diff --git a/README.md b/README.md
index 30b3300752f10c1ef76c663ca1d6303af6bc8647..46a7a5a52dc43d3e9e6b26708e177926d2a68a02 100644
--- a/README.md
+++ b/README.md
@@ -52,13 +52,13 @@ HySoP "CPU_Intel" Docker Image can be retrieved and submitted as a [Docker Conta
As a jupyter notebook with the following command:
```
-docker run -p 8888:8888 --rm -ti gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-master
+docker run -p 8888:8888 --rm -ti gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-cpu-intel-master
```
Or to start a terminal session:
```
-docker run -it --rm --entrypoint="/bin/bash" gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-master:latest
+docker run -it --rm --entrypoint="/bin/bash" gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-cpu-intel-master:latest
```
In both cases, you will end up with a fully-fonctionnal installation of Hysop software (in a [Docker Container](https://www.docker.com/resources/what-container/) ) and will be able to quickly test HySoP using [examples in the documentation](https://particle_methods.gricad-pages.univ-grenoble-alpes.fr/hysop-doc/getting_started/index.html).
@@ -72,7 +72,7 @@ In both cases, you will end up with a fully-fonctionnal installation of Hysop so
* *By default, the Docker container is completely isolated from the host machine's disk space! As a result, it's impossible to write or read data on your hard disk. To share a directory between your host and the docker container, update the docker command like this:
```
- docker run -v HOST_DIRECTORY:/home/hysop-user/shared -p 8888:8888 --rm -ti gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-master
+ docker run -v HOST_DIRECTORY:/home/hysop-user/shared -p 8888:8888 --rm -ti gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-gpu-nvidia-master
```
HOST_DIRECTORY (use full path!) will be available in the container in directory 'shared'.
diff --git a/ci/docker_images/ci_cpu_intel/Dockerfile b/ci/docker_images/ci_cpu_intel/Dockerfile
deleted file mode 100644
index 7e7f24988dccd140487dce3902cc049671b9275d..0000000000000000000000000000000000000000
--- a/ci/docker_images/ci_cpu_intel/Dockerfile
+++ /dev/null
@@ -1,224 +0,0 @@
-##
-## Copyright (c) HySoP 2011-2024
-##
-## This file is part of HySoP software.
-## See "https://particle_methods.gricad-pages.univ-grenoble-alpes.fr/hysop-doc/"
-## for further info.
-##
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-##
-## http://www.apache.org/licenses/LICENSE-2.0
-##
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-##
-
-# Docker muti-stage builds or buildkit (parallel stages)
-# https://docs.docker.com/build/building/multi-stage/
-#
-FROM mambaorg/micromamba AS mambahysop
-LABEL authors="hysop_team@univ-xxx.fr"
-USER root
-ARG PYTHON_VERSION=3.12.4
-ENV PYTHON_EXECUTABLE=python3.12
-
-#
-# Install somme linux tools, compilers and libs
-#
-RUN apt update && apt upgrade -y && apt install -y -qq \
- wget \
- git-core \
- make \
- pkg-config \
- g++ \
- gfortran \
- libopenmpi-dev \
- libclfft-dev && \
- apt autoclean -y && \
- apt autoremove -y && \
- rm -rf /var/lib/apt/lists/* && \
- rm -rf $HOME/.cache/pip/*
-
-#
-# Install conda/mamba packages listed in ci/hysopenv_cpu_intel.yaml file
-#
-COPY --chown=$MAMBA_USER:$MAMBA_USER ci/hysopenv_cpu_intel.yaml /home/hysopenv_cpu_intel.yaml
-
-RUN micromamba config prepend channels conda-forge && \
- micromamba self-update && \
- micromamba config set channel_priority strict && \
- micromamba install -n base python=${PYTHON_VERSION} -c conda-forge && \
- micromamba install -y -f /home/hysopenv_cpu_intel.yaml && \
- micromamba clean --all --yes
-
-ARG MAMBA_DOCKERFILE_ACTIVATE=1 # (otherwise python will not be found)
-
-########
-# HPTT # (longest time compilation)
-########
-FROM mambahysop AS hptt
-
-RUN cd /tmp && \
- git clone https://gitlab.com/keckj/hptt.git && \
- cd hptt && \
- sed -i "s#-mavx##g" CMakeLists.txt && \
- sed -i "s#-march=native##g" CMakeLists.txt && \
- sed -i "s#-mtune=native##g" CMakeLists.txt && \
- mkdir build && \
- cd build && \
- cmake -DCMAKE_BUILD_TYPE=Release .. && \
- make -j$(nproc) && \
