Scientific Computing

Intel oneAPI / oneMKL includes Scalapack. MKL Scalapack library & include files are found under the MKLROOT environment variable. Scalapack MKL is used in CMake via MKLConfig.cmake (found under $ENV{MKLROOT}/lib/cmake/MKLConfig.cmake) like:

set(ENABLE_BLACS true)
set(ENABLE_SCALAPACK true)

set(MKL_INTERFACE "lp64")
# "lp64" is the 32-bit interface, "ilp64" is the 64-bit interface

set(MKL_SYCL_MPI false)
set(MKL_SYCL_LINK false)
# for Intel oneAPI 2025.2, we don't need SYCL

find_package(MKL CONFIG REQUIRED)

add_executable(mytest main.f90)
target_link_libraries(mytest PRIVATE MKL::MKL_SCALAPACK)

The MKL_SYCL* variables control whether SYCL is enabled for Intel oneAPI 2025.2 and later, which usually we don’t want.

The exact link flags and compile flags (that are automatically handled by MKLConfig.cmake) for a particular system are obtained from Intel Link Line Advisor.

Intel MKL Scalapack example project

Netlib Scalapack examples can also be used with non-MKL Scalapack.

While we generally recommend using WSL for MPI on Windows, MS-MPI is available and works with MSYS2 / MinGW GCC Gfortran on Windows. MSYS2 is a popular choice to use GCC, Clang and many other developer tools from the Windows Command Prompt, PowerShell or the MSYS Terminal itself.

Continuous Integration for Windows MPI applications on GitHub Actions is accomplished as in fortran-mpi-examples Windows CI workflows. Set inter-step environment variables using GitHub Actions environment files.

GNU Octave and other interactive terminal program use GNU Readline for command line editing. If the Readline library is incompatible with GNU Octave, it may become unusable by not being able to type in GUI or non-GUI modes. A workaround for non-GUI mode only is to disable interactive console input like:

octave --no-line-editing

For example Readline 8.3 has a known bug with a patch already released.

SSH-agent remembers SSH Public Key authentication, which can be time-limited by the user. This avoids the user having to type the password for each SSH connection, especially relevant to using Git over SSH. Windows has SSH built-in from Microsoft including SSH-agent. WSL also can use SSH-agent within each of the WSL images. SSH-agent works well with Git over SSH.

To use SSH-agent, add SSH keys like:

ssh-add ~/.ssh/mykey

This will persist the key in the SSH-agent until the SSH-agent is stopped, the user logs out,or the key is removed.

Remove all SSH-agent keys from RAM (if desired):

ssh-add -D

List all SSH-agent keys loaded:

ssh-add -L

Time limit for SSH-agent keys

Except for Windows, a time limit can be set for how long the key is remembered:

ssh-add -t 30m ~/.ssh/mykey

-t 30m

remember authentication for a period of time (here, 30 minutes)

Currently, the OpenSSH implemenation of SSH-agent on Windows does NOT support the -t option. If the -t option is used on Windows, it will fail like:

Could not add identity <key>: agent refused operation

Each operating system has a distinct method of enabling SSH-agent.

Windows SSH-agent

SSH-agent can be enabled from PowerShell. Note that the OpenSSH Client and OpenSSH server must both be installed.

Check if Windows SSH-Agent is running:

Get-Service ssh-agent

Start SSH Agent:

Set-Service -StartupType Automatic -Name ssh-agent

Start-Service ssh-agent

if status of Windows SSH-Agent in Powershell is “Running” then SSH-agent should be working.

Get-Service ssh-agent

If you still have trouble, try setting the permissions for the $HOME/.ssh directory more conservatively with this Powershell script.

