Reimplement build system

.gitignore

@@ -1,10 +1,224 @@
-# Exclude binary files
+# Prerequisites
+*.d
+
+# Object files
 *.o
-*.so
+*.ko
+*.obj
+*.elf
+
+# Linker output
+*.ilk
+*.map
+*.exp
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
 *.a
-*.mod
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
 *.exe
-**/__pycache__
-doc/*
-build*/*
-include/version.h
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
+*.su
+*.idb
+*.pdb
+
+# Kernel Module Compile Results
+*.mod*
+*.cmd
+.tmp_versions/
+modules.order
+Module.symvers
+Mkfile.old
+dkms.conf
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# VSCode
+.vscode/
+
+# Custom build options file
+custom.cmake
+
+# Build directories
+*build*/

.gitlab-ci.yml

@@ -56,11 +56,11 @@ cmake-config-nvidia:
     before_script:
         - export NVARCH=`uname -s`_`uname -m`
         - export NVCOMPILERS=/opt/nvidia/hpc_sdk
-        - export PATH=$NVCOMPILERS/$NVARCH/2023/compilers/bin:$PATH
+        - export PATH=$NVCOMPILERS/$NVARCH/2024/compilers/bin:$PATH
     script:
         - mkdir build_nvidia
         - cd build_nvidia
-        - cmake -DCMAKE_C_COMPILER=`which nvc` -DCMAKE_CXX_COMPILER=`which nvcc` -DCMAKE_Fortran_COMPILER=`which nvfortran` -DCMAKE_BUILD_TYPE=RELEASE -DHDF5_ROOT=/opt/nvidia/hdf5-1.12.2 ..
+        - cmake -DCMAKE_C_COMPILER=`which nvc` -DCMAKE_CXX_COMPILER=`which nvcc` -DCMAKE_Fortran_COMPILER=`which nvfortran` -DCMAKE_BUILD_TYPE=RELEASE -DWITH_HDF5=FALSE ..
     artifacts:
         paths:
             - build_nvidia
@@ -87,10 +87,11 @@ compile-C:
     script:
         - cd build
         - make C_test_programs
-        - make utility_programs
+        - make openmmpol_utils
     artifacts:
         paths:
             - build/bin
+            - build/app
     only:
         - pushes
         - schedules
@@ -130,10 +131,11 @@ compile-C-intel:
     script:
         - cd build_intel
         - make C_test_programs
-        - make utility_programs
+        - make openmmpol_utils
     artifacts:
         paths:
             - build_intel/bin
+            - build_intel/app
     only:
         - schedules
 
@@ -177,10 +179,11 @@ compile-C-nvidia:
     script:
         - cd build_nvidia
         - make C_test_programs
-        - make utility_programs
+        - make openmmpol_utils
     artifacts:
         paths:
             - build_nvidia/bin
+            - build_nvidia/app
     only:
         - schedules