Scientific Computing

A recent PyHC presentation given by Ian of US-RSE had a discussion where a few journals relevant to publishing research software were noted. We have used engrXiv for software preprints. Refereed journals include:

• JOSS: briefest, a summary of software
• Astronomy & Computing
• SoftwareX
• Data Science Journal

When using Intel oneAPI compilers on Windows, you may get a message like:

INTERNAL ERROR: pgopti_Create_Full_Path: buffer too small

This is probably caused by a filepath that’s more than 139 characters. You may not see the paths printed as being that long, because CMake with Ninja does preprocessing on each Fortran file that lengthens the filename.

The fix is to make the project paths shorter. Users may have to build code from a directory nearer the top of the filesystem hierarchy.

ExFAT is faster than NTFS by up to several percent hard drive write speed. ExFAT allows a hard drive to easily be read across operating systems. Windows Subsystem for Linux can read ExFAT drives. Formatting a disk deletes all data on the drive. The system hard drive %SYSTEMDRIVE% for Windows OS MUST be NTFS.

NOTE: If the hard drive is unformatted, it will not have a drive letter. Once sure the drive is empty or want to erase the contents to make it ExFAT, do this through Disk Management.

Format a drive to ExFAT from Windows Explorer by right-clicking on the drive to format and selecting “Format” → File System: “ExFAT”

Alternatively, format a drive to ExFAT from Command Prompt or PowerShell by:

format driveletter /FS:exFAT /Q

Format a drive to ExFAT from Disk Management by running diskmgmt.msc and right click the new drive → Format. If NTFS is the only option, use Windows Explorer to format to ExFAT after first formatting to NTFS here.

Switching to CMake from autotools or plain Makefiles gives generally better support of many operating systems, in particular Windows. Another benefit is generally faster speed of configuration and build. In 2020, MonetDB switched from autotools to CMake. They observed MonetDB with CMake builds in 40% of the original time. Note also the improvement due to Ninja instead of GNU Make.

We have converted a number of projects from autotools to CMake. Consider automated autotools to CMake script and then manually compare or redo by inspection of the autotools scripts.

In general, livestream data bandwidth depends on the video content (lots of motion vs. talking head) and wireless conditions.

YouTube Live has a wide range of livestreaming modes. Consider 480p to start to keep the connection from dropping out, with data bandwidth of 500 - 2,000 kbps ~ 16 Mbyte/minute. Use variable bitrate to dramatically reduce upload bandwith needed for typical livestreaming scenes. OBS Studio is among streaming software supporting HLS for ease and robustness or low latency RTMPS.

Hugo shortcodes are a powerful, easy way to template code used in blogs and websites. Ana Ulin describes a one-line Hugo shortcode to inline HTML in Hugo:

Under the top-level Hugo website Git directory, add file “layouts/shortcodes/rawhtml.html” containing:

{{.Inner}}

Then in the Markdown file for the particular blog post, do like (removing the space between the left brace and the left caret):

{{ < rawhtml >}}
<p>arbitrary HTML here</p>
{{ < /rawhtml >}}

This example demonstrates inline HTML in a Hugo Markdown page.

Compare files between Git branches with a GUI like VS Code or Meld, showing all files different between the current Git branch to another Git branch “develop”:

git difftool develop

Compare a single file to another Git branch “develop”:

git difftool develop -- src/myfile.c

For projects consisting of more than a few files, or of files in different code languages, it can sometimes be beneficial to only run certain workflows depending on which files changed. For example, consider a Fortran-based simulation where the CI takes minutes or hours to run, with associated Python plotting code. If only the plotting code is changed, it might not be necessary to CI the entire simulation, but instead test just the Python code. This can be arranged via separate .yml files under the repo’s .github/workflows/ directory.

Example: only run Python analysis script tests (say, under “scripts/”) when analysis scripts are changed. If Fortran code or Python interface scripts are changed, run other CI.

File .github/workflows/ci_scripts.yml

name: ci_scripts

on:
  push:
    paths:
      - "scripts/**.py"
      - .github/workflows/ci.yml
  pull_request:
    paths:
      - "scripts/**.py"
      - .github/workflows/ci.yml

jobs:

  linux:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout
    - uses: actions/setup-python
      with:
        python-version: '3.x'

    - run: pip install .
    - run: pip install flake8 mypy pytest

    - run: flake8
    - run: mypy

    - run: pytest

File: .github/workflows/ci.yml

name: ci

on:
  push:
    paths:
      - "**.f90"
      - "**.cmake"
      - "**/CMakeLists.txt"
      - ".github/workflows/ci.yml"
  pull_request:
    paths:
      - "**.f90"
      - "**.cmake"
      - "**/CMakeLists.txt"
      - ".github/workflows/ci.yml"

jobs:

  linux:
    runs-on: ubuntu-latest
    timeout-minutes: 5
    steps:
    - uses: actions/checkout
    - uses: actions/setup-python
      with:
        python-version: '3.x'

    - name: Install packages
      run: |
        sudo apt update
        sudo apt install --no-install-recommends gfortran libopenmpi-dev openmpi-bin

    - run: cmake -B build
    - run: cmake --build build
    - run: ctest --test-dir build -V

Matlab mustBeA is used in function argument validation to check that a variable is in one of multiple classes, instead of the single class coercion used by Matlab arguments block by default.

Simply create a file in the project directory “mustBeA.m”, or under private/mustBeA.m

function mustBeA(x, classes)
% for Matlab < R2020b
arguments
  x
  classes (1,:) string
end

mustBeMember(class(x), classes)

end

Matlab mustBeFile and mustBeFolder can fail to validate when the filename starts with a tilde “~”. Tilde is used by most terminal shells to indicate the user home directory. However, Matlab does not currently recognize tilde.

Workaround this issue with expanduser.m in the mustBe* call.

Example: myfun.m:

function myfun(A, B)
arguments
  A {mustBeA(A, ["string", "char"])}
  B (1,1) {mustBeNumeric}
end

...

end

A summary of public Windows Subsystem for Linux changes for the latest Windows Fast Ring build and recent builds is provided. A master listing of current build vs. Ring is also available.

Additional notes:

• Windows Subsystem for Linux release notes
• Windows Subsystem for Linux: About with link to issue trackers, presentations, etc.
• Microsoft Commandline Blog