- make install && \
- cd ../pythonAPI && \
- pip install --upgrade . && \
- cd /tmp && \
- rm -rf /tmp/hptt
-
-#########
-# FLINT #
-#########
-FROM mambahysop AS flint
-
-#
-# python flint (FLINT2 + ARB + python-flint)
-#
-# flint 3.0.1 version is the last version (16 nov 2023)
-# (now ARB has been merged into flint 3)
-#
-RUN cd /tmp && \
- wget -q https://github.com/flintlib/flint/archive/refs/tags/v3.0.1.tar.gz && \
- tar -xzf v*.tar.gz && \
- rm -f v*.tar.gz && \
- cd flint* && \
- mkdir build && \
- cd build/ && \
- cmake .. -DBUILD_SHARED_LIBS=ON && \
- make -j$(nproc) && \
- make install && \
- cd /tmp && \
- rm -rf /tmp/flint*
-
-#####################
-# HDF5_mpi and H5PY #
-#####################
-FROM mambahysop AS hdf5_mpi_h5py
-
-ENV MPICC "mpicc"
-ARG pip_install_opts='--upgrade --no-binary=h5py --no-deps --no-build-isolation'
-RUN cd /tmp && \
- wget -q https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.3/src/hdf5-1.14.3.tar.gz && \
- tar -xzf hdf5-*.tar.gz && \
- rm -f hdf5-*.tar.gz && \
- cd hdf5-* && \
- CC="${MPICC}" ./configure --prefix=/usr/local --enable-parallel \
- --enable-shared=yes --enable-static=no && \
- make -j$(nproc) && \
- make install && \
- cd /tmp && \
- rm -rf /tmp/hdf5-* && \
- CC="${MPICC}" HDF5_MPI="ON" HDF5_VERSION="1.14.3" \
- HDF5_DIR=/usr/local H5PY_SETUP_REQUIRES=0 \
- pip install ${pip_install_opts} h5py==3.11.0
-
-##########
-# Stage #
-##########
-FROM mambahysop AS stage2
-
-# Some python packages are not available in micromamba!
-RUN pip install --upgrade \
- tee colors.py primefac \
- argparse_color_formatter \
- tox memory-tempfile
-
-# gpyFFT
-# WARNING: Old package!
-RUN cd /tmp && \
- git clone https://github.com/geggo/gpyfft.git && \
- cd gpyfft && \
- sed 's#finalize(self, _destroy_plan, self.plan)##' -i gpyfft/gpyfftlib.pyx && \
- pip install . && \
- cd - && \
- rm -rf /tmp/gpyfft
-
-#
-# FFTW latest version nov 2023
-# Compilation is necessary because there is no mpi version
-# with the float precisions requested by hysop (single, double, long)
-#
-ENV FFTW_ROOT="/usr/local"
-RUN cd /tmp && \
- wget -q http://www.fftw.org/fftw-3.3.10.tar.gz && \
- tar -xzf fftw-*.tar.gz && \
- rm -f fftw-*.tar.gz && \
- cd fftw-* && \
- ./configure --enable-openmp --enable-threads --enable-mpi --enable-shared --with-pic --prefix="${FFTW_ROOT}" --enable-single && \
- make -j$(nproc) && make install && make clean && \
- ./configure --enable-openmp --enable-threads --enable-mpi --enable-shared --with-pic --prefix="${FFTW_ROOT}" && \
- make -j$(nproc) && make install && make clean && \
- ./configure --enable-openmp --enable-threads --enable-mpi --enable-shared --with-pic --prefix="${FFTW_ROOT}" --enable-long-double && \
- make -j$(nproc) && make install && make clean && \
- cd /tmp && \
- rm -rf /tmp/fftw-*
-
-#
-# PYFFTW git version (last test: july 2024)
-# pyfftw is linked to fftw3 compiled above
-
-#ARG pip_install_opts='--no-binary=pyfftw --no-deps --no-build-isolation'
-ARG pip_install_opts='--no-binary=pyfftw --no-deps'
-RUN cd /tmp && \
- git clone https://github.com/pyFFTW/pyFFTW.git && \
- cd pyFFTW && \
- PYFFTW_INCLUDE="/include" \
- pip install ${pip_install_opts} . && \
- cd /tmp && \
- rm -rf /tmp/pyFFTW
-
-###############
-# Final-Stage #
-###############
-FROM stage2 AS final-stage
-
-# Copy only necessary files from previous stages
-COPY --from=hptt /usr/local/include /usr/local/include
-COPY --from=hptt /usr/local/lib /usr/local/lib/
-COPY --from=flint /usr/local/include/flint/ /usr/local/include/flint/
-COPY --from=flint /usr/local/lib/libflint.so /usr/local/lib/
-COPY --from=hdf5_mpi_h5py /usr/local/bin /usr/local/bin/
-COPY --from=hdf5_mpi_h5py /usr/local/lib /usr/local/lib
-COPY --from=hdf5_mpi_h5py /usr/local/include /usr/local/include
-
-# Copy only necessary parts of /opt/conda
-COPY --from=hptt /opt/conda/lib/python3.12/site-packages/hptt \
- /opt/conda/lib/python3.12/site-packages/hptt
-
-COPY --from=hdf5_mpi_h5py /opt/conda/lib/python3.12/site-packages/h5py \
- /opt/conda/lib/python3.12/site-packages/h5py
-
-# Important for f2py command summit in meson build system!
