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Commit dda6e01b authored by Thomas Purcell's avatar Thomas Purcell
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Revert some changes from sissopp gitlab repo

Dockerfile and .gitlab-ci; remove bindings.*pp files
parent e54d4cc0
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image: registry.gitlab.com/sissopp_developers/sissopp image: gitlab-registry.mpcdf.mpg.de/tpurcell/cpp_sisso
stages: stages:
- build - build
...@@ -6,16 +6,118 @@ stages: ...@@ -6,16 +6,118 @@ stages:
- bin_test - bin_test
- doc_builds - doc_builds
build-intel:
stage: build
script:
- python -m venv cpp_sisso_env
- source cpp_sisso_env/bin/activate
- mkdir build_intel/
- cd build_intel/
- export I_MPI_ROOT=/home/runner/intel/oneapi/mpi/latest/
- export INTEL_COMP_ROOT=/home/runner/intel/oneapi/compiler/latest/linux/
- export MKLROOT=/home/runner/intel/oneapi/mkl/latest/
- export LD_LIBRARY_PATH=$I_MPI_ROOT/lib/:$I_MPI_ROOT/lib/release:$MKLROOT/lib/intel64:$INTEL_COMP_ROOT/lib/:$INTEL_COMP_ROOT/compiler/lib/intel64/:$LD_LIBRARY_PATH:$HOME/intel/oneapi/intelpython/latest/lib/:$HOME/intel/oneapi/intelpython/latest/lib/python3.7
- export PYTHONPATH=$HOME/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/:cpp_sisso_env/lib/python3.7/site-packages/
- export PATH=$INTEL_COMP_ROOT/bin/:$INTEL_COMP_ROOT/bin/intel64:$I_MPI_ROOT/bin:$PATH
- cmake -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILE=icc -DCMAKE_CXX_FLAGS="-O3" -DBUILD_TESTS=ON -DBUILD_PARAMS=ON -DBUILD_PYTHON=ON ../
- make
- make install
- cd ../
artifacts:
when: always
paths:
- bin/sisso++
- lib/libsisso.so
- lib/boost/*
- lib/gtest/*
- lib/coin-or/*
- lib/nlopt/*
- lib/gtest/*
- lib/fmt/*
- tests/googletest/sisso_test
- cpp_sisso_env/*
expire_in: 1 days
test-intel-py:
stage: unit_test
dependencies:
- build-intel
script:
- source cpp_sisso_env/bin/activate
- export I_MPI_ROOT=/home/runner/intel/oneapi/mpi/latest/
- export INTEL_COMP_ROOT=/home/runner/intel/oneapi/compiler/latest/linux/
- export MKLROOT=/home/runner/intel/oneapi/mkl/latest/
- export LD_LIBRARY_PATH=$I_MPI_ROOT/lib/:$I_MPI_ROOT/lib/release:$MKLROOT/lib/intel64:$INTEL_COMP_ROOT/lib/:$INTEL_COMP_ROOT/compiler/lib/intel64/:$LD_LIBRARY_PATH:$HOME/intel/oneapi/intelpython/latest/lib/:$HOME/intel/oneapi/intelpython/latest/lib/python3.7
- export PYTHONPATH=$HOME/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/:cpp_sisso_env/lib/python3.7/site-packages/
- export PATH=$INTEL_COMP_ROOT/bin/:$INTEL_COMP_ROOT/bin/intel64:$I_MPI_ROOT/bin:$PATH
- export OMP_NUM_THREADS=2
- export OMP_PLACES=cores
- pytest tests/pytest
test-intel-googletest:
stage: unit_test
dependencies:
- build-intel
script:
- source cpp_sisso_env/bin/activate
- export I_MPI_ROOT=/home/runner/intel/oneapi/mpi/latest/
- export INTEL_COMP_ROOT=/home/runner/intel/oneapi/compiler/latest/linux/
- export MKLROOT=/home/runner/intel/oneapi/mkl/latest/
- export LD_LIBRARY_PATH=$I_MPI_ROOT/lib/:$I_MPI_ROOT/lib/release:$MKLROOT/lib/intel64:$INTEL_COMP_ROOT/lib/:$INTEL_COMP_ROOT/compiler/lib/intel64/:$LD_LIBRARY_PATH:$HOME/intel/oneapi/intelpython/latest/lib/:$HOME/intel/oneapi/intelpython/latest/lib/python3.7
