Scientific Computing

grep is a ubiquitous command-line tool for searching plain-text data sets for lines that match a regular expression. Ripgrep is a modern alternative to grep that is designed to be faster and more efficient at recursive text file searches common to code developers. Ripgrep is used internally by VS Code for its search functionality.

Install ripgrep with:

• Windows: winget install BurntSushi.ripgrep.GNU
• macOS: brew install ripgrep
• Linux: apt install ripgrep or similar

The rg command is used to invoke ripgrep, and it supports a wide range of options for customizing search behavior.

Examples:

Search for the term “TODO” in all .cpp files in the current directory and its subdirectories:

rg "TODO" --glob "*.cpp"

Case-insensitive search:

rg -i todo

Show line numbers and filename only:

rg -n TODO

Search only certain file types:

rg TODO -g "*.cpp" -g "*.hpp"

Include hidden and ignored files (like .gitignore):

rg TODO --hidden --no-ignore

Literal string search (not regex):

rg -F a+b*c

List only matching file names:

rg -l TODO

Show files that do not match:

rg -L TODO

Valgrind is a dynamic analysis tool that can detect memory leaks and other problems in programs including C, C++, and Fortran. Valgrind is available on Linux and BSD for x86 and ARM CPU architectures.

For macOS on Intel x86 CPUs, Valgrind is available in Homebrew.

For macOS on Apple Silicon ARM64 CPU, Valgrind can be used from an aarch64 Linux virtual machine in native mode for best performance. There is a development fork of Valgrind for Apple Silicon, but it may not yet ready for production use.

Weather radio broadcast alerts USA NOAA NWR are receivable on dedicated 162 MHz weather (WX) radio receivers. Many two-way communications radios such as CB radio, GMRS, and MURS can also have 162 MHz WX radio receiver capability. The advantage of these alerts is that mobile phone service is not required, just a small portable radio and a clear path to the WX radio transmitter, so audio alerts are heard only when a selected hazard type is determined to be in the area.

162 MHz WX radio is a one-way broadcast radio service carrying weather information and emergency alerts across much of the USA and Mexico. Unfortunately, the Canada WX radio service was shutdown in March 2026. Currently, Canadian weather broadcasts use the Coast Guard Continuous Marine Broadcast (CMB) to relay weather information. When determining which WX channel to receive on, it can be confusing because there is no standard WX channel number to 162 MHz frequency mapping. Use the NOAA USA search to find nearby WX radio transmitter frequencies.

WX radio channel number to frequency mapping: a common practice is to start with the lowest frequency and go up across the 7 WX radio frequencies. This is perhaps the most common channel number to frequency mapping.

Non-sequential channel order is used by some CB radios such as Radioddity / Anytone radios made by Qixiang.

Comparing reception performance on a known frequency vs. a handheld radio can give a quick indication that an antenna system is working OK, even if, as with 27 MHz CB radio, the designed antenna frequency is far from the 162 MHz weather radio frequency. Comparing WX radio reception on a CB radio with base or mobile antenna versus a handheld radio on the same 162 MHz WX radio frequency indicates that the CB radio antenna coax is perhaps not severely damaged or lossy, and the radio is working OK.

Modern receivers may allow arbitrary VFO tuning. This is important in Canada, where marine weather broadcasts are not always on WX radio frequencies. Some WX radios are 10 channel and may include frequencies like 161.650 MHz, 161.775 MHz and 163.275 Mhz or such, which may help in Canada, but other VHF frequencies are also used for weather broadcasts, so VFO tuning is important to receive all broadcasts.

On macOS, when started from the Applications icon, Matlab does NOT source shell configuration files. Any environment variables set in these files such as those added by package managers like Homebrew or Conda will not be available in the Matlab environment.

On macOS, only if Matlab is started from the Terminal like /Applications/MatlabR20*.app/bin/matlab will Matlab source the shell configuration file, leading to the expected environment variables as default in an interactive login shell also available in Matlab.

• .matlab7rc.sh,
• ~/.zshrc or ~/.bashrc.

Instead of depending on how the user launched Matlab, a more uniform approach is to have users set environment variables in the Matlab startup.m script, which will be sourced regardless of how Matlab is launched. Set desired environment variables in the Matlab startup.m script like:

edit(fullfile(userpath,'startup.m'))

Add lines like

setenv('PATH', [getenv('HOMEBREW_PREFIX') '/bin/' pathsep getenv('PATH')])

We recommend not running system() scripts in startup.m unless truly necessary to avoid delaying Matlab startup time or affecting startup stability.

Then programs installed by Homebrew like CMake, GCC, etc. will be on Path environment variable in Matlab.