-ENV FC="mpif90"
-ENV MPICC "mpicc"
-ARG MPI_HOME=/usr
-ENV MPIRUN_EXECUTABLE="${MPI_HOME}/bin/mpirun.openmpi"
-ENV MPIEXEC_EXECUTABLE="${MPI_HOME}/bin/mpiexec.openmpi"
-
-# To run MPI test as root on docker image
-ENV OMPI_ALLOW_RUN_AS_ROOT=1
-ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-
-# ensure all libraries are known by the runtime linker
-# clean cached packages
-ENV LD_LIBRARY_PATH=/opt/conda/lib:/usr/local/lib:${LD_LIBRARY_PATH}
-RUN ldconfig && \
- rm -rf /var/lib/apt/lists/* && \
- rm -rf $HOME/.cache/pip/* && \
- rm -rf /tmp/*
-
-WORKDIR /home
-ENV CI_PROJECT_DIR /home
diff --git a/ci/docker_images/ci_gpu_nvidia/Dockerfile b/ci/docker_images/ci_gpu_nvidia/Dockerfile
deleted file mode 100644
index ab993f8fe98d01c8e4e7b24aea272d22c237393a..0000000000000000000000000000000000000000
--- a/ci/docker_images/ci_gpu_nvidia/Dockerfile
+++ /dev/null
@@ -1,236 +0,0 @@
-##
-## Copyright (c) HySoP 2011-2024
-##
-## This file is part of HySoP software.
-## See "https://particle_methods.gricad-pages.univ-grenoble-alpes.fr/hysop-doc/"
-## for further info.
-##
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-##
-## http://www.apache.org/licenses/LICENSE-2.0
-##
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-##
-
-# Docker muti-stage builds or buildkit (parallel stages)
-# https://docs.docker.com/build/building/multi-stage/
-#
-FROM mambaorg/micromamba AS mambahysop
-LABEL authors="hysop_team@univ-xxx.fr"
-USER root
-ARG PYTHON_VERSION=3.12.4
-ENV PYTHON_EXECUTABLE=python3.12
-
-#
-# Install somme linux tools, compilers and libs
-#
-RUN apt update && apt upgrade -y && apt install -y -qq \
- wget \
- git-core \
- make \
- pkg-config \
- g++ \
- gfortran \
- libopenmpi-dev \
- libclfft-dev && \
- apt autoclean -y && \
- apt autoremove -y && \
- rm -rf /var/lib/apt/lists/* && \
- rm -rf $HOME/.cache/pip/*
-
-#
-# Install conda/mamba packages listed in ci/hysopenv_gpu_nvidia.yaml file
-#
-COPY --chown=$MAMBA_USER:$MAMBA_USER \
- ci/hysopenv_gpu_nvidia.yaml \
- /home/hysopenv_gpu_nvidia.yaml
-
-RUN micromamba config prepend channels conda-forge && \
- micromamba self-update && \
- micromamba config set channel_priority strict && \
- micromamba install -n base python=${PYTHON_VERSION} -c conda-forge && \
- micromamba install -y -f /home/hysopenv_gpu_nvidia.yaml && \
- micromamba clean --all --yes
-
-ARG MAMBA_DOCKERFILE_ACTIVATE=1 # (otherwise python will not be found)
-
-# Nvidia library path.
-# The nvidia libraries are intalled/copied when docker container is created!
