Scientific Computing

CMake version recommendations and install

Downloading the latest release of CMake is usually easy. Admin / sudo is not required.

  • Linux: snap install cmake
  • macOS: brew install cmake
  • Windows: winget install Kitware.CMake
  • PyPI CMake package: python -m pip install cmake

For platforms where CMake binaries aren’t easily available, build CMake using scripts/build_cmake.cmake.

To see the merge requests for a certain release, use a URL like: https://gitlab.kitware.com/cmake/cmake/-/merge_requests?milestone_title=3.32.0&scope=all&state=all


CMake 3.32 enables CMAKE_LINK_WARNING_AS_ERROR boolean option sets most compilers to error if a compile warning occurs, which is generally a good setting for CI systems. target_link_libraries() can use a LINKER: prefix to abstract options. CTest –interactive-debug-mode is particularly useful on Windows to enable debug dumps and error popup windows.


CMake 3.31 warns if cmake_minimum_required() is < 3.10. TLS ≥ 1.2 is required by default for internet operations e.g. file(DOWNLOAD), ExternalProject, FetchContent, and similar. file(ARCHIVE_CREATE) gained a long-needed WORKING_DIRECTORY parameter that is essentially necessary to avoid machine-specific paths being embedded in the archive. CMAKE_LINK_LIBRARIES_STRATEGY allows specifying a strategy for ordering target direct link dependencies.


CMake 3.30 adds C++26 support. CMAKE_TLS_VERIFY environment variable was added to set TLS verification (true, false). CMake 3.31 defaults CMAKE_TLS_VERIFY to on, where previously it was off.


CMake 3.29 adds cmake_language(EXIT code) to exit CMake script mode with a specific return code. This is useful when using CMake as a platform-agnostic scripting language instead of shell script.

Environment variable CMAKE_INSTALL_PREFIX is used to set the default install prefix across projects–it can be overridden as typical by cmake -DCMAKE_INSTALL_PREFIX= option.

Target property TEST_LAUNCHER allows specifying a test launcher. For MPI program this allows deduplicating or making more programmatic test runner scripts.

Linker information variables including CMAKE__COMPILER_LINKER_ID have been added to allow programmatic logic like setting target_link_options() based on the particular linker.

ctest --parallel without a number or 0 will use unbounded test run parallelism.


CMake 3.28 changes PATH behavior for Windows find_{library,path,file}() to no longer search PATH. This may break some projects that rely on PATH for finding libraries. The MSYS2-distributed CMake is patched to include PATH like earlier CMake, which can be confusing for CI etc. not using MSYS CMake with that patch. Windows CI/user may need to specify CMAKE_PREFIX_PATH like

cmake -DCMAKE_PREFIX_PATH=$Env:SYSTEMDRIVE/msys64/ucrt64/lib -B build

Support for C++20 modules is considerably improved and most users will want at least CMake 3.28 to make C++ modules usable. Generator expressions $<IF> $<AND> $<OR> now short circuit. Test properties now have a DIRECTORY parameter, useful for setting test parameters from the project’s top level CMakeLists.txt. CMake 3.28.4 fixed a long-standing bug in Ninja Fortran targets that use include statements.


CMake 3.27 emits warning for cmake_minimum_required(VERSION) < 3.5. CTest test properties TIMEOUT_SIGNAL_NAME and TIMEOUT_SIGNAL_GRACE_PERIOD specify a POSIX signal to send to a timed out test process. Interactive CMake debugger added by cmake --debugger is used with an IDE such as Visual Studio. CMake script command cmake_file_api() allows querying CMake File API from within CMake.

ℹ️ Note

Fortran + Ninja was broken for OBJECT libraries in CMake 3.27.0..3.27.8 and fixed in 3.27.9.


Older CMake changelog

No strict aliasing C / C++

Optimizing compilers may enable strict aliasing. For a wide variety of existing projects, strict aliasing provides additional optimization. For some projects, such as MUMPS, memory leaks have been observed that are resolved by disabling strict aliasing using GCC flag “-fno-strict-aliasing”.

Compilers with ability to switch on / off strict aliasing include:

libuv recommends -fno-strict-aliasing due to type punning.

