Scientific Computing

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

Microsoft until 2024 provided Windows virtual machine images at

https://developer.microsoft.com/en-us/windows/downloads/virtual-machines

Currently, there are Windows 11 Enterprise evaulation ISO images that require setup and install, versus the easier to use VM images previously available. Ensure that the ISO image is for the correct CPU architecture (x86-64 or ARM64) or else the ISO won’t work or may run agonizingly slow.

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

ReactOS gives a free, open-source Windows 2003 API level replacement that can use USB devices. Sometimes Linux users need to use a Windows VM when USB devices are required in Windows programs. ReactOS can work in a VM for older Windows programs with a much smaller install than Microsoft Windows.

Install ReactOS in a virtual machine with the VirtualBox version recommended in ReactOS install procedure. Create a new VM with name “ReactOS”, which should auto-populate needed settings.

When installing, use FAT file system instead of buggy, experimental BTRFS at this time. Disable JavaScript in ReactOS Firefox browser as ReactOS might hang at 100% CPU for JavaScript intensive websites. Type about:config in Firefox address bar and Toggle javascript.enabled to false.

ReactOS advantages vs. Windows:

• ReactOS installation takes 90% less space than Windows
• no OS license maintenance with free, open-source ReactOS
• no licensing worries about making many copies of a working ReactOS install. Get a VM working and copy it to many workstations.
• ReactOS theme feels like Windows XP, so there are few concerns about transitioning users reluctant to change

ReactOS Limitations:

ReactOS 0.4.x API level is Windows NT 5.2 (Windows 2003 / XP). Programs requiring Windows NT 6.0 (Vista) or newer will likely not run. Current versions of Python do not work with ReactOS 0.4.x due to the Windows NT 5.2 API level. Consider trying an older version of the program you want to install that is still noted to work with Windows XP when using ReactOS.

NT 6.x API Windows Vista support is important as many programs, including open source programs, have left Windows NT 5.x unsupported and non-functional for their programs.

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