-RUN echo "/usr/lib/x86_64-linux-gnu/libnvidia-opencl.so.1" > \
- /opt/conda/etc/OpenCL/vendors/nvidia.icd
-
-ENV NVIDIA_VISIBLE_DEVICES all
-ENV NVIDIA_DRIVER_CAPABILITIES compute,utility
-
-########
-# HPTT # (longest time compilation)
-########
-FROM mambahysop AS hptt
-
-RUN cd /tmp && \
- git clone https://gitlab.com/keckj/hptt.git && \
- cd hptt && \
- sed -i "s#-mavx##g" CMakeLists.txt && \
- sed -i "s#-march=native##g" CMakeLists.txt && \
- sed -i "s#-mtune=native##g" CMakeLists.txt && \
- mkdir build && \
- cd build && \
- cmake -DCMAKE_BUILD_TYPE=Release .. && \
- make -j$(nproc) && \
- make install && \
- cd ../pythonAPI && \
- pip install --upgrade . && \
- cd /tmp && \
- rm -rf /tmp/hptt
-
-#########
-# FLINT #
-#########
-FROM mambahysop AS flint
-
-#
-# python flint (FLINT2 + ARB + python-flint)
-#
-# flint 3.0.1 version is the last version (16 nov 2023)
-# (now ARB has been merged into flint 3)
-#
-RUN cd /tmp && \
- wget -q https://github.com/flintlib/flint/archive/refs/tags/v3.0.1.tar.gz && \
- tar -xzf v*.tar.gz && \
- rm -f v*.tar.gz && \
- cd flint* && \
- mkdir build && \
- cd build/ && \
- cmake .. -DBUILD_SHARED_LIBS=ON && \
- make -j$(nproc) && \
- make install && \
- cd /tmp && \
- rm -rf /tmp/flint*
-
-#####################
-# HDF5_mpi and H5PY #
-#####################
-FROM mambahysop AS hdf5_mpi_h5py
-
-ENV MPICC "mpicc"
-ARG pip_install_opts='--upgrade --no-binary=h5py --no-deps --no-build-isolation'
-RUN cd /tmp && \
- wget -q https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.3/src/hdf5-1.14.3.tar.gz && \
- tar -xzf hdf5-*.tar.gz && \
- rm -f hdf5-*.tar.gz && \
- cd hdf5-* && \
- CC="${MPICC}" ./configure --prefix=/usr/local --enable-parallel \
- --enable-shared=yes --enable-static=no && \
- make -j$(nproc) && \
- make install && \
- cd /tmp && \
- rm -rf /tmp/hdf5-* && \
- CC="${MPICC}" HDF5_MPI="ON" HDF5_VERSION="1.14.3" \
- HDF5_DIR=/usr/local H5PY_SETUP_REQUIRES=0 \
- pip install ${pip_install_opts} h5py==3.11.0
-
-##########
-# Stage #
-##########
-FROM mambahysop AS stage2
-
-# Some python packages are not available in micromamba!
-RUN pip install --upgrade \
- tee colors.py primefac \
- argparse_color_formatter \
- tox memory-tempfile
-
-# gpyFFT
-# WARNING: Old package!
-RUN cd /tmp && \
- git clone https://github.com/geggo/gpyfft.git && \
- cd gpyfft && \
- sed 's#finalize(self, _destroy_plan, self.plan)##' -i gpyfft/gpyfftlib.pyx && \
- pip install . && \
- cd - && \
- rm -rf /tmp/gpyfft
-
-#
-# FFTW latest version nov 2023
-# Compilation is necessary because there is no mpi version
-# with the float precisions requested by hysop (single, double, long)
-#
-ENV FFTW_ROOT="/usr/local"
-RUN cd /tmp && \
- wget -q http://www.fftw.org/fftw-3.3.10.tar.gz && \
- tar -xzf fftw-*.tar.gz && \
- rm -f fftw-*.tar.gz && \
- cd fftw-* && \
- ./configure --enable-openmp --enable-threads --enable-mpi --enable-shared --with-pic --prefix="${FFTW_ROOT}" --enable-single && \
- make -j$(nproc) && make install && make clean && \
- ./configure --enable-openmp --enable-threads --enable-mpi --enable-shared --with-pic --prefix="${FFTW_ROOT}" && \
- make -j$(nproc) && make install && make clean && \
- ./configure --enable-openmp --enable-threads --enable-mpi --enable-shared --with-pic --prefix="${FFTW_ROOT}" --enable-long-double && \
- make -j$(nproc) && make install && make clean && \
- cd /tmp && \
- rm -rf /tmp/fftw-*
-
-#
-# PYFFTW git version (last test: july 2024)
-# pyfftw is linked to fftw3 compiled above
-
-#ARG pip_install_opts='--no-binary=pyfftw --no-deps --no-build-isolation'
-ARG pip_install_opts='--no-binary=pyfftw --no-deps'
-RUN cd /tmp && \
- git clone https://github.com/pyFFTW/pyFFTW.git && \
- cd pyFFTW && \
- PYFFTW_INCLUDE="/include" \
- pip install ${pip_install_opts} . && \
- cd /tmp && \
- rm -rf /tmp/pyFFTW
-
-###############
-# Final-Stage #
-###############
-FROM stage2 AS final-stage
-
-# Copy only necessary files from previous stages
-COPY --from=hptt /usr/local/include /usr/local/include
-COPY --from=hptt /usr/local/lib /usr/local/lib/
-COPY --from=flint /usr/local/include/flint/ /usr/local/include/flint/
-COPY --from=flint /usr/local/lib/libflint.so /usr/local/lib/
-COPY --from=hdf5_mpi_h5py /usr/local/bin /usr/local/bin/
-COPY --from=hdf5_mpi_h5py /usr/local/lib /usr/local/lib
-COPY --from=hdf5_mpi_h5py /usr/local/include /usr/local/include
-
-# Copy only necessary parts of /opt/conda
-COPY --from=hptt /opt/conda/lib/python3.12/site-packages/hptt \
- /opt/conda/lib/python3.12/site-packages/hptt
-
-COPY --from=hdf5_mpi_h5py /opt/conda/lib/python3.12/site-packages/h5py \
- /opt/conda/lib/python3.12/site-packages/h5py
-
-# Important for f2py command summit in meson build system!