References:

CMake Zstd compression

Zstd is an open file compression standard. Zstd has become widely used and is incorporated in the Linux kernel and GCC. We use Zstd for data archiving particularly for large files where size and speed are a concern. CMake supports Zstd compression throughout, including file(ARCHIVE_CREATE) and file(ARCHIVE_EXTRACT). Zstd is vendored into CMake, so there is no need to worry about system shared libraries for Zstd.

file(ARCHIVE_CREATE ... WORKING_DIRECTORY ...) is necessary to avoid system-specific relative path issues.

set(archive "example.zst")
set(in_dir "data/")

file(ARCHIVE_CREATE
  OUTPUT ${archive}
  PATHS ${in_dir}
  COMPRESSION Zstd
  COMPRESSION_LEVEL 3
  WORKING_DIRECTORY ${in_dir}
  )
COMPRESSION_LEVEL
arbitrary, bigger value is more compressed.
FORMAT
not used for Zstd.

Wouxun KG-S72C antenna

The Wouxun KG-S72C is a modern CB radio with AM and FM capabilities, which are recommended for anyone buying a new CB radio. The KG-S72C has CTCSS and DCS coded squelch, which allows hearing only parties with the same subaudible code. Only a few other models of CB radio have this capability, so most users might only occasionally use coded squelch. An important point to note is that no one sells the KG-S72C factory antenna replacement, so be very careful not to lose or damage the factory antenna. Since the KG-S72C receives an SMA female antenna (the radio has SMA female connector), using long replacement antennas are mechanically fragile and could break the antenna jack.

The sound quality on receive and transmit is good, especially in FM mode as for most AM / FM CB radios.

Cons

The KG-S72C has a few cons, which are tolerable.

  1. Lack of RF gain control, which is a fundamental requirement for any CB radio to make listening tolerable in AM mode. Using the KG-S72C as a mobile radio with an appropriate SMA adapter to the mobile antenna coax is OK, but the lack of RF gain control can be fatiguing and is the second con.
  2. The squelch mode seems to be noise squelch only, which can be frustrating as it closes intermittently on loud AM modulation. It would benefit from a signal strength squelch as traditional CB radios use.

Captive portal public WiFi URLs

Public WiFi often has captive portal login. Portals may coerce users to accept terms and conditions and absolution of liability before accessing the Internet. The portals may be worked around by DNS tunneling, MAC spoofing, etc. Many users just tolerate the portals.

Web browsers may try to trigger captive portals by checking servers, in case the OS hasn’t already triggered the captive portal. Sometimes captive portals aren’t triggered. HSTS blocks HTTP captive portal redirects. Try visiting a deliberately non-HTTPS portal-triggering site like http://neverssl.com

Devices on networks that block the platform’s automatic network checking may indicate like:

Connected, no Internet

If there’s not a captive sign-in webpage, the network connection may still work to non-Google sites.

Check connectivity manually using curl like:

curl -s -w %{response_code} -o /dev/null URL
-o /dev/null
discard the webpage content to avoid screen clutter. On Windows, use -o NUL instead.
-s
silent mode
-w %{response_code}
write the HTTP response code to console
URL
the URL of the captive portal server
Platform server HTTPS response code
Firefox detectportal.firefox.com/success.txt 200
Chromium clients3.google.com/generate_204 204
Windows www.msftconnecttest.com/connecttest.txt 200
macOS captive.apple.com/hotspot-detect.html 200
Android connectivitycheck.gstatic.com/generate_204 204
Ubuntu connectivity-check.ubuntu.com 204
Fedora fedoraproject.org/static/hotspot.txt 200

To disable connectivity checking in Ubuntu: Settings → Privacy → “Network Connectivity Checking”

Cobra 19 Ultra 6 CB radio

The Cobra 19 Ultra 6 appears to be a relabeled AnyTone Smart II. While previous Cobra 19 models had significant features missing, the Cobra 19 Ultra 6 has the necessary features to be a good choice in entry-level very compact CB radio.

From practical in-vehicle use, the speaker is adequately loud. Both AM and FM mode work well on transmit and receive. There is no “dual watch” channel capability, but this may not be a requirement for many users.

RF Gain is essential on any CB radio and the RF gain adjustment range of the Cobra 19 Ultra 6 is good. Typically RF gain between 24 and 39 is useful.

