Scientific Computing

When using a virtual machine, and especially if the virtual machine is in emulation mode, which is generally many times slower than virtualization mode, it can greatly help interaction speed to use a console boot rather than graphical desktop. In operating systems like Ubuntu, this can be done by editing /etc/default/grub and setting:

GRUB_CMDLINE_LINUX_DEFAULT="text"
GRUB_TERMINAL=console

Then from Terminal:

update-grub

systemctl set-default multi-user.target

Then the system will boot into a text console on all future boots.

Reference

Windows Subsystem for Linux WSL has Ubuntu LTS releases among other Linux distros on the Microsoft Store. The Microsoft Store is the recommended method to install WSL.

If the Microsoft Store isn’t available on the computer, manual WSL install is also available. The WSL changelog shows the continually expanding WSL feature set.

WSL can use GUI and sound with programs like Spyder via WSLg.

List WSL distros already installed on the computer from PowerShell / Command Prompt:

wsl --list --verbose

Install, list, and switch between Linux distros on Windows default for bash from Command Prompt:

wslconfig

WSL configuration

Limit the amount of RAM WSL2 can use for all installed WSL instances by editing Windows file $HOME/.wslconfig to include:

[wsl2]
swap=0
memory=4GB

Set memory= to less than the total computer physical RAM to help avoid using Windows swap.

A per-WSL instance default that is confusing and slows down WSL program-finding is stuffing Windows PATH into WSL PATH. We normally disable Windows PATH injection into WSL, because it also breaks library finding in build systems like CMake. Additionally, we enable filesystem metadata, as weird permission errors can occur, even causing CMake to fail to configure simple projects.

Add to each WSL instance /etc/wsl.conf file:

[interop]
enabled=false
appendWindowsPath=false

Run Ubuntu apps from Windows Command Prompt or PowerShell:

wsl ls -l

Run Windows program from Ubuntu terminal:

/mnt/c/Windows/System32/notepad.exe

Note that capitalization matters and .exe must be at the end.

CMake uses the bundled curl library by default. When debugging connectivity issues with CMake, a developer may wish to build CMake with a specific curl version. To do so, from the cmake/ project source directory, use options like:

cmake -Bbuild -DCURL_ROOT=/path/to/curl -DCMAKE_USE_SYSTEM_LIBRARY_CURL=yes

Then build CMake as usual.

Verify the Curl version used with this script.

macOS can update system software from Terminal, even macOS itself. However, to complete the upgrade requires using the graphical desktop, perhaps over VNC.

softwareupdate -l

shows the available updates.

softwareupdate -i -a

installs all available updates.

Valgrind is a dynamic analysis tool that can detect memory leaks and other problems in programs including C, C++, and Fortran. Valgrind is available on Linux and BSD for x86 and ARM CPU architectures. For macOS on Intel x86 CPUs, Valgrind is available in Homebrew. For macOS on Apple Silicon ARM64 CPU, Valgrind can be used from an aarch64 Linux virtual machine in native mode for best performance.

Variable length strings are implemented in Fortran 2003 standard like:

character(:), allocatable :: str

Passing such variables to procedures is declared the same as fixed length strings. In fact, we always declare actual arguments with “*” to avoid needing every string an exact length.

subroutine example(str)
character(*), intent(in) :: str

Before Fortran 202X standard, intrinsic Fortran functions need traditional fixed length character variables. For example:

integer :: i, L
character(:), allocatable :: buf

call get_command_argument(1, length=L, status=i)
if (i /= 0) error stop "first command argument not available"
allocate(character(L) :: buf)
call get_command_argument(1, buf)

Fortran function can return allocatable characters. If you run into bugs with this on old compilers, try manually allocating the character variable. Fortran standard compliant compilers auto-allocate character functions like numeric arrays.