-ENV FC="mpif90"
-ENV MPICC "mpicc"
-ARG MPI_HOME=/usr
-ENV MPIRUN_EXECUTABLE="${MPI_HOME}/bin/mpirun.openmpi"
-ENV MPIEXEC_EXECUTABLE="${MPI_HOME}/bin/mpiexec.openmpi"
-
-# To run MPI test as root on docker image
-ENV OMPI_ALLOW_RUN_AS_ROOT=1
-ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-
-ENV PYOPENCL_COMPILER_OUTPUT=1
-
-# ensure all libraries are known by the runtime linker
-# clean cached packages
-ENV LD_LIBRARY_PATH=/opt/conda/lib:/usr/local/lib:${LD_LIBRARY_PATH}
-RUN ldconfig && \
- rm -rf /var/lib/apt/lists/* && \
- rm -rf $HOME/.cache/pip/* && \
- rm -rf /tmp/*
-
-WORKDIR /home
-ENV CI_PROJECT_DIR /home
diff --git a/ci/docker_images/ci_user/Dockerfile b/ci/docker_images/ci_user/Dockerfile
index 81b62a48fa23b202cb86bff1d2f4faf5ea8106f7..344f072ad27b4553e07198b26c2461c994a57dd2 100644
--- a/ci/docker_images/ci_user/Dockerfile
+++ b/ci/docker_images/ci_user/Dockerfile
@@ -192,7 +192,7 @@ ENV PYOPENCL_COMPILER_OUTPUT=1
# --- Image with deps. required to build hysop-doc ---
-FROM hysop-final AS hysop-doc
+FROM hysop-final-cpu AS hysop-doc
# Bibtex !!!
USER root
@@ -204,6 +204,7 @@ RUN apt update && apt upgrade -y && apt install -y -qq \
rm -rf $HOME/.cache/pip/*
USER hysop-user
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
# Install conda/mamba packages listed in ./hysop_doc.yaml file
COPY --chown=hysop-user:hysop-user ci/hysop-doc-env.yaml /home/hysop-doc-env.yaml
RUN micromamba install -y -f /home/hysop-doc-env.yaml && \
diff --git a/ci/docker_images/hysop_cpu_intel/Dockerfile b/ci/docker_images/hysop_cpu_intel/Dockerfile
deleted file mode 100644
index ea2b772ae1724438ad6786d2ee9bfcde69064fe6..0000000000000000000000000000000000000000
--- a/ci/docker_images/hysop_cpu_intel/Dockerfile
+++ /dev/null
@@ -1,12 +0,0 @@
-ARG REGISTRY=gricad-registry.univ-grenoble-alpes.fr
-ARG PROJECT=particle_methods/hysop
-ARG DEFAULT_IMAGE=ci_cpu_intel
-ARG IMAGENAME=$REGISTRY/$PROJECT/$DEFAULT_IMAGE
-
-FROM $IMAGENAME AS hysop_cpu_intel
-
-ARG MAMBA_DOCKERFILE_ACTIVATE=1 # (otherwise meson will not be found)
-
-# TODO: generic path to hysop!
-RUN cd /builds/particle_methods/hysop && \
- pip install --no-build-isolation --no-deps .
diff --git a/ci/docker_images/hysop_gpu_nvidia/Dockerfile b/ci/docker_images/hysop_gpu_nvidia/Dockerfile
deleted file mode 100644
index b3bf8895ee3685154a368ed51458a0ac9229e93c..0000000000000000000000000000000000000000
--- a/ci/docker_images/hysop_gpu_nvidia/Dockerfile
+++ /dev/null
@@ -1,12 +0,0 @@
-ARG REGISTRY=gricad-registry.univ-grenoble-alpes.fr
-ARG PROJECT=particle_methods/hysop
-ARG DEFAULT_IMAGE=ci_gpu_nvidia
-ARG IMAGENAME=$REGISTRY/$PROJECT/$DEFAULT_IMAGE
-
-FROM $IMAGENAME AS hysop_gpu_nvidia
-
-ARG MAMBA_DOCKERFILE_ACTIVATE=1 # (otherwise meson will not be found)
-
-# TODO: generic path to hysop!