- export PYTHONPATH=$HOME/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/:cpp_sisso_env/lib/python3.7/site-packages/
- export PATH=$INTEL_COMP_ROOT/bin/:$INTEL_COMP_ROOT/bin/intel64:$I_MPI_ROOT/bin:$PATH
- export OMP_NUM_THREADS=2
- export OMP_PLACES=cores
- cd tests/
- googletest/sisso_test
test-intel-bin:
stage: bin_test
dependencies:
- build-intel
script:
- source cpp_sisso_env/bin/activate
- export I_MPI_ROOT=/home/runner/intel/oneapi/mpi/latest/
- export INTEL_COMP_ROOT=/home/runner/intel/oneapi/compiler/latest/linux/
- export MKLROOT=/home/runner/intel/oneapi/mkl/latest/
- export LD_LIBRARY_PATH=$I_MPI_ROOT/lib/:$I_MPI_ROOT/lib/release:$MKLROOT/lib/intel64:$INTEL_COMP_ROOT/lib/:$INTEL_COMP_ROOT/compiler/lib/intel64/:$LD_LIBRARY_PATH:$HOME/intel/oneapi/intelpython/latest/lib/:$HOME/intel/oneapi/intelpython/latest/lib/python3.7
- export PYTHONPATH=$HOME/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/:cpp_sisso_env/lib/python3.7/site-packages/
- export PATH=$INTEL_COMP_ROOT/bin/:$INTEL_COMP_ROOT/bin/intel64:$I_MPI_ROOT/bin:$PATH
- export OMP_NUM_THREADS=1
- cd tests/exec_test/default/
- mpiexec -n 1 ../../../bin/sisso++
- python ../check_model.py
- cd ../classification/
- mpiexec -n 1 ../../../bin/sisso++
- python check_model.py
- cd ../gen_proj
- mpiexec -n 2 ../../../bin/sisso++
- python ../check_model.py
- cd ../log_reg
- mpiexec -n 2 ../../../bin/sisso++
- python check_model.py
- cd ../max_corr
- mpiexec -n 2 ../../../bin/sisso++
- python ../check_model.py
- cd ../param
- mpiexec -n 2 ../../../bin/sisso++
- python ../check_model.py
- cd ../reparam
- mpiexec -n 2 ../../../bin/sisso++
- cd ../../../
build-gnu: build-gnu:
stage: build stage: build
script: script:
- /opt/anaconda/3/2021.05/bin/python -m venv sissopp_env - conda info --envs
- source sissopp_env/bin/activate - python -m venv cpp_sisso_env
- export LD_LIBRARY_PATH=/opt/anaconda/3/2021.05/lib/:/opt/anaconda/3/2021.05/lib/python3.8:$LD_LIBRARY_PATH - source cpp_sisso_env/bin/activate
- export PYTHONPATH=/opt/anaconda/3/2021.05/lib/python3.8/site-packages/:sissopp_env/lib/python3.8/site-packages/ - export LD_LIBRARY_PATH=$HOME/intel/oneapi/intelpython/latest/lib/:$HOME/intel/oneapi/intelpython/latest/lib/python3.7:$LD_LIBRARY_PATH
- export PYTHONPATH=$HOME/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/:cpp_sisso_env/lib/python3.7/site-packages/
- mkdir build_gcc/ - mkdir build_gcc/
- cd build_gcc/ - cd build_gcc/
- cmake -C ../cmake/toolchains/gnu_param_py.cmake -DBUILD_TESTS=ON ../ - cmake -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILE=gcc -DCMAKE_CXX_FLAGS="-O3" -DBUILD_TESTS=ON -DBUILD_PARAMS=ON -DBUILD_PYTHON=ON ../
- make - make
- make install - make install
- cd ../ - cd ../
...@@ -23,33 +125,37 @@ build-gnu: ...@@ -23,33 +125,37 @@ build-gnu:
when: always when: always
paths: paths:
- bin/sisso++ - bin/sisso++
- lib/libsisso.so
- lib/boost/* - lib/boost/*
- lib/gtest/* - lib/gtest/*
- lib/coin-or/* - lib/coin-or/*
- lib/nlopt/* - lib/nlopt/*
- lib/gtest/* - lib/gtest/*
- lib/fmt/* - lib/fmt/*
- lib/libsisso.so
- sissopp_env/*
- tests/googletest/sisso_test - tests/googletest/sisso_test
