Scientific Computing

LWN.net reports on changes to Python 3.13 urllib standard library. It was deduced that Apple rejected Python 3.12 apps due to a string in the Python stdlib that was rejected, regardless of code execution. There naturally was some very good discussion linked to in the LWN.net article that illustrates the conflict between closed commercial platforms with great financial might and open source software. The Python 3.13 patch has already been merged. A pull request backport patch for Python 3.12 has also been created, and illustrates the clean nature of the patch and new configure flag.

GitHub Actions jobs can dynamically set environment variables with job scope using a run: step to write the variable to an environment file.

Append to PATH: All job steps after the “run:” stanzas have the new PATH value “~/.local/bin” appended. Windows defaults to PowerShell.

- name: set Unix PATH
  if: runner.os != 'Windows'
  run: echo "${HOME}/.local/bin" >> $GITHUB_PATH

- name: set Windows PATH
  if: runner.os == 'Windows'
  run: echo "${HOME}/.local/bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append

Any environment variable can be set in this way. Example: set environment variables “CMAKE_INSTALL_PREFIX” and “CMAKE_PREFIX_PATH” to “~/libs” for the following job steps:

- name: set Unix
  if: runner.os != 'Windows'
  run: |
    echo "CMAKE_INSTALL_PREFIX=~/libs" >> $GITHUB_ENV
    echo "CMAKE_PREFIX_PATH=~/libs" >> $GITHUB_ENV

- name: set Windows
  if: runner.os == 'Windows'
  run: |
    echo "CMAKE_INSTALL_PREFIX=$HOME/libs" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
    echo "CMAKE_PREFIX_PATH=$HOME/libs" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append

GitHub Actions environment variables have distinct scopes:

• Workflow
• Job
• Step

It’s trivial to set static environment variables in each of these scopes. Dynamically setting environment variables is also possible.

Workflow

Set static workflow environment variables in GitHub Actions by using env: at the top level of a “.github/workflows/ci.yml” file like:

name: ci

env:
  CTEST_PARALLEL_LEVEL: 0
  CMAKE_BUILD_PARALLEL_LEVEL: 4
  CTEST_NO_TESTS_ACTION: error
  CMAKE_GENERATOR: Ninja
  CC: gcc

Job

Static job environment variables are set like:

jobs:

  base:
    runs-on: macos-latest

    strategy:
      matrix:
        cc: [gcc-13, clang]

    env:
      CMAKE_GENERATOR: Ninja
      CC: ${{ matrix.cc }}

Step

Set static step environment variables like:

    - run: cmake -B build
      env:
        CMAKE_GENERATOR: Ninja

MinGW brings GNU compiler tools to Windows since the late 1990s. MSYS2 provides numerous developer tools including MinGW on Windows using pacman package manager.

Install MSYS2 by downloading msys2-x86_64-*.exe and run the installer, installing to $HOME/msys64. MSYS2 needs to be on a non-FAT / non-ExFAT drive capable of symbolic links such as NTFS.

Start the MSYS2 console in the Windows Start menu. Update MSYS2 to get the latest packages in the MSYS2 terminal. Run this command multiple times until it says “nothing to do”.

pacman -Syuu

To use GCC and other MSYS2 / MinGW64 programs from PowerShell without disrupting other compiler use, create file “gcc.ps1” containing:

$r="$HOME/msys64/ucrt64"
$b="$r/bin"

$Env:CC="$b/gcc"
$Env:FC="$b/gfortran"
$Env:CXX="$b/g++"

# important to put UCRT first to avoid "collect2.exe: error: ld returned 116 exit status" and DLL Hell
$Env:Path = "$b;$Env:Path"

$Env:CMAKE_PREFIX_PATH="$r"

If MSYS2 was installed to the system drive like “C:/msys64” replace $HOME/msys64 with $Env:SystemDrive/msys64

When it’s desired to use MSYS from a PowerShell prompt run “gcc.ps1”.

