Scientific Computing

If upon attempting Pacman operations a failure occurs like:

failed to synchronize all databases (unable to lock database)

This may occur if the system was interrupted during a Pacman operation, leaving a lock file that prevents further package management operations. The lock file is located by:

$(pacman-conf DBPath)/db.lck

which is typically “/var/lib/pacman/db.lck”. Check no other Pacman process is running:

ps -ef | grep pacman

Then the Pacman lock file can be removed:

rm $(pacman-conf DBPath)/db.lck

Anecdotally we have observed that during GitHub outages, Git over SSH operations may have a better chance of succeeding than Git over HTTPS operations. This includes cloning repositories.

Rather than reconfiguring .gitconfig to use SSH, simply clone using the SSH URL instead of the HTTPS URL.

For example, instead of:

git clone https://github.com/user/repo.git

Assuming Git over SSH is setup on the computer:

git clone git@github.com:user/repo.git

The CMake variable CMAKE_GENERATOR can be used with GitHub Actions to specify the Visual Studio 18 2026 generator. Currently, the runner image GitHub Actions runner image windows-2025-vs2026 is used until the “windows-latest” runner image incorporates VS 2026.

jobs:

  msvc:
    runs-on: windows-2025-vs2026

    steps:
    - uses: actions/checkout

    - name: Print CMake version
      run: cmake --version

    - name: Configure CMake
      run: cmake -B build -G "Visual Studio 18 2026"

    # and so on

CMake build directories might contain 100s of megabytes of files for large projects. Over time, a developer computer might contain forgotten build directories that waste disk space. With Python, a script using send2trash allows safe removal of CMake build directories by first moving them to the OS trash/recycle bin. In distinction from shutil.rmtree, this send2trash approach allows recovery of files if the deletion was accidental. The heuristic used to detect a CMake build directory was inspired by ctest_empty_binary_directory.

use mpi_f08 is recommended for Fortran across computing platforms, including Windows.

For native x86 (Intel / AMD CPU) binaries, currently only free Intel oneAPI has mpi_f08 for Fortran. As time progresses and ARM64 CPUs are increasingly widespread, including for Windows PCs, and the complexity / disk space requirements of setting up Visual Studio for Intel oneAPI on Windows, it may be better (easier, faster, performance) to use WSL for Windows MPI. WSL can use OpenMPI or MPICH to access mpi_f08. For Windows ARM CPU users, WSL is the only straightforward option for mpi_f08 in Fortran.

The setup-wsl GitHub Action configures WSLv2 environment in Windows GitHub Actions runners. This allows testing certain quirks and corner cases one might encounter when running software on Windows Subsystem for Linux. For scientific computing Windows users, WSL is often the best way to run computational software on Windows, including software using performance code for GPU and MPI.

Git projects using submodules can be set to default shallow Git clone submodules to save space and time. Edit the “.gitmodules” file to have the “shallow = true” option for each Git submodule. This is particularly useful when the top-level project uses third party libraries or libraries with a large Git revision history.

Example .gitmodules file with shallow Git submodules:

[submodule "proj1"]
	path = proj1
	url = https://github.invalid/nobody/proj1
    shallow = true

Then Git clone with the --recurse-submodules option or Git submodule update with the --init --recursive options:

git clone --recurse-submodules <url>

or if already Git cloned

git submodule update --init --recursive

performs a shallow clone of the Git submodules.

Confirm that the submodules are shallow cloned by checking the Git log of the submodule:

git -C ./proj1 rev-parse --is-shallow-repository

These each return “true” indicating that the submodule is shallow cloned.

USB-C dock display adapters (HDMI, DisplayPort) are generally seen as a preferable replacement for proprietary docking ports on old bulky laptops. A symptom is USB-C adapter works on one laptop, but not on another almost identical laptop model.

For Apple hardware, USB-C docks might only work with DisplayPort connection, not HDMI. This may be because some USB-C docks use “DisplayPort Alternate Mode”, which macOS seems not to recognize with an HDMI connection even on the same monitor that works with a DisplayPort cable connection.

General symptoms across hardware and operating systems include the dock display not being detected by the operating system, to showing a black screen, or very low resolution.

The solution seems to be to stick with expensive OEM display adapters, or at least long established brands. The temptation of a cheap adapter can quickly turn to frustration or botched presentations. Another thing to watch for is cheap adapters may fail intermittently when using more than one high bandwidth feature. For example, using Gigabit Ethernet and HDMI on the cheap USB-C adapter simultaneously may fail intermittently during a conference call or teaching a class, which can be frustrating.

Workarounds

Some adapters that charge the laptop with a USB-C input for power may experience improper operations if the display adapter is plugged into the laptop while the USB-C power input is powered. This problem may persist upon re-plugging the adapter to laptop and/or power cycling the monitor and laptop. A workaround we’ve found is to unplug USB-C power input to the adapter, plug into the laptop with all the desired accessories, then finally plug USB-C power input into the adapter. That is unexpected, but has worked for us sometimes.

The COMMENT field of CMake’s add_custom_target() is intended to print messages during the build. However, this field is a no-op when using CMake Generators like Ninja and GNU Make. To reliably print messages during the build regardless of the Generator used, create a custom echo command using CMake’s built-in cmake -E echo functionality.

set(_out ${PROJECT_BINARY_DIR}/output.txt)

add_custom_target(
    COMMAND ${CMAKE_COMMAND} -E touch ${_out}
    COMMAND ${CMAKE_COMMAND} -E echo "Touch ${_out}"
)

Major projects with CPU arch-specific code may distribute binaries for multiple CPU architectures for operating systems. Apple Silicon or Microsoft Prism are key examples of emulated binaries. Programs, especially computational programs like Anaconda Python should have the native matching CPU arch software installed. Example code to programatically check if a C++, GNU Octave, Matlab, or Python executable on:

• Apple Silicon is using native or Rosetta
• Windows on ARM64 is using native or Prism