- cpp_sisso_env/*
test-gnu-py: test-gnu-py:
stage: unit_test stage: unit_test
dependencies: dependencies:
- build-gnu - build-gnu
script: script:
- source sissopp_env/bin/activate - source cpp_sisso_env/bin/activate
- export LD_LIBRARY_PATH=/opt/anaconda/3/2021.05/lib/:/opt/anaconda/3/2021.05/lib/python3.8:$LD_LIBRARY_PATH - export LD_LIBRARY_PATH=$HOME/intel/oneapi/intelpython/latest/lib/:$HOME/intel/oneapi/intelpython/latest/lib/python3.7:$LD_LIBRARY_PATH
- export PYTHONPATH=/opt/anaconda/3/2021.05/lib/python3.8/site-packages/:sissopp_env/lib/python3.8/site-packages/ - export PYTHONPATH=$HOME/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/:cpp_sisso_env/lib/python3.7/site-packages/
- /opt/anaconda/3/2021.05/bin/pytest tests/pytest - export OMP_NUM_THREADS=2
- export OMP_PLACES=cores
- pytest tests/pytest
test-gnu-googletest: test-gnu-googletest:
stage: unit_test stage: unit_test
dependencies: dependencies:
- build-gnu - build-gnu
script: script:
- source sissopp_env/bin/activate - source cpp_sisso_env/bin/activate
- cd tests/ - export OMP_NUM_THREADS=2
- export OMP_PLACES=cores
- cd tests/
- googletest/sisso_test - googletest/sisso_test
test-gnu-bin: test-gnu-bin:
...@@ -57,30 +163,36 @@ test-gnu-bin: ...@@ -57,30 +163,36 @@ test-gnu-bin:
dependencies: dependencies:
- build-gnu - build-gnu
script: script:
- source sissopp_env/bin/activate - source cpp_sisso_env/bin/activate
- export LD_LIBRARY_PATH=/opt/anaconda/3/2021.05/lib/:/opt/anaconda/3/2021.05/lib/python3.8:`pwd`/lib/:$LD_LIBRARY_PATH - export LD_LIBRARY_PATH=$HOME/intel/oneapi/intelpython/latest/lib/:$HOME/intel/oneapi/intelpython/latest/lib/python3.7:$LD_LIBRARY_PATH
- export PYTHONPATH=/opt/anaconda/3/2021.05/lib/python3.8/site-packages/:sissopp_env/lib/python3.8/site-packages/ - export PYTHONPATH=$HOME/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/:cpp_sisso_env/lib/python3.7/site-packages/
- ls lib - export OMP_NUM_THREADS=1
- cd tests/exec_test/default/ - cd tests/exec_test/default/
- mpiexec -n 1 ../../../bin/sisso++ - mpiexec -n 1 ../../../bin/sisso++
- python ../check_model.py - python ../check_model.py
- cd ../classification/ - cd ../classification/
- mpiexec -n 1 ../../../bin/sisso++ - mpiexec -n 1 ../../../bin/sisso++
- python check_model.py - python check_model.py
- cd ../gen_proj/ - cd ../gen_proj
- mpiexec -n 1 ../../../bin/sisso++ - mpiexec -n 1 ../../../bin/sisso++
- python ../check_model.py - python ../check_model.py
- cd ../log_reg/ - cd ../log_reg
- mpiexec -n 1 ../../../bin/sisso++ - mpiexec -n 1 ../../../bin/sisso++
- python check_model.py - python check_model.py
- cd ../max_corr/ - cd ../max_corr
- mpiexec -n 1 ../../../bin/sisso++ - mpiexec -n 1 ../../../bin/sisso++
- python ../check_model.py - python ../check_model.py
- cd ../param
- mpiexec -n 1 ../../../bin/sisso++
- python ../check_model.py
- cd ../reparam
- mpiexec -n 1 ../../../bin/sisso++
- cd ../../../
pages: pages:
stage: doc_builds stage: doc_builds
script: script:
- source sissopp_env/bin/activate - source cpp_sisso_env/bin/activate
- cd docs/ - cd docs/
- make html - make html
- mv _build/html/ ../public - mv _build/html/ ../public
......
