Scientific Computing

Git uses per-user ~/.gitconfig, per-repository .git/config configuration files, and environment variables to customize Git behavior. The system gitconfig file is not covered here. A common pattern is a developer makes most of their settings in the per-user Git config file, occasionally overriding them in the per-repository config file.

We have several articles on Git configuration, leading to a per-user Git config file with sections like:

pull HTTPS for speed, push SSH for security

[url "ssh://github.com/"]
	pushInsteadOf = https://github.com/
[url "ssh://gitlab.com/"]
	pushInsteadOf = https://gitlab.com/
[url "ssh://gist.github.com/"]
	pushInsteadOf = https://gist.github.com/scivision/
[url "ssh://gitlab.kitware.com/"]
    pushInsteadOf = https://gitlab.kitware.com/

Use Meld for diff and merge

[diff]
	tool = meld
[merge]
	tool = meld

Maintain linear Git history with fast-forward only by default with pull.ff only

[pull]
    ff = only

Check upon “git push” if all Git submodules have first been “git push” before the consuming repository, to avoid broken builds for others with push.recurseSubmodules check

[push]
	recurseSubmodules = check

For any Git operation (except “git clone”) that changs references to Git submodules commit hashes, automatically update the Git submodules to match the new commit hashes with option submodules.recurse true

[submodule]
	recurse = true

Maintain default linear Git history with “git pull” by default allowing fast-forward only. If encountering a Git remote that cannot be fast-forwarded, the user can then either git rebase or git merge to resolve the conflict and / or create a merge commit.

git config --global pull.ff only

Git services such as GitHub allow enforcing linear history.

Reference: Git: rebase vs. merge

Downloading the latest release of CMake is usually easy. Admin / sudo is not required.

• Linux: snap install cmake
• macOS: brew install cmake
• Windows: winget install Kitware.CMake
• PyPI CMake package: python -m pip install cmake

For platforms where CMake binaries aren’t easily available, build CMake using scripts/build_cmake.cmake.

To see the merge requests for a certain release, use a URL like: https://gitlab.kitware.com/cmake/cmake/-/merge_requests?milestone_title=3.32.0&scope=all&state=all

CMake 4.3 additions include:

• Common Package Specification (CPS) officially supported. This provides a solution for the long-standing program of build system-agnostic JSON package configuration files, which can be generated by CMake’s install(EXPORT) and consumable by other build systems.
• cmake --version=json-v1 tells details of the libraries vendored into CMake, which is useful for debugging and reporting issues with CMake’s bundled dependencies. This is complementary to cmake -E capabilities which reports specific capabilities of the CMake.
• CMake command line and file(ARCHIVE_CREATE) commands can specify compression level and algorithm in more detail
• numerous generator string expressions were added

CMake 4.2 additions include:

• Visual Studio 18 2026 generator added
• cmake_language(TRACE) enables tracing just selected nestable portions of CMake script, which is important for debugging CMake projects due to the large volume of trace output.
• FASTBuild generator has impressive benchmarks. FASTBuild supports more modern platforms including Windows, versus ccache or distcc.
• ExternalProject added options to modify environment variables at each step by CONFIGURE_ENVIRONMENT_MODIFICATION, BUILD_ENVIRONMENT_MODIFICATION, INSTALL_ENVIRONMENT_MODIFICATION, TEST_ENVIRONMENT_MODIFICATION
• Target property SPDX_LICENSE

CMake 4.1 additions include:

• project() added COMPAT_VERSION that propagates to subdirectories and can be queried for the top-level COMPAT_VERSION.

CMake 4.0 additions include:

• CMAKE_LINK_WARNING_AS_ERROR boolean option sets most compilers to error if a compile warning occurs, which is generally a good setting for CI systems.
• target_link_libraries() can use a LINKER: prefix to abstract options.
• CMAKE_POLICY_VERSION_MINIMUM allows a user or project to call other projects that haven’t been updated to a newer CMake minimum version.
• SARIF output allows IDEs to better parse build status.
• CTest –interactive-debug-mode is particularly useful on Windows to enable debug dumps and error popup windows.

CMake 3.31 additions include:

• CMake warns if cmake_minimum_required() is < 3.10.
• TLS ≥ 1.2 is required by default for internet operations e.g. file(DOWNLOAD), ExternalProject, FetchContent, and similar.
• file(ARCHIVE_CREATE) gained a long-needed WORKING_DIRECTORY parameter that is essentially necessary to avoid machine-specific paths being embedded in the archive.
• CMAKE_LINK_LIBRARIES_STRATEGY allows specifying a strategy for ordering target direct link dependencies.