Linux SSH-agent

For Linux, including Windows Subsystem for Linux:

Add to ~/.profile:

if [ -z "$(pgrep ssh-agent)" ]; then
   rm -rf ${TMPDIR}/ssh-*
   eval $(ssh-agent -s) > /dev/null
else
   export SSH_AGENT_PID=$(pgrep ssh-agent)
   export SSH_AUTH_SOCK=$(find ${TMPDIR}/ssh-* -name agent.*)
fi

macOS SSH-agent

On macOS, SSH-agent is enabled by default.

SSH agents can have vulnerabilities, as noted for Windows and Linux.

Related: Disable Gnome Keyring SSH Agent

reference

GNU Data Language (GDL) can use GDLDE Workbench GUI for graphical development.

Download and install GDL.

• Windows: installer includes GDLDE Workbench: gdlsetup-Windows-x86_64-standard.exe. Simply install and look in Windows Start menu for “GDL Workbench”
• macOS: use weekly Release gdl-macOS-arm64-standard.dmg
• Ubuntu Linux: apt install gnudatalanguage

Download and extract GDLDE.

Matlab CI is often a better choice than Octave below.

Cross-platform developers run into numerous compatibility issues. Rather than wait for frustrated users to report such a bug, use continuous integration.

Here are CI templates using GNU Octave tests of .m code. Octave oruntests() is incompatible with the advanced functionality of Matlab runtests(),

GitHub Actions: “.github/workflows/ci.yml”:

name: ci

on:
  push:
    paths:
    - "**.m"
    - ".github/workflows/ci.yml"

jobs:

  linux:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout

    - run: |
        sudo apt update
        sudo apt install --no-install-recommends octave

    - run: octave --eval "test_myfuncs"
      working-directory: tests

  windows:
    runs-on: windows-2025
    steps:
    - uses: actions/checkout
    - run: winget install GNU.Octave --disable-interactivity --accept-source-agreements --accept-package-agreements

    - run: octave --eval "test_myfuncs"
      working-directory: tests

WinGet can be used on Windows GitHub Actions runners where a Windows program needs to be installed. In this example, environment variable FFMPEG_ROOT tells Python where to find the ffmpeg.exe program. One could more generally append to the GITHUB_PATH environment variable.

jobs:
  windows:
    runs-on: windows-2025

    steps:

    - name: install prereqs (Windows)
      if: runner.os == 'Windows'
      run: winget install ffmpeg --disable-interactivity --accept-source-agreements --accept-package-agreements

    - name: FFMPEG_ROOT Windows
      if: runner.os == 'Windows'
      run: echo "FFMPEG_ROOT=$env:LOCALAPPDATA/Microsoft/WinGet/Links/" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append

    - name: PyTest
      run: pytest

import functools
import shutil
import os


@functools.cache
def get_exe(name: str) -> str:

    for p in (os.environ.get("FFMPEG_ROOT"), None):
        if exe := shutil.which(name, path=p):
            return exe

    raise FileNotFoundError(name)

GNU Octave offers the syntax of Matlab in an open-source software suite. Octave binaries are readily installed:

• macOS: brew install octave
• Windows: winget install GNU.Octave
• Linux: Flatpak

For Linux, Flatpak may already be installed by the Linux distro. The flathub repo is added by:

flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo

Matlab Addons are packages / toolboxes that can be installed into Matlab. Addons may come from the Mathworks or third-party developers. One can disable non-Mathworks addons to ensure that the project code works as expected in diverse environments.

Check Matlab Addon packages installed:

addons = matlab.addons.installedAddons;

disp(addons)

Disable a non-Mathworks addon by the matlab.addons.disableAddon function. It isn’t possible to disable Mathworks addons; the following results:

Enable/Disable not supported for MathWorks products, MathWorks toolboxes, or support packages.

Check logical status of the addon:

matlab.addons.isAddonEnabled("MyCustomAddon")

If alert boxes (like “note”, “warning”) are not built into a site’s Hugo theme, they can be added with a bit of CSS and partial template.

Edit / add to the Hugo site as in this Gist to enable alert boxes.