Scientific Computing

Matplotlib / Matlab log axis plots

In Python Matplotlib or Matlab, making a plot with log-scaled (instead of default linear-scaled) axes can use the functions like “loglog()”, “semilogx()”, or “semilogy()”. Here we show the more general object-oriented syntax for each of a 2-D line “plot()” and 2-D pseudocolor “pcolor()” and then set the axes scale properties.

We arbitrarily use log abscissa scale and linear ordinate scale, but the same syntax applies to other combinations.

Python

2-D line plot:

import numpy as np
from matplotlib.pyplot import figure, show

x = np.logspace(0, 10, 100)
y = np.log(x)**2

fg = figure()
ax = fg.gca()

ax.plot(x, y)
ax.set_xscale('log')

ax.set_xlabel('x')
ax.set_ylabel('y')

show()

pseudocolor pcolormesh(): observe the stretching of the ticks along the y-axis. In some cases it’s helpful to set the axis limits manually to avoid whitespace past the last data point.

import numpy as np
from matplotlib.pyplot import figure, show

d = np.random.rand(10, 10)
x = np.linspace(1, 10, d.shape[0])
y = np.logspace(0, 1, d.shape[1])

fg = figure()
ax = fg.gca()

ax.pcolormesh(x, y, d)
ax.set_yscale('log')
ax.set_ylim(y[0], y[-1])

ax.set_xlabel('x')
ax.set_ylabel('y')

show()

Matlab

2-D line plot:

x = logspace(0, 10, 100);
y = log(x).^2;

fg = figure();
ax = axes(fg);

plot(ax, x, y);
ax.XScale = 'log';

xlabel(ax, 'x');
ylabel(ax, 'y');

pseudocolor pcolor(): observe the stretching of the ticks along the y-axis. In some cases it’s helpful to set the axis limits manually to avoid whitespace past the last data point.

d = rand(10, 10);
x = linspace(1, 10, size(d, 1));
y = logspace(0, 1, size(d, 2));

fg = figure();
ax = axes(fg);

pcolor(ax, x, y, d);
ax.YScale = 'log';

xlabel(ax, 'x');
ylabel(ax, 'y');

Troubleshooting DNS problems

If one suspects a website has been compromised, don’t use a standard web browser to access the site as there could be zero-day malware on the site. Consider Terminal programs that don’t have JavaScript enabled like curl or lynx if necessary to browse the site, preferably from a VM or other isolated computing resource. These programs are also not immune from security vulnerabilities.

DNSViz helps visualize the DNS chain. Keep in mind DNS and nameserver updates can take minutes to hours to propagate.

macOS:

dscacheutil -q host -a name host.invalid

Linux / macOS / WSL:

dig +trace host.invalid

If the DNS entries seem valid, consider that the web hosting server (that sends the HTML files to browser) may be compromised.

Compile Matlab .m code executable

Matlab Compiler compiles existing .m Matlab script to run as an executable on another PC without Matlab. Matlab Compiler Runtime MCR is used on computers that don’t have Matlab to run the compiled Matlab code.

Caveats:

  • Matlab Compiler does not in general speedup Matlab code execution
  • in general, compiled binaries might be disassembled to reverse-engineer the underlying code
  • MCR version on each computer running the executable must match the Matlab version of the compiling Matlab, and the compiling computer must have the same operating system as the MCR running computers.

Compiling computer: ensure Matlab Compiler is installed:

assert(license('test', 'compiler') == 1)

Example program “mymcc.m”:

function Y = mymcc()

X = 0:0.01:2*3.14;
Y = sin(X);
plot(X,Y)
title('Test of MCR')
xlabel('x')
ylabel('y')
disp('I ran an MCR program!')

end

Compile “.m” file in Matlab:

mcc -m -v mymcc.m

Run compiled Matlab program:

./run_mymcc.sh mymcc

I ran an MCR program!

and show a Matlab plot window showing a sine wave. Close the plot window to end the execution of your program.


Notes:

Reference

GNU Octave does not currently have the ability to compile “.m” files. Octave mkoctfile is to distribute C / C++ code that calls Octave functions–and ABI-compatible Octave must be installed on the user computers

Using Intel oneAPI and MKL with CMake

There can be substantial speed boosts from Intel compilers with Intel CPUs. Intel oneAPI gives advanced debuggers and performance measurements. Intel oneMKL can give a significant speed boost to ABI-compatible compilers for certain math operations.

For Windows, use the oneAPI Command Prompt. Otherwise, specify environment variables CC, CXX, FC to indicate desired compilers via script:

Build with CMake:

cmake -B build

cmake --build build

Example CMakeLists.txt

To see the compiler commands CMake is issuing, use

cmake --build build -v

Refer to Intel Link Advisor for supported compiler / operating system / MKL combinations.


Get runtime confirmation that MKL is being used via MKL_VERBOSE.

  • Linux:

    MKL_VERBOSE=1 ./mytest
  • Windows

    set MKL_VERBOSE=1
    mytest.exe

That gives verbose text output upon use of MKL functions. That runtime option does slow down MKL performance, so normally we don’t use it.

Apple Silicon virtual machines

Native virtualization has a “guest” OS with the same CPU architecture as the “host” physical CPU. Non-native emulation generally runs slower than native virtualization. Non-native virtualization means a host computer (such as Apple Silicon) can emulate any supported CPU architecture. Apple Silicon is ARM64, but with virtualization such as UTM / QEMU the Apple Silicon CPU can emulate ARM32, x86_64, MIPS, RISC-V, PowerPC, and more within the container.

QEMU emulator is available on Homebrew for Apple Silicon and can emulate a different CPU architecture or run native architecture at nearly full performance. UTM is a containerized emulation based off of QEMU for iOS and macOS–like QEMU, the same CPU architecture is virtualized at near full performance, while non-native virtualization is emulated with slower performance. When creating a new virtual machine in UTM, the first questions include whether the VM will be virtualized (native) or emulated (non-native) and the CPU architecture. UTM works with native virtualized Windows 11 for ARM, Linux, and emulates many architectures, even old PowerPC macOS guest images.

VirtualBox is an open-source native virtualization application that generally targets x86_64 CPUs. VirtualBox “Developer Preview” for Apple Silicon is available from the Nightly Builds as “macOS/ARM64 BETA”. The Oracle developer notes that the VirtualBox Apple Silicon beta is not yet ready for production use.


Commercial paid Apple Silicon virtualization: these native virtualization applications are not open-source. They run native virtual machines on Apple Silicon including Windows 11 ARM.

  • Parallels is paid-only software
  • VMWare Fusion is paid software, but has a no-cost personal-use license for home users.

GUI viewers for HDF5 / NetCDF4 data

HDF5 is a popular data container format, a filesystem within a file. Many programs supporting HDF5 like Matlab can read and plot data. It is useful to have a standalone simple data browser like HDFview.

HDFview from the HDF Group can read HDF5, NetCDF4, and FITS. HDFview enables editing (writing) as well as reading HDF5. One can simply download the HDFview binaries, or use package managers:

  • Linux: apt install hdfview
  • macOS: brew install hdfview

ViTables is a Python-based HDF5 GUI.


The Java-based PanoplyJ is available for macOS, Linux and Windows.

CMake compiler flag precedence

To ensure the user set compile flags take precedence by appearing later in the command line vs. CMake’s automatic flags, use add_compile_options to set language-specific or project-wide compiler options. target_compile_options is similar, but applies to only one target.

The generator expression $<$<COMPILE_LANGUAGE:C>:...> is used to only add the flag for the C language. This is important as many compiler options are language-specific, particularly for C / C++ and Fortran projects.

If one truly needs to wipe out all CMake automatic flags, try settingCMAKE_FLAGS variable to an empty string.

Matlab arguments validation

Matlab function arguments validation syntax is generally recommended over legacy validateattributes() and inputParser(). Function arguments validation specification coerces the input and/or output variables to the class declaration given if possible, and errors otherwise.

  • Default values are easily specified, which required such verbose syntax before.
  • only a single class can be specified
  • recall the .empty method of most Matlab classes e.g. datetime.empty() that allows initializing an empty array.

Matlab argument validation syntax coerces class at runtime.

Git default text editor

Git uses the EDITOR environment variable to determine which text editor to use for commit messages. Since the commit message editing is typically small and simple, it may be desired to set a distinct text editor just for Git. This is done via Git global config:

git config --global core.editor "nano"