CMake 3.30 additions include:

• C++26 support.
• CMAKE_TLS_VERIFY environment variable was added to set TLS verification (true, false).
• defaults CMAKE_TLS_VERIFY to on, where previously it was off.
• CTest can use the --test-dir argument with --preset, which avoids needing to be locked into a specific build directory.

CMake 3.29 additions include:

• cmake_language(EXIT code) to exit CMake script mode with a specific return code. This is useful when using CMake as a platform-agnostic scripting language instead of shell script.
• Environment variable CMAKE_INSTALL_PREFIX is used to set the default install prefix across projects–it can be overridden as typical by cmake -DCMAKE_INSTALL_PREFIX= option.
• Target property TEST_LAUNCHER allows specifying a test launcher. For MPI program this allows deduplicating or making more programmatic test runner scripts.
• Linker information variables including CMAKE__COMPILER_LINKER_ID have been added to allow programmatic logic like setting target_link_options() based on the particular linker.
• ctest --parallel without a number or 0 will use unbounded test run parallelism.

CMake 3.28 additions include:

• changes PATH behavior for Windows find_{library,path,file}() to no longer search PATH. This may break some projects that rely on PATH for finding libraries. MSYS2-distributed CMake is patched to include PATH like earlier CMake, which can be confusing for CI etc. not using MSYS CMake with that patch. Windows CI/user may need to specify CMAKE_PREFIX_PATH like

  cmake -DCMAKE_PREFIX_PATH=$Env:SYSTEMDRIVE/msys64/ucrt64/lib -B build

• Support for C++20 modules is considerably improved and most users will want at least CMake 3.28 to make C++ modules usable.

• Generator expressions $<IF> $<AND> $<OR> now short circuit.

• Test properties now have a DIRECTORY parameter, useful for setting test parameters from the project’s top level CMakeLists.txt.

• CMake 3.28.4 fixed a long-standing bug in Ninja Fortran targets that use include statements.

CMake 3.27 additions include:

• emits warning for cmake_minimum_required(VERSION) < 3.5.
• CTest test properties TIMEOUT_SIGNAL_NAME and TIMEOUT_SIGNAL_GRACE_PERIOD specify a POSIX signal to send to a timed out test process.
• Interactive CMake debugger added by cmake --debugger is used with an IDE such as Visual Studio.
• CMake script command cmake_file_api() allows querying CMake File API from within CMake.

ℹ️ Note

Fortran + Ninja was broken for OBJECT libraries in CMake 3.27.0..3.27.8 and fixed in 3.27.9.

Older CMake changelog

The Matlab version can be obtained “brute force” by running Matlab, but this can take tens of seconds on a network drive system such as HPC.

matlab -batch "disp(version)"

A much faster way to get the Matlab version is to read the VersionInfo.xml file that is included in the Matlab installation directory. This file contains the version information in XML format, as is available at least back to Matlab R2016a.

This Python script quickly parses the VersionInfo.xml file to extract the Matlab version information without needing to run Matlab itself.

Environment variables that start with DYLD_ are restricted by macOS, and are not passed to child processes by default for security reasons. A workaround for this is to use a dummy environment variable that does not start with DYLD_, and then use a wrapper script to read that variable and set the DYLD_LIBRARY_PATH environment variable accordingly. This is necessary because DYLD_LIBRARY_PATH is read at program startup, and setting it within a program will not have any effect on the dynamic linker used by that program. The wrapper script can be used to set the DYLD_LIBRARY_PATH environment variable before executing the desired program, allowing it to find the necessary libraries without being blocked by macOS security restrictions.

Continuous integration (CI) systems generally rely on an integer return code to detect success (== 0) or failure (!= 0). The error() and assert() functions of Matlab / GNU Octave return non-zero status that works well with CI systems. The Matlab unittest framework is the primary method for testing Matlab code.

Matlab -batch option to run from the command line completely replaces -r and is more robust.

matlab -batch "assertSuccess(runtests)"

For pre-buildtool releases of matlab (< R2022b) we use a helper script that invokes runtests with appropriate parameters for the Matlab release used. To test across Matlab releases without a specific CI Matlab version fanout, we can use Python Pytest as in this wrapper script that tests Matlab from R2017a to R2025b and beyond.

There are several ways to reboot a computer from the terminal. For Linux or macOS the “reboot” command (or shutdown -r) is commonly used. For Windows, the PowerShell command Restart-Computer is a standard way to reboot the system from Terminal.

