Scientific Computing

Intel oneAPI is a useful, performant compiler for CI with the C, C++, and Fortran languages. oneAPI compilers give useful debugging output at build and run time. If having trouble determining the oneAPI APT package name, examine the APT repo Packages file on the developer computer like:

curl -O https://apt.repos.intel.com/oneapi/dists/all/main/binary-amd64/Packages.gz

gunzip Packages.gz

less Packages

This examples oneAPI GitHub Actions workflow works for C, C++, and Fortran.

Matlab .mltbx toolbox packaged toolbox format is proprietary to Matlab. Oftentimes we desire to distribute a Matlab package as a set of .m source files instead. To add a “toolbox” or “package” to Matlab and use functions from that toolbox requires using “addpath” or “import” Matlab syntax. This example makes those paths persistent in Matlab and Octave, using example toolbox directories ~/mypkg1 and ~/mypkg2.

Normally use addpath() instead of cd(). Do not put brackets or braces around the multiple paths.

Prepend a package to the Matlab path by editing the startup.m file from Matlab or Octave:

edit(fullfile(userpath,'startup.m'))

put in addpath() commands to the desired Matlab packages paths like:

addpath('~/mypkg1','~/mypkg2')

Restart Matlab/Octave and type

path

and the new toolbox directories will be at the top.

Matlab requires compilers for mex -setup langage used (C / C++ / Fortran) and Matlab Engine for the respective code language. Windows Matlab supported compiler locations are communicated to Matlab via environment variables.

One-time setup MEX:

mex -setup C
mex -setup C++
mex -setup Fortran

Inspect Matlab MEX parameters:

mex.getCompilerConfigurations('c')
mex.getCompilerConfigurations('c++')
mex.getCompilerConfigurations('fortran')

It’s possible to switch between compilers that are setup with MEX. Choosing compilers is generally not possible on Linux or macOS from within Matlab. If a oneAPI version compatible with Matlab is installed on Windows, Matlab may detect it and allow switching compilers. If a different compiler is detected and allowed by Matlab, commands to choose the compiler will be at the bottom of the output when using the “mex -setup” commands below.

If having trouble with mex -setup for example if setup fails on macOS like:

“sh: /var/folders/…/mex_…: No such file or directory”

Try running the mex -setup command from Terminal using Matlab batch mode to see if Matlab’s shell was breaking setup. This usually fixes the setup issue. In our cases, we found that environment variables MATLAB_SHELL and SHELL were already set appropriately (not the generic /bin/sh), but we still had to run the mex -setup command from Terminal.

matlab -batch "mex -setup C -v"
matlab -batch "mex -setup C++ -v"
matlab -batch "mex -setup Fortran -v"

Once MEX is working, consider using Matlab buildtool build system for simple, terse syntax to build and test MEX and Matlab Engine code.

Windows MinGW MEX

Using MinGW on Windows with Matlab requires having an exact version of MinGW supported by Matlab. For example, the version of MinGW with MSYS2 is generally not supported by Matlab.

Tell Matlab the supported MinGW compiler path via Windows environment variable MW_MINGW64_LOC.

Find the MinGW compiler location from PowerShell:

(Get-Item((Get-Command gfortran.exe).Path)).Directory.parent.FullName

This would be something like “C:\msys64\ucrt64”.

Put that path in Matlab:

setenv('MW_MINGW64_LOC', '<path of gcc.exe>')

Do “mex -setup” as above.

C MEX Example

Compile built-in C example

mex(fullfile(matlabroot,'extern/examples/mex/yprime.c'))

Run

yprime(3, [4,2,7,1])

ans = 2.0000 5.9924 1.0000 2.986

Fortran MEX example

Compile built-in Fortran example:

mex(fullfile(matlabroot,'extern/examples/refbook/timestwo.F'))

Run:

timestwo(3)

ans = 6.0

Matlab might not use newly-compiled MEX functions if the function cache is not cleared. This can happen when the MEX function was previously called before building the MEX code. Detect if the MEX implementation of a function is being used in memory:

function y = is_mex_fun(name)
  y = endsWith(which(name), mexext());
end

Example: Matlab function timestwo.m and optionally MEX compiled function also called timestwo.