It is proper to manually allocate character variable actual arguments when bind(C) interfaces are used.

function greet(b)

logical, intent(in) :: b

character(:), allocatable :: greet

!! Manual allocation of character variable. This could be necessary on old or buggy compilers.

if(b) then
  allocate(character(5) :: greet)
  greet = 'hello'
else
  allocate(character(3) :: greet)
  greet = 'bye'
endif

end function greet

GitHub Actions workflows can use different compilers per job by writing the compiler name or path to environment files in each job. This is useful for programs and libraries that need distinct compiler versions. An example of this is Matlab, where each Matlab release has a range of compatible compilers.

• Matlab R2021a, R2021b: GCC-8
• Matlab R2022a and newer: GCC-10

Implement in GitHub Actions:

jobs:

  linux:
    runs-on: ubuntu-latest

    strategy:
      matrix:
        release: [R2021b, R2024a, latest-including-prerelease]

    steps:

    - name: GCC-8 - Matlab < R2022a
      if: ${{ matrix.release < 'R2022a' && matrix.release != 'latest-including-prerelease' }}
      run: |
        echo "CC=gcc-8" >> $GITHUB_ENV
        echo "CXX=g++-8" >> $GITHUB_ENV
        echo "FC=gfortran-8" >> $GITHUB_ENV

    - name: GCC-10 - Matlab >= R2022a
      if: ${{ matrix.release >= 'R2022a' || matrix.release == 'latest-including-prerelease' }}
      run: |
        echo "CC=gcc-10" >> $GITHUB_ENV
        echo "CXX=g++-10" >> $GITHUB_ENV
        echo "FC=gfortran-10" >> $GITHUB_ENV

    - name: Install MATLAB
      uses: matlab-actions/setup-matlab
      with:
        release: ${{ matrix.release }}
        cache: true

Battery time remaining estimates for computing devices can vary widely in accuracy. The estimates are based on assumptions about future behavior based on prior usage trends, from a mix of current and prior charge usage. Windows updates can disable battery time remaining, and devices may come from the factory with battery time estimates disabled.

Hovering over the battery icon on the Windows taskbar can show the estimated battery time remaining along with the percent battery charge. The estimated battery time remaining is the same shown under System / Power & Battery.

The usual precautions on modifying the Windows Registry apply–do a Windows System Recovery milestone first. These keys are under:

HKLM\SYSTEM\CurrentControlSet\Control\Power

Reboot after making these changes. It may take a minute or two after first reboot for the estaimted battery life to show up.

If these registry keys exist, set their value to 0. If they don’t exist, that’s fine too.

EnergyEstimationDisabled=0
UserBatteryDischargeEstimator=0

Create this DWORD32 value (if not existing) and set to 1

EnergyEstimationEnabled=1

Reference: forum

JSON can hold several data types including arrays. This example iterates over a JSON array in CMake.

Suppose file “json.cmake” contains:

cmake_minimum_required(VERSION 3.19)

set(jarr "{
\"c\":[3,4,5]
}")

string(JSON L LENGTH "${jarr} ""c")
math(EXPR L "${L}-1")

string(JSON t TYPE "${jarr}" "c")
message(STATUS "type: ${t}")

foreach(i RANGE ${L})
  string(JSON v GET "${jarr}" "c" ${i})
  string(JSON t TYPE "${jarr}" "c" ${i})
  message(STATUS "c[${i}] = ${v}  ${t}")
endforeach()

This results in:

$ cmake -P json.cmake

-- type: ARRAY
-- c[0] = 3  NUMBER
-- c[1] = 4  NUMBER
-- c[2] = 5  NUMBER

Using HDF5 / NetCDF4 / HDF4 from any language can be intimidating if directly using the low-level API. Interfaces have sprung up for popular languages that make HDF5 trivially easy to use, such as Python h5py.

The stdlib for Matlab provides functions making HDF5, NetCDF4, and HDF4 much easier to use in Matlab.

The “h5*” functions are for HDF5, “nc*” functions are for NetCDF4, and “h4*” functions are for HDF4. The functions are polymorphic, typecasting user data.

The h5*, nc*, and h4* functions work very similarly. For simplicity, we only show the h5* functions.

• h5save() save a variable to a file
• h5variables() list all the variable in a file
• h5size() get the size (shape) of a variable in a file
• h5exists() check if a variable exists in a file