Scientific Computing

HDFView is a Java-based application to view, create, and modify HDF5 files in a tabular format. HDFView can also make 1-D (line) plots and 2-D (raster) plots of the data in an HDF5 file. For example data see Neon.

To view a plot of data, right click on the dataset name and select “Open As” and then set the parameters to view the data. It’s important to use a recent version of HDFView, as a long-time issue especially with Linux distributions is having old, broken versions of HDFView. A typical problem with old HDFView versions is that HDFView won’t start.

Overleaf paid accounts can edit Overleaf LaTeX documents offline and Git push / pull with Git direct to Overleaf. Direct Git access does not require special GitHub permissiongs and works with GitLab, GitHub, Bitbucket, etc.

Once the procedure below is done, you’ll be able to:

git push

push local changes (after git commit) to Git provider and Overleaf simultaneously

git push provider

push local changes to only Git provider

git push origin

push local changes to only Overleaf

git pull

pull from Overleaf

For simplicity, this procedure assumes the LaTeX project is existing on Overleaf to start. Starting with a project from the Git provider is more complicated since Overleaf cannot accept force push.

Connect existing Overleaf to Git Hosting provider

Check your current Overleaf LaTeX repo

cd ~/Dissertation
git remote -v

You should see:

origin  https://git.overleaf.com/hash (fetch)
origin  https://git.overleaf.com/hash (push)

Create a new repo Dissertation in the Git hosting provider. Do not create any README, LICENSE, or .gitignore. Then connect Git provider as origin:

git remote add provider ssh://git.invalid/username/Dissertation

git remote set-url origin --add --push https://git.overleaf.com/hash
git remote set-url origin --add --push ssh://git.invalid/username/Dissertation

Verify Overleaf git remote setup

Verify setup by

git remote -v

should be like

provider ssh://git.invalid/username/Dissertation (fetch)
provider ssh://git.invalid/username/Dissertation (push)
origin  https://git.overleaf.com/<hash> (fetch)
origin  ssh://git.invalid/username/Dissertation (push)
origin  https://git.overleaf.com/<hash> (push)

Notes

• SSH Public Key Authentication is in general recommended for Git (besides Overleaf)
• One can simultaneously use Overleaf, GitLab, Dropbox, OneDrive, Bitbucket. Just remember to NOT put a LaTeX Git project into a synced Dropbox / OneDrive folder or you’ll get synchronization errors.

LaTeX code highlighting is possible using the “minted” package, which uses Pygments as a backend. To install minted:

tlmgr install minted

python -m pip install pygments

If using a GUI, the “–shell-escape” option may need to be added. In TeXmaker / TeXstudio, under “Options → Configure → Commands” add --shell-escape right after the compiler executable.

When using TeXLive, the “tlmgr” program allows installing many LaTeX-related packages. For example, to enable Tikz diagrams via \usepackage{tikz}, install the “pgf” package:

tlmgr install pgf

Packages can also be added to TeXLive by the GUI TeX Live Manager. Under Package List select Status: All.

Generally LaTeX bibliographies can use clickable URLs if the LaTeX document specifies:

\usepackage{hyperref}

and for software, data, etc. entries that don’t have a specific type in the bibliography style:

@misc{myref1,
author={lorem ipsum},
note={\url{https://github.invalid/user/repo}}
}

Note that HTML percent “%” codes do not work. The HTML percent must be translated to their ASCII character. For example, %3A is “:” colon.

On Windows computers, after upgrading software or having left the computer on for days since last reboot (closing lid and reopening included), a memory Access Violation may occur:

• exit code “-1073741819”
• hex code 0x0005
• Exception Code: 0xC0000005

The simplest and most common fix is to simply reboot the Windows computer.

We see these errors also during software development when building or configuring the build system such as CMake. Looking at the build directory file CMakeConfigureLog.yaml can provide more insights into the issue.

The world is full of inexpensive USB charging adapters. Since the adapters connect to AC mains power, a very large amount of energy is available that can result in damage to the device or even the home / office the charger is in under catastrophic failure. Since nearly every person in the world needs multiple USB charge adapters, the manufacturers compete aggressively on size and price. This leads the OEMs to be tempted to cut back on safety and interfere-reducing components.

Ethical and responsible manufacturers find a way to keep the quality and safety circuitry intact, and may even go beyond the chip manufacturer and safety regulator requirements. These extra measures help protect the charger brand image. A distinct retailer known for quality USB charger adapters is IKEA. It’s speculated that since they’re putting their own brand on the charger, IKEA is perhaps taking notable care to ensure the chargers don’t damage devices or the surroundings.

Unix-like shells typically have a syntax that allows running a command with one or more environment variables having values that don’t persist after the command. For example, in Unix-like shells:

CC=clang CXX=clang++ make

Runs the program “make” with environment variables CC and CXX temporarily set. Subsequent commands use the original value, if any, of CC and CXX.

In PowerShell this syntax doesn’t directly exist, but can be effected like:

pwsh -c { $env:CC="clang"; $env:CXX="clang++"; make }

Another example:

PowerShell:

pwsh -c { $env:hi="hello"; python -c "import os; print(os.getenv('hi'))" }

Unix-like shell:

hi="hello" python -c "import os; print(os.getenv('hi'))"

YaML is used by GitHub Actions workflow expressions. The “if” conditional logic for a task uses comparison operators that also work to compare strings, especially useful for version numbers.

jobs:

  core:

    strategy:
      matrix:
        release: [R2022a, R2023b]

    steps:

    - name: Run
      if: ${{ matrix.release >= 'R2022b' || matrix.release == 'latest-including-prerelease' }}
      ...

On Windows, program faults can cause an modal window to appear regarding reporting the issue to Microsoft. This window stops automated scripts from further progress. This is a problem for long-running programs or scripts that call other programs, perhaps on a Task Schedule.

Disable Windows Reporting modal windows on Windows Pro and non-Pro by simply opening “services.msc” and disable “Windows Error Reporting Service”.

Windows Pro only

Alternatively, for Windows Pro:

Press ⊞+r and type

gpedit.msc

Go to Computer Configuration → Administrative Templates → Windows Components → Windows Error Reporting and configure as desired.

Reference