function y = timestwo(x)
  disp("this is plain Matlab script")
  y = 2 * x;
end

If one builds the MEX function with the same name and then calls the function, Matlab may not use the MEX compiled version until the function cache is cleared. Clear the Matlab function cache, thereby enabling newly-compiled MEX functions to be used by command

clear functions

% or

clear all

% then

assert(is_mex_fun("timestwo"))

These commands do NOT clear the function cache:

% these don't help
rehash
rehash path
clear mex

Eavesdropping / injection vulnerabilities allow unencrypted wireless mouse connection to be used as a keyboard by attackers to inject unwanted keystrokes, possibly taking over your PC. Force pairing allows unauthorized input to the PC. Logitech device firmware has distinct per-OS update procedures.

On Windows, the Logitech Unifying software:

winget install Logitech.UnifyingSoftware

is used to update firmware and pair receivers with mice and keyboards. In Logitech Unifying software click Advanced → Update Firmware

On Linux, fwupd supports updating Logitech Unifying receivers. Modern Linux distros will raise a prompt to seamlessly update Logitech receiver firmware.

On Linux, check firmware version and pair devices to the Logitech Unifying receiver with Solaar.

Fwupd: list all recognized devices, including firmware versions where applicable:

fwupdmgr get-devices

For C or C++ projects with incorrect #define logic or due to compiler bugs, it may be necessary to avoid CMake internally set definitions like -DNDEBUG. CMake internally sets -DNDEBUG when the CMAKE_BUILD_TYPE is set to Release, RelWithDebInfo, or MinSizeRel.

This can be done in scope like:

string(REPLACE "-DNDEBUG" "" CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE}")
string(REPLACE "-DNDEBUG" "" CMAKE_C_FLAGS_RELWITHDEBINFO "${CMAKE_C_FLAGS_RELWITHDEBINFO}")
string(REPLACE "-DNDEBUG" "" CMAKE_C_FLAGS_MINSIZEREL "${CMAKE_C_FLAGS_MINSIZEREL}")

remove_definitions(-DNDEBUG) does not work here because -DNDEBUG is set internal to CMake.

The same may be accomplished per target by manipulating target COMPILE_DEFINITIONS:

get_target_property(_cf my_target COMPILE_DEFINITIONS)

string(REPLACE "-DNDEBUG" "" _cf "${_cf}")

set_target_properties(my_target PROPERTIES COMPILE_DEFINITIONS "${_cf}")

In general, Matplotlib figures look better with constrained_layout. The older tight_layout is not as flexible and can lead to overlapping text, particularly with “suptitle”.

To make figures with subplots and suptitle work better, use:

matplotlib.pyplot.figure(layout='constrained')

# or

matplotlib.figure.Figure(constrained_layout=True)

Example:

import matplotlib.pyplot as plt

fg = plt.figure(layout='constrained')
ax = fg.subplots(3, 1)

for i in range(3):
    ax[i].plot(range(5+5*i))

fg.suptitle('lots of lines')

plt.show()

These are CMake MRs (Merge Requests) that have been or may be merged. They are not yet in a CMake release, but they may be included in future releases.

• ExternalProject set environment variables for each of the configure, build, test, and install steps. Previously this was a cumbersome syntax invoking cmake -E env or similar.
• Fix Windows Console handling: CMake 4.1 aims to enable CMake Windows color console output and fix long-standing race conditions in Windows Console handling.

Xarray can write and load netCDF4 files into datasets. Warning messages may appear when using older netCDF4 files with newer versions of Xarray or NumPy like:

RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject

This may indicate underlying incompatibilities between the versions of Xarray, Pandas, NumPy, and the netCDF4 library.

Advantages of conda over pip include:

• distributing per-platform optimized libraries
• prioritized channels resolve version conflicts, helping mitigate Python package dependency hell

Conda channel priority order is ordered by which channel appears first (highest) in .condarc. We generally recommend adding per-environment channels rather than modifying the global configuration to avoid corrupting multiple environments with incompatible packages`.

In general “strict” channel priority is recommended to mitigate compatibility problems.

conda config --set channel_priority strict

conda config --get channel_priority

Add a conda per-environment channel:

conda activate <env-name>

conda config --env --add channels <channel-name>

Get the current channel list for an environment:

conda activate <env-name>

conda config --env --show channels