-RUN cd /builds/particle_methods/hysop && \
- pip install --no-build-isolation --no-deps .
diff --git a/ci/docker_images/hysop_user_cpu_intel/Dockerfile b/ci/docker_images/hysop_user_cpu_intel/Dockerfile
deleted file mode 100644
index d15777c807847072d2c1f3b3c449a59d0b0d7813..0000000000000000000000000000000000000000
--- a/ci/docker_images/hysop_user_cpu_intel/Dockerfile
+++ /dev/null
@@ -1,25 +0,0 @@
-ARG REGISTRY=gricad-registry.univ-grenoble-alpes.fr
-ARG PROJECT=particle_methods/hysop
-ARG DEFAULT_IMAGE=hysop_cpu_intel
-ARG IMAGENAME=$REGISTRY/$PROJECT/$DEFAULT_IMAGE
-
-FROM $IMAGENAME
-ARG UID
-ARG GID
-ARG LOGIN
-ARG GROUP
-
-# Update the package list, install sudo, create a non-root user,
-# and grant password-less sudo permissions
-RUN addgroup --force-badname --gid $GID $GROUP && \
- adduser --uid $UID --gid $GID --disabled-password --gecos "" $LOGIN && \
- echo "$LOGIN ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
-
-# Set the non-root user as the default user
-USER $LOGIN
-
-# Set the working directory
-ARG WKD=/home/$LOGIN
-WORKDIR $WKD
-
-# End
diff --git a/ci/docker_images/hysop_user_gpu_nvidia/Dockerfile b/ci/docker_images/hysop_user_gpu_nvidia/Dockerfile
deleted file mode 100644
index 0620dc8deed797cbd9eb520ebd9c1b6c32dd0f9c..0000000000000000000000000000000000000000
--- a/ci/docker_images/hysop_user_gpu_nvidia/Dockerfile
+++ /dev/null
@@ -1,25 +0,0 @@
-ARG REGISTRY=gricad-registry.univ-grenoble-alpes.fr
-ARG PROJECT=particle_methods/hysop
-ARG DEFAULT_IMAGE=hysop_gpu_nvidia
-ARG IMAGENAME=$REGISTRY/$PROJECT/$DEFAULT_IMAGE
-
-FROM $IMAGENAME
-ARG UID
-ARG GID
-ARG LOGIN
-ARG GROUP
-
-# Update the package list, install sudo, create a non-root user,
-# and grant password-less sudo permissions
-RUN addgroup --force-badname --gid $GID $GROUP && \
- adduser --uid $UID --gid $GID --disabled-password --gecos "" $LOGIN && \
- echo "$LOGIN ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
-
-# Set the non-root user as the default user
-USER $LOGIN
-
-# Set the working directory
-ARG WKD=/home/$LOGIN
-WORKDIR $WKD
-
-# End
diff --git a/ci/hysop-doc-env.yaml b/ci/hysop-doc-env.yaml
index aab41072a645c7ee53c7ca8560ffb5b3e240a40d..66fa4e80b16a5c012c704b8ffddb24ebea626103 100644
--- a/ci/hysop-doc-env.yaml
+++ b/ci/hysop-doc-env.yaml
@@ -21,6 +21,41 @@ name: base
channels:
- conda-forge
dependencies:
+ - python=3.12
+ - clinfo
+ - cmake
+ - cython
+ - editdistance
+ - gmpy2
+ - jsonpickle
+ - matplotlib
+ - meson
+ - meson-python # need for pip install --no-build-isolation --no-deps .
