOINT ["/tini", "--", "jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"]
Expand All @@ -397,31 +268,7 @@ LABEL description="Bempp Jupyter Lab (Numba only)"

WORKDIR /tmp
RUN git clone https://github.com/bempp/bempp-cl
RUN cd bempp-cl && python3 setup.py install
RUN cp -r bempp-cl/notebooks /root/example_notebooks
RUN rm /root/example_notebooks/conftest.py /root/example_notebooks/test_notebooks.py

# Clear /tmp
RUN rm -rf /tmp/*

WORKDIR /root

ARG TINI_VERSION
ADD https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini /tini
RUN chmod +x /tini && \
pip3 install --no-cache-dir jupyter jupyterlab plotly
EXPOSE 8888/tcp

ENTRYPOINT ["/tini", "--", "jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"]

########################################

FROM bempp-dev-env-with-dolfin as fenics-lab
LABEL description="Bempp Jupyter Lab with legacy FEniCS"

WORKDIR /tmp
RUN git clone https://github.com/bempp/bempp-cl
RUN cd bempp-cl && pip3 install .
RUN cd bempp-cl && python3 -m pip install .
RUN cp -r bempp-cl/notebooks /root/example_notebooks
RUN rm /root/example_notebooks/conftest.py /root/example_notebooks/test_notebooks.py

Expand All @@ -433,7 +280,7 @@ WORKDIR /root
ARG TINI_VERSION
ADD https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini /tini
RUN chmod +x /tini && \
pip3 install --no-cache-dir jupyter jupyterlab plotly
python3 -m pip install --no-cache-dir jupyter jupyterlab plotly
EXPOSE 8888/tcp

ENTRYPOINT ["/tini", "--", "jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"]
4 changes: 2 additions & 2 deletions bempp/api/assembly/blocked_operator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ def __init__(self, m, n):
"""Construct an (m x n) blocked boundary operator."""
super().__init__()

self._operators = _np.empty((m, n), dtype=_np.object)
self._operators = _np.empty((m, n), dtype=object)
self._rows = m * [False]
self._cols = n * [False]

Expand Down Expand Up @@ -592,7 +592,7 @@ def __init__(self, ops):

self._ndims = (rows, cols)

self._operators = _np.empty((rows, cols), dtype=_np.object)
self._operators = _np.empty((rows, cols), dtype=object)
self._rows = -_np.ones(rows, dtype=int)
self._cols = -_np.ones(cols, dtype=int)

Expand Down
2 changes: 1 addition & 1 deletion bempp/api/utils/remote_operator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -272,7 +272,7 @@ def __init__(self, ops):

self._ndims = (rows, cols)

self._operators = _np.empty((rows, cols), dtype=_np.object)
self._operators = _np.empty((rows, cols), dtype=object)
self._tags = _np.empty((rows, cols), dtype=_np.int)
self._rows = -_np.ones(rows, dtype=int)
self._cols = -_np.ones(cols, dtype=int)
Expand Down