Note that the Matlab commands below only affect commands within that same command line:

!source ~/.zshrc && ls

system("source ~/.zshrc && ls")

In larger projects, one might not remember if they or a colleague has opened or commented on a prior Issue topic. To search the issues by a username, use this search syntax in the GitHub Issues search bar:

• Issue created by a user:

is:issue author:username

• Issue commented on by a user:

is:issue commenter:username

Note that the search term is not user:.

This maps into the GitHub API as a query parameter:

?q=is:issue+author:username

For example at the Bootstrap project for one’s self “@me”:

https://github.com/twbs/bootstrap/issues?=q=is%3Aissue+author%3A%40me

C has long had the __FILE__ macro, which expands to a string literal containing the name or path to the current source file. C++ provides a much more powerful mechanism to programmatically determine the source file location via source_location in the <source_location> header introduced in C++20. This capability is particularly powerful for logging and debugging, as shown in the example linked above that a function’s caller can be located by source file and line number without the caller needing to explicitly pass that information.

Sometimes when opening the Matlab Desktop, the Command Window where one types commands might not be visible. This can be restored from the “Home” tab on the top ribbon, click the “Layout” button on the Environment section, and click “Two Column (default)”. Notice that one can also “Save Layout” to store the current layout for future use and easily select between layout suitable for different tasks.

At the the writing, UTM didn’t have a known way to work with RISC-V, so we use QEMU directly on macOS (or Linux). Obtain QEMU - on macOS via brew install qemu or on Linux via the package manager (e.g. apt install qemu). We need a uboot.elf. One way to get it is from a Linux machine or VM if on macOS by apt install u-boot-qemu and then copy the file from /usr/lib/u-boot/qemu/riscv64/uboot.elf to the machine where you want to run QEMU.

cp /usr/lib/u-boot/qemu-riscv64_smode/uboot.elf ~/uboot.elf

Then obtain the Ubuntu LTS RISCV image.

Extract the image like:

unxz ubuntu-24.04.4-preinstalled-server-riscv64.img.xz

It’s important to increase the disk size, otherwise the image will run of space quickly when installing compilers etc. Add say 10 GB of virtual HD space by:

qemu-img resize -f raw ubuntu-*-preinstalled-server-riscv64.img +10G

Then run QEMU like (perhaps make a little script):

img=$HOME/riscv_vm/ubuntu-24.04.4-preinstalled-server-riscv64.img
uboot=$HOME/riscv_vm/uboot.elf

qemu-system-riscv64 \
-machine virt -nographic -m 2048 -smp 4 \
-kernel ${uboot} \
-device virtio-net-device,netdev=eth0 -netdev user,id=eth0 \
-device virtio-rng-pci \
-drive file=${img},format=raw,if=virtio

This should boot the Ubuntu image and in a few minutes get to the login prompt. The default username is ubuntu and the password is ubuntu.

When using Git pre-commit hooks with the wide range of files typical of scientific computing, it may occur that the hooks modify files that should be excluded, such as FITS files that have a text header and a binary data part. Exclude such files by using case-insensitive regex patterns in the .pre-commit-config.yaml file by top level exclude key, for example to case-insensitively exclude files with the .fit or .fits extension, use:

exclude: (?i)\.fits?$

Because it’s considered an anti-pattern to have a global pre-commit config, such exclusions and all other pre-commit configuration on a per-repo basis.

To compile legacy Fortran code, certain compiler flags can be used to enable non-standard Fortran syntax that was common before the Fortran 95 standard became widely adopted. It’s hard to pin an exact year for when developers transitioned to more standard Fortran code, but the mid-2000s is a reasonable estimate for when Fortran codebases started to modernize in significant numbers. Gfortran took over from g77 as the default Fortran compiler circa 2005 and was the first widely used free Fortran compiler capable of the Fortran 95 standard. Here are legacy-enabling flags for currently maintained Fortran compilers.

In addition to the flags below, it may be necessary to provide default real and / or integer precision flags to compile old code that relies on the default precision being different than the modern default of 4 bytes for real and 4 bytes for integer.

GNU GFortran

• -std=legacy enables pre-Fortran 77 arbitrary length arrays, where A(1) was declared instead of A(*) in Fortran 77 or A(:) in modern Fortran.
• -fdec- options enable various non-standard extensions in the DEC Fortran style.
• see also Gfortran runtime options for issues reading binary files.

LLVM Flang

Flang compiler flags have a “-std” option that might be checked to see if the project sets it too restrictively.

Intel oneAPI

• -nostand does not change compiler behavior–it disables standard-based warnings.
• -f66 apples Fortran 66 semantic rules, including Do loops that always run at least once.

IBM OpenXL

• -qlanglvl=extended disables compiler language level checks, and is the default.
• several more options may be employed if needed for compatibility

Cray Fortran

The ftn compiler can disable some checks with flags like -d C