+ - mpi4py
+ - networkx
+ - ninja
+ - numba
+ - numcodecs
+ - numpy
+ - openmpi # no hack for mpi, use conda
+ - portalocker
+ - psutil
+ - py-cpuinfo
+ - pyopencl==2024.1
+ - pytest
+ - python-flint
+ - pyvis
+ - scipy
+ - sympy
+ - wheel
+ - zarr
+ - hdf5=*=mpi*
+ - h5py=*=mpi*
+ - fftw=*=mpi*
+ - tox
+ - pyfftw
+ - jupyterlab
+ - intel-opencl-rt
- doxygen
- graphviz
- sphinx
@@ -30,7 +65,17 @@ dependencies:
- sphinx-rtd-theme
- strip-hints
- pandoc
- - ipykernel
+ - antlr4-python3-runtime
+ #- ipykernel
- pip
- pip:
- nbsphinx
+ - tee
+ - colors.py
+ - primefac
+ - argparse_color_formatter
+ - memory-tempfile
+channels:
+ - numba
+dependencies:
+ - llvmlite
diff --git a/ci/hysopenv.yaml b/ci/hysopenv.yaml
index 6272fe3ced83c98fba9a7dd879ccbfe92cd3ca96..d3d7566e4124adfd18def46578ed5cad7ec4c9f6 100644
--- a/ci/hysopenv.yaml
+++ b/ci/hysopenv.yaml
@@ -71,6 +71,7 @@ dependencies:
- tox
- pyfftw
- jupyterlab
+ - pip
- pip:
- tee
- colors.py
diff --git a/ci/hysopenv_cpu_intel.yaml b/ci/hysopenv_cpu_intel.yaml
deleted file mode 100644
index accb71ca7c11a007737f131c5553e800ea93be01..0000000000000000000000000000000000000000
--- a/ci/hysopenv_cpu_intel.yaml
+++ /dev/null
@@ -1,62 +0,0 @@
-##
-## Copyright (c) HySoP 2011-2024
-##
-## This file is part of HySoP software.
-## See "https://particle_methods.gricad-pages.univ-grenoble-alpes.fr/hysop-doc/"
-## for further info.
-##
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-##
-## http://www.apache.org/licenses/LICENSE-2.0
-##
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-##
-name: base
-channels:
- - conda-forge
-dependencies:
- - python=3.12
- - clinfo
- - cmake
- - cython
- - editdistance
- - gmpy2
- - intel-opencl-rt
- - jsonpickle
- - matplotlib
- - meson
- - meson-python # need for pip install --no-build-isolation --no-deps .
- - mpi4py
- - networkx
- - ninja
- - numba
- - numcodecs
- - numpy
- - openmpi=4.1.6=external_* # more info at the end of this file
- - portalocker
- - psutil
- - py-cpuinfo
- - pyopencl==2024.1
- - pytest
- - python-flint
- - pyvis
- - scipy
- - sympy
- - wheel
- - zarr
-channels:
- - numba
-dependencies:
- - llvmlite
-
-
- # openmpi=4.1.6=external_* :
- # Forces conda to use system openmpi already installed!
- # (https://conda-forge.org/docs/user/tipsandtricks.html#
- # using-external-message-passing-interface-mpi-libraries)
diff --git a/ci/hysopenv_gpu_nvidia.yaml b/ci/hysopenv_gpu_nvidia.yaml
deleted file mode 100644
index 940d36acbab3eb6fb1a5847feaa089267c6c0eac..0000000000000000000000000000000000000000
--- a/ci/hysopenv_gpu_nvidia.yaml
+++ /dev/null
@@ -1,59 +0,0 @@
-##
-## Copyright (c) HySoP 2011-2024
-##
-## This file is part of HySoP software.
-## See "https://particle_methods.gricad-pages.univ-grenoble-alpes.fr/hysop-doc/"
-## for further info.
-##
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-##
-## http://www.apache.org/licenses/LICENSE-2.0
-##
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-##
-name: base
-channels:
- - conda-forge
-dependencies:
- - clinfo
- - cmake
- - cython
- - editdistance
- - gmpy2
- - jsonpickle
- - matplotlib
- - meson
- - meson-python # need for pip install --no-build-isolation --no-deps .
- - mpi4py
- - networkx
- - ninja
- - numba
- - numcodecs
- - numpy
- - openmpi=4.1.6=external_* # more info at the end of this file
- - portalocker
- - psutil
- - py-cpuinfo
- - pyopencl==2024.1
- - pytest
- - python-flint
- - pyvis
- - scipy
- - sympy
- - wheel
- - zarr
-channels:
- - numba
-dependencies:
- - llvmlite
-
- # openmpi=4.1.6=external_* :
- # Forces conda to use system openmpi already installed!
