Add example application: sqd-hdf5-chemistry

.github/workflows/coverage.yml

@@ -31,7 +31,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y g++ clang cmake ninja-build
+          sudo apt-get install -y g++ clang cmake ninja-build libhdf5-dev libopenblas-dev pkg-config libssl-dev libomp-dev libeigen3-dev openmpi-bin libopenmpi-dev
       - name: Install tox
         run: |
           python -m pip install --upgrade pip

.github/workflows/lint.yml

@@ -35,7 +35,7 @@ jobs:
       - name: Install via apt-get
         run: |
           sudo apt-get update
-          sudo apt-get install -y fd-find clang-tidy-21 clang-format-21
+          sudo apt-get install -y fd-find clang-tidy-21 clang-format-21 libhdf5-dev libopenblas-dev pkg-config libomp-dev libgomp-dev openmpi-bin libopenmpi-dev
           sudo ln -fs clang-format-21 /usr/bin/clang-format
           sudo ln -fs clang-tidy-21 /usr/bin/clang-tidy
           sudo ln -fs /usr/bin/fdfind /usr/local/bin/fd

.github/workflows/test_development_versions.yml

@@ -50,7 +50,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y g++ clang cmake ninja-build
+          sudo apt-get install -y g++ clang cmake ninja-build libhdf5-dev libopenblas-dev pkg-config libssl-dev libomp-dev libeigen3-dev openmpi-bin libopenmpi-dev
       - name: Configure CMake
         run: >-
           cmake -S . -B build

.github/workflows/test_latest_versions.yml

@@ -71,7 +71,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y g++ clang cmake ninja-build
+          sudo apt-get install -y g++ clang cmake ninja-build libhdf5-dev libopenblas-dev pkg-config libssl-dev libomp-dev libeigen3-dev openmpi-bin libopenmpi-dev
       - name: Configure CMake
         run: >-
           cmake -S . -B build

.github/workflows/test_without_exceptions_rtti.yml

@@ -32,7 +32,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y g++ clang cmake ninja-build
+          sudo apt-get install -y g++ clang cmake ninja-build libhdf5-dev libopenblas-dev pkg-config libomp-dev libgomp-dev openmpi-bin libopenmpi-dev
       - name: Configure CMake
         run: >-
           cmake -S . -B build

.gitmodules

@@ -40,3 +40,15 @@
 [submodule "deps/boost/mp11"]
 	path = deps/boost/mp11
 	url = https://github.com/boostorg/mp11.git
+[submodule "deps/sbd"]
+	path = deps/sbd
+	url = https://github.com/r-ccs-cms/sbd.git
+[submodule "deps/highfive"]
+	path = deps/highfive
+	url = https://github.com/highfive-devs/highfive.git
+[submodule "deps/xtl"]
+	path = deps/xtl
+	url = https://github.com/xtensor-stack/xtl.git
+[submodule "deps/xtensor"]
+	path = deps/xtensor
+	url = https://github.com/xtensor-stack/xtensor.git

CMakeLists.txt

@@ -21,6 +21,27 @@ include_directories(include)
 add_subdirectory(deps/doctest)
 add_subdirectory(deps/nanobench)
 
+function(find_package_fallback package_name subdir)
+    find_package(${package_name} QUIET)
+    if(${package_name}_FOUND)
+        message(STATUS "${package_name} found")
+    else()
+        message(STATUS "${package_name} not found, using version in ${subdir}")
+        set("${package_name}_VENDORED" TRUE PARENT_SCOPE)
+        add_subdirectory(${subdir})
+    endif()
+endfunction()
+
+# FIXME: These are required only by the sqd-hdf5-chemistry executable;
+# ideally we could make them optional overall
+find_package_fallback(HighFive deps/highfive)
+find_package(MPI REQUIRED)
+find_package(OpenMP REQUIRED)
+set(xtensor_INCLUDE_DIRS
+    deps/xtensor/include
+    deps/xtl/include
+)
+
 # boost::dynamic_bitset
 add_library(boost_dynamic_bitset INTERFACE)
 target_include_directories(boost_dynamic_bitset INTERFACE
@@ -38,6 +59,23 @@ target_include_directories(boost_dynamic_bitset INTERFACE
     ${CMAKE_CURRENT_SOURCE_DIR}/deps/boost/type_traits/include
 )
 
+# sbd library
+find_package(BLAS REQUIRED)
+add_library(sbd INTERFACE)
+target_include_directories(sbd INTERFACE
+    ${CMAKE_CURRENT_SOURCE_DIR}/deps/sbd/include
+    ${MPI_CXX_INCLUDE_DIRS}
+    ${BLAS_INCLUDE_DIRS}
+)
+target_link_libraries(sbd
+    INTERFACE
+    ${BLAS_LIBRARIES}
+    OpenMP::OpenMP_CXX
+    MPI::MPI_CXX
+)
+
+add_definitions(-DH5_USE_XTENSOR)
+
 add_executable(sqd_tests
     test/doctest_main.cpp
     test/test_postselection.cpp
@@ -60,3 +98,16 @@ add_executable(sqd_benchmarks
 )
 target_include_directories(sqd_benchmarks PRIVATE deps/nanobench/src/include)
 target_link_libraries(sqd_benchmarks PRIVATE nanobench)
+
+add_executable(sqd-hdf5-chemistry src/sqd-hdf5-chemistry.cpp)
+target_include_directories(sqd-hdf5-chemistry
+    PRIVATE
+    ${xtensor_INCLUDE_DIRS}
+)
+target_link_libraries(sqd-hdf5-chemistry
+    PRIVATE
+    HighFive
+    boost_dynamic_bitset
+    sbd
+    MPI::MPI_CXX
+)

docs/index.rst

@@ -19,5 +19,6 @@ Table of Contents
 
    Compilation flags <compilation-flags>
    API Reference <apidocs/index>
+   Example app: tutorials <tutorials/index>
    GitHub <https://github.com/Qiskit/qiskit-addon-sqd-hpc>
    Release Notes <release-notes>

docs/tutorials/01_compile.rst

@@ -0,0 +1,51 @@
+Compile example app on the target machine
+=========================================
+
+Option 1: Manual compilation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Install dependencies
+^^^^^^^^^^^^^^^^^^^^
+
+- C++ compiler (must support C++17 or later)
+- cmake
+- MPI implementation
+- ...
+
+On RHEL systems, some of these can be installed with
+
+.. code:: sh
+
+    export sudo dnf install cmake mpich-devel
+
+Make sure ``mpicxx`` is in ``$PATH``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For instance, with ``mpich``, this may look like
+
+.. code:: sh
+
+    export PATH=/usr/lib64/mpich/bin:$PATH
+    export LD_LIBRARY_PATH=/usr/lib64/mpich/lib:$LD_LIBRARY_PATH
+
+Obtain the addon source code
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code:: sh
+
+    git clone https://github.com/Qiskit/qiskit-addon-sqd-hpc.git
+    cd qiskit-addon-sqd-hpc
+    git submodule update --init --recursive
+
+Build using ``cmake``
+^^^^^^^^^^^^^^^^^^^^^
+
+.. code:: sh
+
+    mkdir -p build
+    cd build
+    cmake ..
+    cmake --build . -j4
+
+Option 2: Compile using Spack
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~