From MSYS2 command prompt, search for packages like:

pacman -Ss gcc

MSYS2 packages of interest for scientific computing include: gcc, gdb, gcc-fortran, clang, boost, lapack, scalapack, HDF5, ninja, make, pkgconf, aspell. Install packages with environment prefix “mingw-w64-ucrt-x86_64-” for x86_64 Windows applications for example Gfortran “mingw-w64-ucrt-x86_64-gcc-fortran”. On ARM64 Windows, use “mingw-w64-clang-aarch64-” environment prefix for example Clang “mingw-w64-clang-aarch64-clang”.

You may need to reorder directories in the Windows Path variable. For example GNU Octave may need to be moved lower in the Path list or removed from Path.

If you find that MSYS2 is using more 500 MB, try clearing the package cache of old package versions

pacman -Sc

The MSYS2 latest package update feed shows recently updated packages. The MSYS2 Install reference is also useful. PowerShell per-session variable set is useful to set CC, FC, CXX to single intended compiler to build systems.

Alternatives

As compared to Cygwin, MSYS2 works from the Windows Command Prompt or PowerShell. MSYS2 provides native Window binaries. Cygwin does not have a command-line package installer.

Windows Subsystem for Linux is strongly supported, but does not give Windows binaries unless cross-compiling.

Clang, LLVM Flang Fortran compiler, GCC, Boost and many more packages are easily available on Windows via MSYS2. Clang is also available via direct download.

it’s often useful to have separate development environments for each compiler. The Powershell script “clang.ps1” creates a Clang LLVM environment. We don’t permanently put Clang on the user or system PATH to avoid DLL conflicts. Running “clang.ps1” in Powershell enables Clang until that Powershell window is closed.

For MSYS2 Clang and LLVM Flang Fortran compiler, create “clang.ps1” like:

$r="$Env:SystemDrive/msys64/ucrt64"
$b="$r/bin"

$Env:CC="$b/clang"
$Env:CXX="$b/clang++"
$Env:FC="$b/flang"

# important to put UCRT first to avoid "collect2.exe: error: ld returned 116 exit status" and DLL Hell
$Env:Path = "$b;$Env:Path"

$Env:CMAKE_PREFIX_PATH="$r"

For standalone (non-MSYS2) Clang make “clang.ps1” like:

$Env:CC="clang"
$Env:CXX="clang++"
$Env:Path = "$Env:ProgramFiles/LLVM/bin;$Env:Path"

If you need to use the MSVC CL-like clang driver clang-cl, create “clang-cl.ps1” and run it when desired.

$Env:CC="clang-cl"
$Env:CXX="clang-cl"
$Env:Path = "$Env:ProgramFiles/LLVM/bin;$Env:Path"

HDF4 is a predecessor to the industry-standard HDF5 data file format. This HDF4 CMake example shows how to build and link HDF4 seamlessly with Fortran example code.

Users and developers might accidentally build a program or library without optimizations when they are desired. This could make the runtime 10 to 1000 times or more slower than it would be with optimizations. This could be devastating in computational cost on HPC and cause needless schedule delays. Programmatically detecting or using a heuristic to determine if a program was built with optimizations can help prevent this. Such methods are language-specific.

• CMake, NDEBUG is set if CMAKE_BUILD_TYPE is Release or RelWithDebInfo.
• Meson: NDEBUG is set if buildtype is release or debugoptimized with

project(..., default_options: ['b_ndebug=if-release'])

C / C++

There is currently no universal language standard method in C / C++ to determine if optimization was used on build. The presence of macro NDEBUG is used by the standard library to disable assertions. One could use if NDEBUG is defined as an indication if optimizations were used.

bool fs_is_optimized(){
// This is a heuristic, trusting the build system or user to set NDEBUG if optimized.
#if defined(NDEBUG)
  return true;
#else
  return false;
#endif
}

Fortran

If the Fortran code is compiled with preprocessing, a method using NDEBUG as above could be used. Fortran iso_fortran_env provides functions compiler_version and compiler_options. These could be used in a fine-grained, per compiler way to determine if optimizations were used.

Python

Distributed Python environments would virtually always be optimized. One can use heuristic checks to help indicate if the Python executable was built in debug mode. I am not yet aware of a universal method to determine if the CPython executable was built with optimizations.

import sysconfig

debug = bool(sysconfig.get_config_var('Py_DEBUG'))

HDF5 command line tools h5dump and h5ls are handy to quickly explore HDF5 files from the command line. Backup link to old documentation. They are particularly useful when accessing a remote computer such as HPC where the HDF5 files may be very large and would take a while to transfer to a local computer.

h5ls provides a high-level look at objects in an HDF5 file. Typically we start examining HDF5 files by printing the dataset hierarchy:

h5ls --recursive my.h5

Determine the filters used (e.g. was the data compressed):

h5ls --verbose my.h5

h5dump can print the entire contents of an HDF5 file to the screen. This can be overwhelming, so we typically print only the headers to start:

h5dump --header my.h5

Individual variables can be printed like:

h5dump --dataset=myvar my.h5

Determine the filters used (e.g. was the data compressed):

h5dump --properties --header --dataset=myvar my.h5

Related: HDF5 data GUI

Mid-range radio control (1 km to 10+ km) and other data telemetry has long been legal in the 27 MHz 11m band across the world. In the USA, FCC Rules Part 95 subpart C addresses 27 MHz data transmissions. 27 MHz is still actively used for data telemetry, with manufacturers claiming up to 15 miles range with a 10 Watt 27.255 MHz data FSK transceiver. Another long-time 27 MHz data telemetry application is 27 MHz paging.

Wireless mice and keyboards in the early 2000’s decade widely used the 27 MHz band. Unfortunately those devices operating on 27.195 MHz “19A” would significantly interfere with the popular CB channel 19 27.185 MHz, and could be heard even just driving by a house with a CB radio in the vehicle. Likewise for the other 27 MHz channels that bleed across several CB radio channels if in a neighboring house or passing within say 50 meters of a CB radio. This is due to the liberal emissions mask of FCC Part 95.779(a) allowing significant bleedover of unwanted modulation products into adjacent channels. Thankfully, these 27 MHz mice and keyboards have limited users these days. 27 MHz mice and keyboards are still sold as low-end inexpensive devices, so they might still be heard in some locales.

The data telemetry or mouse/keyboard transmissions typically use FSK modulation. On an AM receiver, FSK might sound like a quiet transmission with little modulation. Using an FM receiver, FSK typically sounds like a loud buzz or tone.

Detecting band openings in the 10m, 11m, and 12m radio bands can be done by listening to popular frequencies in these bands. The 10m and 12m bands are licensed amateur radio bands capable of global communications when ionospheric conditions are favorable. The 11m band is license-free and typically has more users such that an amateur radio operator may listen to 11m to determine if 12m and/or 10m are also experiencing enhanced skywave propagation.

A good 10m frequency to listen to is in the vicinity of 28.074 MHz and 28.078 MHz, which are the FT8 and JS8call suppressed carrier frequency as tuned in upper-sideband (USB) mode. This can be tuned by a converted CB radio in AM mode on 28.075 MHz. An AM mode radio tuned to 28.075 MHz will hear a seemingly random series of tones with a 15 second interval. The tones heard in an AM receiver come from multiple FT8 or JS8Call signals heterodyning.

For 12m, listen to FT8 / JS8Call USB 24.915 MHz or USB 24.922 MHz. If only having a converted AM CB radio, tune 24.915 MHz or 24.925 MHz.

11m DX frequencies to monitor include:

• AM 27.025 MHz (CB channel 6, high powered calling frequency)
• AM 27.185 MHz (CB channel 19, road calling channel)
• AM 27.065 MHz (CB channel 9, Spanish language calling frequency in Central and South America)
• FM 26.805 MHz (FM 11m DX calling frequency)
• USB 27.245 MHz (CB channel 25, JS8Call frequency)