From 4580566247c29aa6d7275199cee93e0b5cd2323a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?=
<franck.perignon@univ-grenoble-alpes.fr>
Date: Mon, 16 Sep 2024 18:35:20 +0200
Subject: [PATCH] =?UTF-8?q?[docker-build-cpu-intel-user]=20[docker-build-g?=
=?UTF-8?q?pu-nvidia-user]=20-=C2=A0Try=20to=20fix=20docker=20images=20gen?=
=?UTF-8?q?=20with=20CI=20(symlink=20loop=3F)=20-=20Use=20pyfft=20from=20m?=
=?UTF-8?q?icromamba=20=20(last=20version=20is=20now=20available)?=
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Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
ci/docker_images/ci_user/Dockerfile | 73 +++++++++++------------------
ci/hysopenv.yaml | 1 +
2 files changed, 29 insertions(+), 45 deletions(-)
diff --git a/ci/docker_images/ci_user/Dockerfile b/ci/docker_images/ci_user/Dockerfile
index 79647cfad..7261525ec 100644
--- a/ci/docker_images/ci_user/Dockerfile
+++ b/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
diff --git a/ci/hysopenv.yaml b/ci/hysopenv.yaml
index d25247755..3a0aeadfb 100644
--- a/ci/hysopenv.yaml
+++ b/ci/hysopenv.yaml
@@ -69,6 +69,7 @@ dependencies:
- h5py=*=mpi*
- fftw=*=mpi*
- tox
+ - pyfftw
channels:
- numba
dependencies:
--
GitLab