[docker-build-cpu-intel-user] [docker-build-gpu-nvidia-user]

- Try to fix docker images gen with CI (symlink loop?)
- Use pyfft from micromamba  (last version is now available)

ci/docker_images/ci_user/Dockerfile

@@ -88,60 +88,42 @@ RUN micromamba config prepend channels conda-forge                     && \
 # HPTT # (longest time compilation)
 ########
 FROM hysop-base-python AS hptt
-
+USER hysop-user
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
 RUN 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
 RUN cmake -S hptt -B build-hptt -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX && \
-    cmake --build build-hptt -j$(nproc)                             && \
-    cmake --install build-hptt                             
+    cmake --build build-hptt -j$(nproc)         && \
+    cmake --install build-hptt                           
 ENV HPTT_ROOT /opt/conda
 RUN cd hptt/pythonAPI                             && \
-    pip install --no-cache-dir --upgrade .                     
-RUN rm -rf hptt build-hptt
+    pip install --no-cache-dir --upgrade .  && rm -rf hptt build-hptt
 
 #########
 # FLINT #
 #########
 FROM hysop-base-python AS flint
-
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+USER hysop-user
 #
 # 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)
 #
+# Requires gmp and mpfr -> from micromamba env
 RUN 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                                                            && \
     mv flint* flint
 RUN cmake -S flint -B build-flint -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX && \  
     cmake --build build-flint -j$(nproc)                                       && \
-    cmake --install build-flint
-# RUN rm -rf flint* build-flint
-
-#####################
-# HDF5_mpi and H5PY #
-#####################
-# NOT USED !
-FROM hysop-base-python  AS hdf5_mpi_h5py
-
-ENV MPICC "mpicc"
-ARG pip_install_opts='--upgrade --no-binary=h5py --no-deps --no-build-isolation'
-RUN 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     
-RUN cd hdf5-*               && \
-    CC="${MPICC}" ./configure --prefix=$CONDA_PREFIX --enable-parallel     \
-                              --enable-shared=yes --enable-static=no && \
-    make -j$(nproc)         && \
-    make install            
-RUN rm -rf hdf5-*      && \
-    CC="${MPICC}" HDF5_MPI="ON" HDF5_VERSION="1.14.3"          \
-    HDF5_DIR=$CONDA_PREFIX H5PY_SETUP_REQUIRES=0                  \
-    pip install ${pip_install_opts} h5py==3.11.0
+    cmake --install build-flint && \
+    rm -rf flint* build-flint
+
 
 ##########
 # Stage  #
@@ -159,8 +141,7 @@ RUN pip install --no-cache-dir --upgrade    \
 RUN git clone https://github.com/geggo/gpyfft.git                           && \
  cd gpyfft                                                                  && \
  sed 's#finalize(self, _destroy_plan, self.plan)##' -i gpyfft/gpyfftlib.pyx && \
- pip install --no-cache-dir . 
-RUN rm -rf gpyfft
+ pip install --no-cache-dir .  && rm -rf gpyfft
 
 # #
 # FFTW latest version nov 2023
@@ -186,12 +167,12 @@ RUN rm -rf gpyfft
 # pyfftw is linked to fftw3 compiled above
 
 #ARG pip_install_opts='--no-binary=pyfftw --no-deps --no-build-isolation'
-ARG pip_install_opts='--no-cache-dir --no-binary=pyfftw --no-deps'
-RUN git clone https://github.com/pyFFTW/pyFFTW.git                           && \
-    cd pyFFTW                                                                && \
-#    PYFFTW_INCLUDE="/include"                                                   \
-    pip install ${pip_install_opts} .   
-RUN rm -rf pyFFTW
+#ARG pip_install_opts='--no-cache-dir --no-binary=pyfftw --no-deps'
+#RUN git clone https://github.com/pyFFTW/pyFFTW.git                           && \
+#    cd pyFFTW                                                                && \
+##    PYFFTW_INCLUDE="/include"                                                   \
+#    pip install ${pip_install_opts} .  && \
+#    cd && rm -rf pyFFTW
 
 ###############
 # Final-Stage #
@@ -199,13 +180,16 @@ RUN rm -rf pyFFTW
 FROM hysop-full-python AS hysop-final
 
 # Copy only necessary files from previous stages
-COPY --from=hptt /opt/conda/lib/libhptt* /opt/conda/lib
-COPY --from=hptt /opt/conda/include /opt/conda/include
-COPY --from=flint /opt/conda/include/flint /opt/conda/include/flint
-COPY --from=flint /opt/conda/lib/libflint* /opt/conda/lib
-# 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=hptt --chown=hysop-user:hysop-user /opt/conda/lib/libhptt.so /opt/conda/lib/
+COPY --from=hptt --chown=hysop-user:hysop-user /opt/conda/include/compute_node.h /opt/conda/include/hptt*.h \ 
+    /opt/conda/include/macros.h /opt/conda/include/plan.h /opt/conda/include/utils.h /opt/conda/include/transpose.h /opt/conda/include/
+COPY --from=hptt --chown=hysop-user:hysop-user /opt/conda/lib/python3.12/site-packages/hptt \
+    /opt/conda/lib/python3.12/site-packages/hptt
+
+COPY --from=flint --chown=hysop-user:hysop-user /opt/conda/include/flint /opt/conda/include/flint
+RUN mkdir -p /home/hysop-user/temp/lib
+COPY --from=flint --chown=hysop-user:hysop-user /opt/conda/lib/libflint* /home/hysop-user/temp/lib/
+RUN mv /home/hysop-user/temp/lib/libflint* /opt/conda/lib/ && rm -rf /home/hysop-user/temp
 
 # Important for f2py command summit in meson build system!
 ENV MPIFC mpif90
@@ -223,7 +207,6 @@ ENV MPIEXEC_EXECUTABLE="${MPI_HOME}/bin/mpiexec"
 RUN rm -rf $HOME/.cache/pip/*   && \
     rm -rf /tmp/*
 
-
 # ---- cpu image ---
 FROM hysop-final AS hysop-final-cpu
 

ci/hysopenv.yaml

@@ -69,6 +69,7 @@ dependencies:
   - h5py=*=mpi*
   - fftw=*=mpi*
   - tox
+  - pyfftw
 channels:
   - numba
 dependencies: