Scientific Computing

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.

This process to install GNU Radio on the Raspberry Pi assumes:

• Raspberry Pi OS is installed on the headless Raspberry Pi.
• At least a 16 GB filesystem in the Raspberry Pi.
• Raspberry Pi 3 or newer, as GNU Radio can tax the CPU and IO of modest ARM processors. GNU Radio requires at least an ARMv7 processor. However many applications benefit from Raspberry Pi 4 or newer. Get at least the 4 GB RAM model.

Install GNU Radio. This takes more than 10 minutes even with a fast SD card.

apt install gnuradio gnuradio-dev git

For Red Pitaya with Raspberry Pi GNU Radio, also install

apt install gr-hpsdr

Configure the Red Pitaya for six HPSDR receivers

If needed, rename Ethernet interface to eth0

wpa_supplicant reference

Git uses the GIT_EDITOR environment variable to determine the text editor to use for commit messages. Alternatively, to keep the editor configuration in the ~/.gitconfig file, set the Git text editor via the core.editor configuration variable. This is done via Git global config:

git config --global core.editor "nano"

Most environment variable have alphanumeric names and don’t need any special consideration to access. On Windows, some important programs still use the “Program Files (x86)” directory, denoted by environment variable “ProgramFiles(x86)”.

cmake_minimum_required(VERSION 3.10)

set(px $ENV{ProgramFiles\(x86\)})

message(STATUS "${px}")

Most other code languages don’t have any particular issues using environment variables named with special characters.

All of the following print like:

C:\Program Files (x86)

Matlab:

getenv("ProgramFiles(x86)")

Python:

python -c "import os; print(os.environ['ProgramFiles(x86)'])"

C++:

#include <cstdlib>
#include <iostream>

int main()
{
    std::cout << std::getenv("ProgramFiles(x86)") << "\n";
    return EXIT_SUCCESS;
}

Fortran:

program env

implicit none

integer :: i
character(100) :: path

call get_environment_variable('ProgramFiles(x86)', path, status=i)
if (i/=0) error stop "env var ProgramFiles(x86) not found"

print '(a)', path

end program env

Matplotlib plots with datetime axes can benefit from rotating axes tick labels or concise tick labels to avoid overlapping text.

Example code used in this post with synthetic data:

from matplotlib.pyplot import Figure
import matplotlib.dates as mdates
from datetime import datetime, timedelta

def datetime_range(start: datetime, end: datetime, step: timedelta) -> list[datetime]:
    """like range() for datetime"""
    return [start + i * step for i in range((end - start) // step)]

t = datetime_range(datetime(2021, 1, 1), datetime(2021, 1, 2), timedelta(minutes=30))
y = range(len(t))

Rotate datetime tick labels

If rotating tick labels, the overall axes typically need to be positioned to allow for the rotated labels, otherwise the tick labels can be cut off the figure edges. The axes position is updated automatically with constrained_layout option of figure().

import matplotlib.pyplot as plt

fg = plt.figure(layout='constrained')
ax = fg.gca()

ax.plot(t, y)
ax.set_xlabel('time')
ax.set_ylabel('y')
ax.tick_params(axis="x", labelrotation=30)  # arbitrary rotation amount

plt.show()

Matplotlib date formatting

Matplotlib datetime axes have numerous formatting options. Here we show the ConciseFormatter, which may avoid the need to rotate tick labels.

import matplotlib.pyplot as plt

fg = plt.figure(layout='constrained')
ax = fg.gca()

ax.plot(t, y)
ax.set_xlabel('time')
ax.set_ylabel('y')

ax.xaxis.set_major_formatter(
    mdates.ConciseDateFormatter(ax.xaxis.get_major_locator()))

plt.show()

If a DLL conflicts with a programs needed DLLs, the program may quit with a specific message, or it may silently exit. The return code may correspond to segfault or other error. To help see if a DLL conflict is occurring, use gdb to run the program. This works even for general programs that weren’t built on the system. We suggest obtaining GDB via MSYS2. If there is a problem with a DLL, GDB will often print the name of the DLL. If the DLL is in an unexpected location, this may indicate a directory that should not be in environment variable Path.

Start GDB Fortran debugger: assuming executable myprog

gdb myprog.exe

Run program from (gdb) prompt:

r

CMake has built-in support for C/C++ static code analysis tools such as CppCheck. Apply CppCheck to CMake targets with CMakeLists.txt by setting CMAKE_CXX_CPPCHECK.

File “cppcheck.supp” contains suppressions for false positives. NOTE: CMake runs cppcheck from an arbitrary directory, so per-file suppressions in the file don’t work as usual. To suppress a warning for a specific file, use the --suppress option to cppcheck in CMakeLists.txt like:

set_property(TARGET MyTarget PROPERTY CXX_CPPCHECK "${CMAKE_CXX_CPPCHECK};--suppress=containerOutOfBounds")

Don’t just blindly modify code based on CppCheck output. Like any code analysis tool there are false positives and false negatives.

A Windows short path can be converted to long path and vice versa using the Windows C library as in this standalone, single source file example.

Users (or developers!) may not realize that the shell expands glob asterisk * unless enclosed in quotes. This can surprise users unfamiliar with this shell behavior, say when using Python argparse with position-based arguments. Say a user has a single file to process in a directory, and doesn’t want to type the long filename, so they type:

python myScript.py ~/data/*.h5 32

Here we assume myScript.py expects two positional arguments, the first being a filename, and the second being an integer. If more than one “*.h5” file subsequently exists and myScript.py is run, the actual input to Python would be like:

python myScript.py ~/data/file1.h5 ~/data/file2.h5 32

Which causes a Python argparse exception.

To see what the shell is going to expand to, with default keybindings and Bash or Zsh at least, press after typing the command these keys:

CMake ExternalProject works for many types of sub-projects across CMake generators. An implementation detail of Ninja is by default ExternalProject doesn’t print progress until each ExternalProject step is finished. For large external projects that take several minutes to download and build, users could be confused thinking CMake has frozen up. To make ExternalProject show live progress as it does with Makefiles generators, add the USES_TERMINAL_* true arguments to ExternalProject_Add.

ExternalProject_Add(
  BigProject
  ...
  USES_TERMINAL_DOWNLOAD true
  USES_TERMINAL_UPDATE true
  USES_TERMINAL_PATCH true
  USES_TERMINAL_CONFIGURE true
  USES_TERMINAL_BUILD true
  USES_TERMINAL_INSTALL true
  USES_TERMINAL_TEST true
)

“USES_TERMINAL* true” forces ExternalProject steps to run sequentially. For large projects this is ordinarily not significant.