WIP: update api for python module, drop python2 (#777)

* restore Python module
* drop Python2 support
* add ci/cd for Python module
* add Python example Si_dft.py

.github/workflows/build.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     container: electronicstructure/sirius
     env:
-      SPEC_GCC: sirius@develop %gcc +tests +apps +vdwxc +scalapack +fortran build_type=RelWithDebInfo ^openblas ^mpich
+      SPEC_GCC: sirius@develop %gcc +python +tests +apps +vdwxc +scalapack +fortran build_type=RelWithDebInfo ^openblas ^mpich
     steps:
       - uses: actions/checkout@v2
       - name: Show the spec
@@ -22,7 +22,7 @@ jobs:
           cd ${GITHUB_WORKSPACE}
           mkdir build
           cd build
-          spack --color always -e gcc-build-env build-env $SPEC_GCC -- cmake .. -DUSE_SCALAPACK=1 -DUSE_VDWXC=1 -DBUILD_TESTING=1 -DCREATE_FORTRAN_BINDINGS=1 -DCMAKE_BUILD_TYPE=RelWithDebInfo
+          spack --color always -e gcc-build-env build-env $SPEC_GCC -- cmake .. -DUSE_SCALAPACK=1 -DUSE_VDWXC=1 -DBUILD_TESTING=1 -DCREATE_FORTRAN_BINDINGS=1 -DCREATE_PYTHON_MODULE=1 -DCMAKE_BUILD_TYPE=RelWithDebInfo
       - name: Build SIRIUS
         run: |
           cd ${GITHUB_WORKSPACE}/build

CMakeLists.txt

@@ -23,7 +23,6 @@ set(USE_PROFILER            ON  CACHE BOOL "measure execution of functions with
 set(USE_MEMORY_POOL         ON  CACHE BOOL "use memory pool")
 set(USE_POWER_COUNTER       OFF CACHE BOOL "measure energy consumption with power counters")
 set(BUILD_TESTING           OFF CACHE BOOL "build test executables") # override default setting in CTest module
-set(PYTHON2                 OFF CACHE STRING "use Python 2.7")
 set(CUDA_ARCH               OFF CACHE STRING "the target GPU architectures; 60 (Pascal), 70 (Volta), etc. Multiple archs are supported too.")
 set(GPU_MEMORY_ALIGMENT "512" CACHE STRING "memory alignment of the GPU")
 set(USE_FP32 "AUTO" CACHE STRING "Enable single precision support.")
@@ -72,15 +71,8 @@ include(GitSubmodule)    # include custom defined FindPackage modules
 include(GNUInstallDirs)  # required to get a proper LIBDIR variable
 
 if (CREATE_PYTHON_MODULE)
-  if(PYTHON2)
-    # force cmake to use python2
-    set(PYBIND11_PYTHON_VERSION 2.7)
-    find_package(Python2 REQUIRED)
-    set(PYTHON_EXECUTABLE ${Python2_EXECUTABLE})
-  else()
-    find_package(Python3 COMPONENTS Interpreter REQUIRED)
-    set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
-  endif()
+  find_package(Python3 COMPONENTS Interpreter REQUIRED)
+  set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
 endif()
 
 # Set release as the default build type.

ci/dockerfiles/Dockerfile

@@ -1,4 +1,4 @@
-FROM nvidia/cuda:11.2.2-devel-ubuntu20.04
+FROM nvidia/cuda:11.4.2-devel-ubuntu20.04
 
 ENV DEBIAN_FRONTEND=noninteractive \
     PATH="$PATH:/spack/bin"
@@ -17,15 +17,15 @@ RUN apt-get install -y gcc g++ gfortran clang git make unzip \
   patchelf
 
 # install CMake
-RUN wget https://github.com/Kitware/CMake/releases/download/v3.24.1/cmake-3.24.1-linux-x86_64.tar.gz -O cmake.tar.gz && \
+RUN wget https://github.com/Kitware/CMake/releases/download/v3.24.3/cmake-3.24.3-linux-x86_64.tar.gz -O cmake.tar.gz && \
     tar zxvf cmake.tar.gz --strip-components=1 -C /usr
 
 # get latest version of spack
 RUN git clone https://github.com/spack/spack.git
 
 # find gcc and clang compilers
-RUN /spack/bin/spack compiler find
-RUN /spack/bin/spack external find --all
+RUN spack compiler find
+RUN spack external find --all
 
 # install yq (utility to manipulate the yaml files)
 RUN wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_386 && chmod a+x /usr/local/bin/yq
@@ -37,24 +37,25 @@ RUN yq -i '.compilers[0].compiler.paths.f77 = "/usr/bin/gfortran"' /root/.spack/
     yq -i '.compilers[1].compiler.paths.fc = "/usr/bin/gfortran"' /root/.spack/linux/compilers.yaml
 
 # create GCC build env.
-RUN /spack/bin/spack env create --with-view /sirius-install gcc-build-env
+RUN spack env create --with-view /sirius-install gcc-build-env
 
-ENV SPEC_GCC="sirius@develop %gcc build_type=Release +scalapack +vdwxc +fortran +tests +nlcglib +elpa +magma +cuda cuda_arch=60 ^openblas ^mpich@3.3.2 ^nlcglib +cuda +wrapper cuda_arch=60 ^kokkos +wrapper cuda_arch=60 ^spfft+single_precision ^magma+cuda cuda_arch=60 target=x86_64"
+ENV SPEC_GCC="sirius@develop %gcc build_type=Release +python +scalapack +vdwxc +fortran +tests +nlcglib +elpa +magma +cuda cuda_arch=60 ^openblas ^mpich@3.3.2 ^nlcglib +cuda +wrapper cuda_arch=60 ^kokkos +wrapper cuda_arch=60 ^spfft+single_precision ^magma+cuda cuda_arch=60 target=x86_64"
 
-RUN /spack/bin/spack -e gcc-build-env spec $SPEC_GCC
+# show spec.
+RUN spack -e gcc-build-env spec $SPEC_GCC
 
-RUN /spack/bin/spack -e gcc-build-env install --fail-fast --only=dependencies $SPEC_GCC
+RUN spack -e gcc-build-env add $SPEC_GCC
+
+RUN spack -e gcc-build-env install --fail-fast --only=dependencies
 
 # create clang build env.
-RUN /spack/bin/spack env create clang-build-env
+RUN spack env create clang-build-env
 
 ENV SPEC_CLANG="sirius@develop %clang build_type=Release +tests ^openblas ^mpich ~fortran ^spfft+single_precision target=x86_64"
 
-RUN /spack/bin/spack -e clang-build-env spec $SPEC_CLANG
+RUN spack -e clang-build-env spec $SPEC_CLANG
 
 # install all packages; don't reuse from gcc
-RUN /spack/bin/spack -e clang-build-env install --fresh --fail-fast --only=dependencies $SPEC_CLANG
+RUN spack -e clang-build-env add $SPEC_CLANG
+RUN spack -e clang-build-env install --fresh --fail-fast --only=dependencies
 
-#WORKDIR /root
-#
-#ENTRYPOINT ["bash", "-l"]