...@@ -17,15 +17,22 @@ RUN apt-get update &&\ ...@@ -17,15 +17,22 @@ RUN apt-get update &&\
apt-get install -y doxygen &&\ apt-get install -y doxygen &&\
apt-get clean apt-get clean
ARG dst=/opt/anaconda/3/2021.05 RUN apt-get install -y gpg-agent wget software-properties-common &&\
wget https://repositories.intel.com/graphics/intel-graphics.key &&\
RUN wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh apt-key add intel-graphics.key &&\
RUN mv Anaconda3-2021.05-Linux-x86_64.sh /tmp/anaconda.sh apt-add-repository 'deb [arch=amd64] https://repositories.intel.com/graphics/ubuntu focal main'
RUN bash /tmp/anaconda.sh -b -f -p ${dst} &&\ RUN apt-get update -y &&\
rm -f /tmp/anaconda.sh apt-get install -y intel-opencl-icd intel-level-zero-gpu level-zero intel-media-va-driver-non-free libmfx1 libcilkrts5
RUN apt-get install -y \
RUN ${dst}/bin/conda install -y -c conda-forge numpy scipy pandas pytest seaborn tornado libigc-dev \
RUN ${dst}/bin/pip install sphinx sphinx-rtd-theme breathe sphinx-sitemap myst_parser libigdfcl-dev \
libigfxcmrt-dev \
level-zero-dev
ARG oneapi_src=oneapi.sh
ADD ${oneapi_src} /tmp/oneapi.sh
ARG hpc_oneapi_src=hpc_oneapi.sh
ADD ${hpc_oneapi_src} /tmp/hpc_oneapi.sh
# Setup the user # Setup the user
RUN useradd -d /home/runner -ms /bin/bash runner RUN useradd -d /home/runner -ms /bin/bash runner
...@@ -33,13 +40,19 @@ RUN useradd -d /home/runner -ms /bin/bash runner ...@@ -33,13 +40,19 @@ RUN useradd -d /home/runner -ms /bin/bash runner
USER runner USER runner
WORKDIR /home/runner WORKDIR /home/runner
RUN sh /tmp/oneapi.sh -s -a --silent --eula accept --components intel.oneapi.lin.python3:intel.oneapi.lin.tbb.devel:intel.oneapi.lin.dpcpp-cpp-compiler:intel.oneapi.lin.dpl:intel.oneapi.lin.mkl.devel:intel.oneapi.lin.dpcpp-ct
RUN sh /tmp/hpc_oneapi.sh -s -a --silent --eula accept --components intel.oneapi.lin.mpi.devel:intel.oneapi.lin.dpcpp-cpp-compiler-pro:intel.oneapi.lin.ifort-compiler
ENV CONDA_DEFAULT_ENV='base' ENV CONDA_DEFAULT_ENV='base'
ENV CONDA_EXE='/opt/anaconda/3/2021.05/bin/conda' ENV CONDA_EXE='/home/runner/intel/oneapi/intelpython/latest/bin/conda'
ENV CONDA_PREFIX='/opt/anaconda/3/2021.05' ENV CONDA_PREFIX='/home/runner/intel/oneapi/intelpython/latest'
ENV CONDA_PROMPT_MODIFIER='(base) ' ENV CONDA_PROMPT_MODIFIER='(base) '
ENV CONDA_PYTHON_EXE='/opt/anaconda/3/2021.05/bin/python' ENV CONDA_PYTHON_EXE='/home/runner/intel/oneapi/intelpython/latest/bin/python'
ENV CONDA_SHLVL='1' ENV CONDA_SHLVL='1'
ENV PATH="/opt/anaconda/3/2021.05/bin:/opt/anaconda/3/2021.05/condabin:$PATH" ENV CPATH='/home/runner/intel/oneapi/dpl/latest/linux/include:/home/runner/intel/oneapi/dev-utilities/latest/include:/home/runner/intel/oneapi/mpi/latest//include:/home/runner/intel/oneapi/mkl/latest/include:/home/runner/intel/oneapi/ccl/latest/include/cpu_gpu_dpcpp:/home/runner/intel/oneapi/compiler/latest/linux/include:/home/runner/intel/oneapi/ipp/latest/include:/home/runner/intel/oneapi/vpl/latest/include:/home/runner/intel/oneapi/dal/latest/include:/home/runner/intel/oneapi/dnnl/latest/cpu_dpcpp_gpu_dpcpp/lib:/home/runner/intel/oneapi/ippcp/latest/include:/home/runner/intel/oneapi/tbb/latest/env/../include'
ENV PATH="/home/runner/intel/oneapi/intelpython/latest/bin:/home/runner/intel/oneapi/intelpython/latest/condabin:$PATH"
ENV _CE_CONDA='' ENV _CE_CONDA=''
ENV _CE_M='' ENV _CE_M=''
RUN /home/runner/intel/oneapi/intelpython/latest/bin/conda install -y numpy scipy pandas pytest seaborn tornado
RUN /home/runner/intel/oneapi/intelpython/latest/bin/pip install sphinx sphinx-rtd-theme breathe sphinx-sitemap myst_parser
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