Scientific Computing

Docker images are useful for reproducibility and ease of setup and for software binary distribution on platforms not natively available on GitHub Actions runner images. While one can setup a custom Docker image, it’s often possible to simply use an existing official image from Docker Hub.

This example GitHub Actions workflow uses the Alpine Linux image with the MUSL C library to build a statically-linked binary.

name: alpine-musl

on: [push]

jobs:
  musl:
    container: alpine

    steps:
    - uses: actions/checkout@v4

    - name: install build tools
      run: apk add --no-cache ninja-build cmake gfortran openmpi-dev

    - name: print MUSL version
      continue-on-error: true
      run: ldd --version

    - name: CMake configure
      run: cmake -B build

    - name: CMake build
      run: cmake --build build

# Good idea to ensure self-tests pass before packaging
    - name: CMake test
      run: ctest --test-dir build

(Optional) If a CPack archive is desired add step:

    - name: CMake package
      if: success()
      run: cpack --config build/CPackConfig.cmake

The binary artifact or CPack archive can be uploaded by step upload-artifact:

    - name: .exe for release
      uses: actions/upload-artifact@v4
      if: success()
      with:
        name: my.exe
        path: build/my.exe

Some folder locations in macOS are not accessible by traversing one level at a time from outside or above that location. In general, it can be convenient to open a terminal window at a specific folder location. The folder may be opened directly by right-clicking on the folder in Finder and selecting “New Terminal at Folder”.

By default, listing the contents of a directory with PowerShell shows file metadata along with the path names within the directory. Other shells typically show only the path names by default, which is convenient for copy-pasting lists of files or directories into other commands or scripts. To list only the path names when listing a directory in PowerShell, use the -Name option:

Get-ChildItem -Name

# or

ls -Name

The POSIX function nanosleep() is not available on Windows with MSVC and certain MinGW architectures. This implementation of nanosleep() for Windows uses Waitable Timer Objects. The clock tick for Windows is 100 ns. The practical achievable timer resolution on Windows is in the millisecond range. This presents a floor on the accuracy achievable for sleep timers. Virtual Machine running of Windows makes the sleep accuracy significantly worse.

In general across general-purpose operating systems, high accuracy sleep timer performance is not guaranteed. For high accuracy sleep timers (i.e., beyond what is needed for gaming and abstract high-level control of hardware interfaces), consider using a real-time operating system (RTOS) or a dedicated microcontroller.

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OpenMP and OpenACC are open standards for parallel programming on CPU and GPU shared memory platforms. While OpenMP has wider compiler support, OpenACC also aims to be portable across compilers and computing architectures. OpenMP standard syntax for C, C++, Fortran, and CUDA can work seamlessly with non-OpenMP systems if code is properly written. While OpenMP is typically built in from the factory in contemporary compilers, the compilers may need flag(s) to enable OpenMP. Build systems like CMake and Meson can manage the OpenMP compiler flags.

OpenMP is well-supported in commercial computation performance-oriented Fortran compilers like:

• Intel oneAPI
• NVIDIA HPC SDK
• AOCC

OpenMP support in open-source Fortran compilers includes LLVM and GCC.

Open-source compilers such as LLVM Flang need to have the proper OpenMP-enabling flags set when building the compiler by the distribution maintainers. For example, Homebrew LLVM Flang was missing Fortran libomp.mod support due to misconfiguration in the Homebrew flang formula.

Examples of Fortran OpenMP code:

• Fortran OpenMP
• C++, Fortran OpenMP

“git clone” clones the default branch of the remote repository as determined by the Git server. The default Git branch is typically “main”, but the repository owner can change it to any other branch. To Git clone a specific branch, use the –branch option:

git clone --branch <branch-name> <repository-url>

This can help workaround problems like a default branch that is very large or is broken in some way.

Symbolic links are useful in any operating system to shorten long, complicated path names like C:/user/foo/data to just C:/data. If encountering problems with user permission, set user permission to create symbolic links on Windows.

Powershell symbolic link creation syntax:

New-Item -ItemType SymbolicLink -Path "Link" -Target "Target"

# for example:
New-Item -ItemType SymbolicLink -Path "my_program.exe" -Target "path/to/my_program.123.exe"

# also for directories:
New-Item -ItemType SymbolicLink -Path "my_fun_dir" -Target "path/to/my_dir"

For clarity, specify the full path to the target file or directory. Especially avoid target “.” or “..” as these can be confusing.

Symbolic links on Windows are a type of Reparse Points. fsutil can tell the type of reparse point:

fsutil reparsepoint query "my_fun_dir"

Reparse Tag Value : 0xa000000c

The reparse tag value corresponds to a symbolic link IO_REPARSE_TAG_SYMLINK.

Python test_symlink.py shows symlinks using Python standard library pathlib.

App Execution Alias

fsutil reparsepoint query $Env:LOCALAPPDATA/Microsoft/WindowsApps/wt.exe

Reparse Tag Value : 0x8000001b

The reparse tag value 0x8000001b is a Windows App Execution Alias IO_REPARSE_TAG_APPEXECLINK. App Execution Aliases are not symbolic links, but are a way for Windows CreateProcess to find the correct executable to run from a user-friendly name like “wt.exe” or “bash.exe”.

Not every language works with App Execution Aliases at this time–Java io and nio don’t work with App Execution Aliases currently. Python does work with App Execution Aliases, for example:

python -c "import shutil; print(shutil.which('wt.exe'))"

Unix-like shell

On a Unix-like shell including WSL, softlinks are created like:

ln -s target link

The Windows error code lookup tool is a useful resource for finding error codes and messages to incorporate into code that needs to handle Windows return codes. The tool allow searching by code or exact message match.

Unit test frameworks should be lightweight to setup and maintain. End users should be able to easily run the unit and integration tests themselves as part of a typical end-user install.

The simplest approach is to write several small test programs and execute them using CMake or Meson. This method can also be an appropriate choice where the program uses complex library interactions that may not mix well with a generic test framework.

The Veggies Fortran test framework is an example of a Fortran unit testing framework. Check the Fortran-lang group for a contemporary discussion on Fortran test frameworks.

Git commands can be lengthy, but Git autocorrect can help with command typos.

git config --global help.autocorrect prompt

This prompts with a suggestion for a mistyped Git command.