Within Windows Subsystem for Linux (WSL), the “reboot” command is only for the particular WSL instance and actually results in a shutdown of the WSL instance, not the entire Windows system. One can verify this by before and after the standard 8 second WSL shutdown time, running in Windows Terminal:

wsl.exe --list --running

The Anytone AT-5000 radio has three modes: Ham, HF, and CB. 99 memories are available in each of Ham mode and HF mode. 16 memories are available in CB mode (even after moving the jumper that enables Ham and HF modes). MEM channels are not shared between frequency modes, so there are 99 Ham and 99 HF channels and 16 CB MEM channels. The radio cover screws are T9 Torx.

Anytone AT-5000 quirks:

• “Dual watch” does not work in VFO mode, even from MEM channels. VFO is only available in Ham or HF profiles, and is how one would normally use the radio in HF or Ham mode.
• If a MEM channel is deleted from the scan list, it’s still scanned when scanning MEM channels. This seems like a firmware bug, present in a radio with LCD version 1.00, RF version 1.00, and radio data version 1.00. The “workaround” is to delete the channel from MEM, which is not so desirable but the only way we know how at this time.

CPS programming

Anytone (Qixiang Electronics) provides a programming cable for the Anytone AT-5000 radio, which connects via the 8P8C modular microphone jack to USB. This is a USB to serial adapter. If the comm port does not appear in the AT-5000 CPS software or in Device Manager under “Ports (COM & LPT)” as “USB-SERIAL CH340 (COMx)”, check Windows Device Manager under “Other devices” for “USB Serial” with a yellow warning icon.

The driver necessary is the GD USB Virtual Comm Port driver, which can be downloaded as part of the Anytone D878 programming software package if not seen as part of the Anytone AT-5000 CPS install package. Don’t install the D878 CPS software, just extract the Zip archive folder titled like “Virtual GD USB Com Drivers (Only If Needed)” and extract the “GD_VirtualComDriver v2.0.2.4944.rar” file to get the driver installer under the “x64” folder. After installing the driver, unplug and replug the programming cable. If it’s still showing a yellow warning icon, right-click on the “USB Serial” entry, select “Update driver”, and choose to browse for drivers on the computer by “let me pick from a list of available drivers on my computer”. Under USB Devices look for “USB-SERIAL CH340” and select it to install the driver. It might be necessary to unplug and replug the programming cable again after installing the driver for it to be recognized properly. There should no longer be a yellow warning icon, and the comm port should appear in the AT-5000 CPS software as “USB-SERIAL CH340 (COMx)” under the “Port” dropdown menu.

Workaround for CPS bugs

These bugs were present in the first release of the AT-5000 CPS software.

• Can’t add or edit memory channels: set the band and working band near the top of the Channel editing window to MEM. Each time a channel is edited, this may need to be done again
• Can’t delete memory channels: channels appear to be deleted, but appear again upon programming the radio. Simply delete them from the radio front panel instead

CMake can show the compile commands that will be issued to compile targets by setting the CMAKE_EXPORT_COMPILE_COMMANDS variable to ON. This generates ${CMAKE_BINARY_DIR}/compile_commands.json file that contains the JSON compilation database for each source file. However, this does not include the link commands used to link the final executable or library.

There are a couple ways to make the build system emit the link commands without actually yet linking the target:

Ninja JSON compilation database method

To show the compile and link commands in JSON compilation database format using Ninja for a specific target including target dependencies use the compdb-targets Ninja tool.

cmake -B build -G Ninja

cmake --build build -- -t compdb-targets MyTarget > compile_and_link_commands.json
# equivalent to
ninja -C build -t compdb-targets MyTarget > compile_and_link_commands.json

GNU Make or Ninja dry-run method

The Ninja compdb-targets method above is preferred, since the drawbacks of this “dry-run” method include:

• have to clean-first to show all the dependecies, otherwise if some dependencies have been built already, they won’t be shown in the output.
• the output is not in JSON format, so it may be harder to parse.

The -n dryrun flag shows the compile and link commands without executing them.

cmake -B build

cmake --build build --target mytarg --verbose --clean-first -- -n

Matlab preferences are stored in <prefdir>/matlab.mlsettings since Matlab R2020a. To reset Matlab preferences, one can rename / move this file–keep it for a backup. The location of <prefdir> can be found by running the following command in Matlab:

prefdir

After moving the matlab.mlsettings file, restart Matlab. Matlab will create a new matlab.mlsettings file with default preferences.

This is particularly helpful if Python is setup with a “bad” distribution that crashes Matlab upon Python py. commands in Matlab, and there isn’t another Python distribution available to switch to in Matlab’s preferences.

The matlab.mlsettings file is a ZIP file of XML and JSON files and folders.