- # (https://conda-forge.org/docs/user/tipsandtricks.html#
- # using-external-message-passing-interface-mpi-libraries)
diff --git a/ci/readme.md b/ci/readme.md
new file mode 100644
index 0000000000000000000000000000000000000000..ae88958ad10d8f5b6111362dfd1298fe22388d7a
--- /dev/null
+++ b/ci/readme.md
@@ -0,0 +1,92 @@
+# CI configuration for Hysop project
+
+
+Req:
+- keep only latest tags
+- exception: releases
+
+
+Steps:
+
+[[_TOC_]]
+
+
+
+## Create and save docker images
+
+**What:**
+
+- build docker images with all the dependencies required to config and build hysop
+- save those images in hysop registries
+
+**Images:**
+
+- ci_cpu_intel: OpenCL/intel, for an host without GPUs --> [saved in hysop registry as ci_cpu_intel](gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/ci_cpu_intel)
+- ci_gpu_nvidia: OpenCL/NVIDIA, for an host with GPUs --> [saved in hysop registry as ci_cpu_nvidia](gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/ci_gpu_nvidia)
+- ci_cpu_intel_doc: same as ci_cpu_intel but with extra-deps required to build the documentation (project [hysop-doc](https://gricad-gitlab.univ-grenoble-alpes.fr/particle_methods/hysop-doc)) --> [saved in hysop-doc registry](gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop-doc/ci_cpu_intel_doc)
+
+
+**When:** only if the last commit message contains [docker-build]
+
+**Requirement**: the same docker images must be generated, whatever the branch is (i.e. ci directory and .gitlab-ci.yml must be properly synchronized between all branches)
+
+
+## Configure hysop
+
+- Run meson setup on OpenCL/intel and OpenCL nvidia images
+- Keep artifacts (build-dir) for build job
+
+## Build hysop
+
+- Run meson compile on OpenCL/intel and OpenCL nvidia images
+- Keep artifacts (build-dir) for tests and install and examples jobs
+
+## Install hysop
+
+- Run meson install on OpenCL/intel and OpenCL nvidia images
+- Try to import hysop and hysop fortran packages
+
+## Tests
+
+Two jobs to:
+- run meson tests on OpenCL/intel and OpenCL nvidia images
+- generate artifacts only if tests fail.
+
+Two jobs to:
+- run examples (run_examples.sh) on OpenCL/intel and OpenCL nvidia images
+- generate artifacts only if tests fail.
+
+## Create 'read-to-use' images
+
+Build and save docker images with a fully functionnal hysop install
+
+- hysopbinderlab, based on 'ci_cpu_intel', source image to create binder repo.
+ Saved in [project hysop-binder](https://gricad-gitlab.univ-grenoble-alpes.fr/particle_methods/hysop_binder)
+
+
+- hysoplab-cpu-intel-<branch-name> master based on 'ci_cpu_intel, jupyter lab for hysop (no GPUs host)
+ [Saved in hysop registry](https://gricad-gitlab.univ-grenoble-alpes.fr/particle_methods/hysop/container_registry)
+
+ usage:
+
+ ```
+ docker run -p 8888:8888 --rm -ti gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-cpu-intel-master
+ ```
+
+- hysoplab-gpu-nvidia-<branch-name> based on 'ci_gpu_nvidia, jupyter lab for hysop (GPUs host)
+ [Saved in hysop registry](https://gricad-gitlab.univ-grenoble-alpes.fr/particle_methods/hysop/container_registry)
+
+ usage:
+
+ ```
+ docker run -p 8888:8888 --runtime=nvidia --gpus all --rm -ti gricad-registry.univ-grenoble-alpes.fr/particle_methods/hysop/hysoplab-gpu-nvidia-master
+ ```
+
+## Build doc
+
+A job to trigger doc. generation in project [hysop-doc](https://gricad-gitlab.univ-grenoble-alpes.fr/particle_methods/hysop-doc)
+
+
+## More
+
+- A job to automatically create a release when a tag is pushed.
diff --git a/ci/scripts/config.sh b/ci/scripts/config.sh
deleted file mode 100755
index 034997e8626de38487d4d515e50b5fdb533bc584..0000000000000000000000000000000000000000
--- a/ci/scripts/config.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env bash
-##
-## Copyright (c) HySoP 2011-2024
-##
-## This file is part of HySoP software.
-## See "https://particle_methods.gricad-pages.univ-grenoble-alpes.fr/hysop-doc/"
-## for further info.
-##
-## Licensed under the Apache License, Version 2.0 (the "License");
-## you may not use this file except in compliance with the License.
-## You may obtain a copy of the License at
-##
-## http://www.apache.org/licenses/LICENSE-2.0
-##
-## Unless required by applicable law or agreed to in writing, software
-## distributed under the License is distributed on an "AS IS" BASIS,
-## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-## See the License for the specific language governing permissions and
-## limitations under the License.
-##
-
-set -feu -o pipefail
-
-# Ensure that required variables are set.
-#: ${CI_PROJECT_DIR:?"Please set environment variable CI_PROJECT_DIR with 'hysop' repository (absolute) path."}
-: ${BUILD_DIR:?"Please set environment variable BUILD_DIR to the required build path."}
-#: ${INSTALL_DIR:?"Please set environment variable INSTALL_DIR to the expected install path."}
-
-meson setup ${BUILD_DIR} --python.install-env prefix --prefix=${BUILD_DIR}/install
-
-exit 0