The radio appears to use audio compandoring, which helps improve apparent audio SNR. The radio has a traditional signal squelch as well as “auto” noise squelch. The general problem with noise squelch across CB radios is that overmodulated AM signals can close the squelch regardless of how strong the signal is.

Setting the RF Gain and Squelch on an AM CB radio is best done by opening the squelch – static is heard. Then set the RF Gain so that only very faint static is heard. Then set the signal squelch just closed.

Channel Scan

On firmware version 1.1, entering scan mode is different than the manual states. To enter channel scan, press and hold the microphone “up” or “down” button until the radio goes once through all 40 channels, then the radio beeps and release the button. The radio then scans all 40 channels repeatedly. Unfortunately, there does not appear to be a way to skip channels in scan mode. This means the radio will often stop on channels 6, 11, etc. with high power stations that may not be what the user wants to listen to.

Matlab read FITS image stacks

In Matlab, fitsread is used to read specific frame(s) from a FITS file. Read frames one at a time from a large multi-frame FITS file in MATLAB. This avoids overwhelming RAM or taking an excessive time to load just one or a few image frames from a FITS file.

Example: sequentially read and plot each frame of a 4096-frame FITS file, with each frame being 256 x 256 pixels.

for i = 1:4096
  currFrame = fitsread('myFile.fits', PixelRegion={[1 256],[1 256],i});
  imagesc(currFrame)
  pause(0.05)
end

GNU Octave FITS reading is done with the cfitsio package using a similar API.


Related: read FITS image stack in Python

Install AMD AOCC C C++ Fortran compiler

The no-cost AMD AOCC compiler is tuned for AMD CPUs, akin to how Intel oneAPI is tuned for Intel CPUs. For a RHEL-based Linux, install the downloaded “.rpm” file like:

dnf install ./aocc-compiler*.x86_64.rpm

Create a source script “~/aocc.sh” like:

root=/opt/AMD/aocc-compiler-5.0.0/

[[ ! -d ${root} ]] && echo "ERROR: ${root} not found" && exit 1

source ${root}/setenv_AOCC.sh

# setenv_AOCC doesn't set these
export CC=clang CXX=clang++ FC=flang

export CXXFLAGS=
export MPI_ROOT=

flang --version

To use the AOCC compiler:

source ~/aocc.sh

AOCL libraries

The AOCL libraries provide accelerated math functions for AMD CPUs for several popular libraries for use in C, C++, or Fortran. AOCL is compatible with AOCC and other compilers as listed in the AOCL downloads.

Android 5G SA no data

5G wireless network providers across the United States and elsewhere are turning on 5G standalone mode (SA), that can enable significantly more data bandwidth and lower connection latency. Some phones, even recent phones, are not properly capable of supporting 5G SA even though they work fine in 5G NSA (non-standalone mode) that operates like 4G LTE. Recent Android releases and carrier updates have disabled 5G SA for certain phones that previously had 5G SA enabled due to data connectivity problems when the carrier enabled 5G SA. A symptom of lost data connectivity, possibly due to 5G SA incompatibility, is the phone signal showing 5G signal bars with an exclamation point.

What may possibly but not always help is to turn off 5G in the phone network settings by setting “Preferred network type” to “LTE” or similar instead of “5G”. This may force the phone to use 4G LTE instead of 5G, which may work better for data connectivity. However this does not always help. If a newer phone on the same network carrier works fine with 5G SA, then the phone with data connectivity problems may need a software update or carrier update to fix the problem, or simply a newer phone may be needed. The Network Cell Info app can show the network type and signal strength, and may help diagnose the problem.

CMAKE_TLS_VERIFY global

TLS verification default is ON since CMake 3.31. Users can override this default for all projects with environment variable CMAKE_TLS_VERIFY. or per-project with CMake variable CMAKE_TLS_VERIFY. The default TLS version may be set by CMAKE_TLS_VERSION. If the system TLS certificate location needs to be specified, this can be done by CMAKE_TLS_CAINFO.

Meson build system uses TLS verification by default, warning if verification fails. TLS verification is part of CMake’s internal nightly testing.

The example uses badssl.com, that purposefully has a variety of certificate problem URLs.


Reference: Issues that would have been caught with this default