Scientific Computing

Free 2-D CAD drawing programs

AutoCAD 2-D libre alternatives are available for Linux, macOS and Windows. They generally require retraining for users coming from AutoCAD. Libre 2-D AutoCAD-like choices include FreeCAD, QCAD and LibreCAD.

FreeCAD is 3-D parametric modeling akin to SolidWorks that can import DXF or DWG. QCAD has distinct paid vs. Community Edition features include DWG and DXF read / write. LibreCAD can read / write DXF and read DWG.

The no-cost ODA File Converter converts DXF to / from DWG.

Install Nvidia HPC C, C++, Fortran compilers

The free-to-use Nvidia HPC SDK offers possible speed improvements and CUDA Fortran. A typical reason for using Nvidia HPC SDK is the Cuda GPU features. Nvidia HPC compilers support C11, C++23, and partial Fortran 2008 including submodule and error stop.

Download and install Nvidia HPC SDK. Create a script nvidia.sh:

To use NVIDIA HPC SDK, source the script:

source ~/nvidia.sh

CMake

In CMake, set NVIDIA HPC compiler-specific options in CMakeLists.txt like:

if(CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC")
  add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-Mdclchk;-Munixlogical>)
endif()

To use newer languages standard features ensure the underlying GCC toolchain is set to a new-enough compiler as per Nvidia HPC SDK documentation. The compiler path can be determined on RHEL-like Linux distros like:

scl enable gcc-toolset-12 "dirname $(which g++)"

If using a CMake toolchain file, instead of CXXFLAGS environment variable, one can set

set(CMAKE_CXX_COMPILER_EXTERNAL_TOOLCHAIN "/opt/rh/gcc-toolset-12/root/usr/")

Visual Studio /utf-8 source files

The MSVC compiler needs the /utf-8 flag when UTF-8 strings are in the source file. If not specified, too many bytes are assigned to each character, leading to incorrect string lengths. This will lead to failures with string width conversions such as WideCharToMultiByte.

Windows Intel oneAPI compiler didn’t need the /utf-8 flag when tested.

In CMake, apply the /utf-8 flag like:

add_compile_options($<$<AND:$<COMPILE_LANGUAGE:CXX>,$<CXX_COMPILER_ID:MSVC>>:/utf-8>)

In Meson, the /utf-8 flag is applied automatically to C++ source files with MSVC compilers.

Matlab upgrade from Terminal

Matlab version upgrade can be initiated from the system Terminal or from the Matlab Help menu. Running the upgrade or Add-On install requires a graphical connection to the computer (Remote Desktop, VNC, or similar).

Matlab release upgrade

The bell icon on the upper right corner of the Matlab Desktop typically shows when a Matlab update is available. To force checking for install, even if the bell is not showing an update, under the Matlab binary directory look for “MathWorksUpdateInstaller”

fullfile(matlabroot, "bin", computer("arch"))

Matlab Add-Ons

Matlab Add-On Explorer is normally launched from the Matlab Desktop. The Add-On Explorer requires a graphical connection. To launch Add-On explorer from the Matlab binary directory look for executable “AddOnInstaller”

Troubleshooting

If the graphical connection has a problem like:

terminating with uncaught exception of type (anonymous namespace)::DisplayError: No display available.

try for diagnosis:

w = matlab.internal.webwindow('www.mathworks.com');

w.bringToFront();

The first command (object instantiation) should not error. The method “bringToFront” should bring up a window if the connection / system allows.


If on Linux with a graphical connection and errors result, try renaming libcrypto.so.1.1 like:

r=$(matlab -batch "disp(fullfile(matlabroot, 'bin', computer('arch')))" | tail -n1)

mv libcrypto.so.1.1 libcrypto.so.1.1.bak

Related: Matlab install on Linux

Datetime vectors in Matlab / Octave

Generating a range of datetime data is a common data analysis and simulation task across programming languages. Matlab and GNU Octave can also generate datetime vectors.

Matlab datetime deprecates datenum. Generate a sequence of datetime like:

t0 = datetime('2020-01-05 12:30:00');
t1 = datetime('2020-01-06 18:15:10');
dt = hours(5.5);

t = t0:dt:t1;

disp(t)

GNU Octave can use many datetime features via the tablicious package.

pkg install -forge tablicious

Load in Octave prompt:

pkg load tablicious

Then use the same Matlab code above.

CMake version recommendations and install

CMake ≥ 3.24 is recommended for general users. 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. 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.

Matlab read FITS image stacks

In Matlab, fitsread is used to read specific frame(s) from a FITS file. That is, you can 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

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