Scientific Computing

Tell current matplotlibrc location:

python -c "import matplotlib; print(matplotlib.matplotlib_fname())"

matplotlibrc location priority

Help end users have the same plotting experience by putting a matplotlibrc file in the Python project directory that users run your script from.

CTest CDash scripts can use the function ctest_empty_binary_directory to recursively remove a CMake build directory to avoid hidden state between test runs in an overall build-test cycle. However, this function will cause the overall CTest run to return a non-zero error code if CMakeCache.txt isn’t present in the build directory. This is confusing in a CI system particularly. While we do appreciate this safety feature over simply using file(REMOVE_RECURSE), it’s necessary to enclose in if() statements like below to avoid false errors.

if(EXISTS ${CTEST_BINARY_DIRECTORY}/CMakeCache.txt)
  ctest_empty_binary_directory(${CTEST_BINARY_DIRECTORY})
endif()

Linux modules are often used by HPC systems allow using more current versions of software than are in the default system repositories. A typical approach is to create an .sh file for a particular job type. To avoid unexpected conflicts or hidden state, load only the modules necessary for a particular project.

Many modules are typically available, listed by:

module avail

The currently loaded modules are listed by:

module list

Load recent GCC:

source gcc.sh

with gcc.sh like:

module load gcc

export CC=gcc CXX=g++ FC=gfortran

Determine available GCC versions:

module avail gcc

Load Intel oneAPI:

source oneapi.sh

with oneapi.sh like:

module load intel-oneapi

export CC=icx CXX=icpx FC=ifx
export MPI_ROOT=$I_MPI_ROOT

Determine available Intel oneAPI versions:

module avail intel-oneapi

Some HPC systems have a too-old GCC version defaulting for Intel oneAPI, which can be fixed by setting GCC toolchain.

Cray PE Programming Environment allows easy switching of compilers for developing and running applications on Cray supercomputers. Use the Cray compiler wrappers cc, CC, and ftn instead of directly referencing the compiler backends gcc, g++, and gfortran.

In CMake script, detect if Cray PE is being used, regardless of compiler backend by detecting if environment variable CRAYPE_VERSION is set.

if(DEFINED ENV{CRAYPE_VERSION})
  message("Cray PE detected")
endif()

CMake superprojects may have one project that builds binary executables with MPI and another project that runs those targets. To avoid the overhead of FindMPI, one can use the following find_program() command to use “mpiexec”.

find_program(MPIEXEC_EXECUTABLE
NAMES mpiexec
HINTS ${MPI_ROOT} ENV MPI_ROOT ENV I_MPI_ROOT
PATHS /usr/lib64 ENV MINGWROOT ENV MSMPI_BIN
PATH_SUFFIXES bin openmpi/bin mpich/bin
DOC "Runs an MPI program"
REQUIRED
)

To ensure expected behavior in a CTest script for ctest_update() when Git is used, set these variables in the CTest script:

set(CTEST_UPDATE_TYPE git)
set(CTEST_UPDATE_COMMAND git)

The CMake generator expression TARGET_FILE yields the full path to a binary target file. This is useful with add_custom_command() and add_test() when a script is used as part of those commands. For CMake native commands, it’s usually not necessary to use TARGET_FILE.

Example:

add_executable(my_exe main.c)

find_package(Python COMPONENTS Interpreter REQUIRED)

add_test(NAME scripted
COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example.py $<TARGET_FILE:my_exe>
)

When using scripts it’s a good practice to also specify the full path as above.

Git doesn’t have any general letter-specific restrictions on branch names. Organizations can implement push restrictions with services like GitHub to restrict branch names–for example bad words or regex patterns.

The Windows operating system has general filename restrictions that restrict several keywords from Git branch names. A list of case-insensitive prohibited branch names includes Windows devices names.

For example on Windows:

> git switch -c con

fatal: cannot lock ref 'refs/heads/con': Unable to create '.git/refs/heads/con.lock': Invalid argument

Note that one can work with those branch names using Windows Subsystem for Linux (WSL), but even if you create such a branch, it will not work from native Windows:

warning: ignoring broken ref refs/heads/con

Speed up Octave startup by a factor of 10-100x by not autoloading packages. For each of the Octave config files that exist, comment out the line:

# pkg ("load", "auto");

Verify GNU Octave speedup fix: in Octave type

pkg list

if all packages are starred, that means you’re autoloading, which greatly slows down Octave startup. The factor of 100 improvement in GNU Octave speedup was estimated with the command

time octave --eval 'exit'

Before fix 4.904 seconds, after fix 0.072 seconds to load Octave.

CMake implements a file(DOWNLOAD INACTIVITY_TIMEOUT) option that uses curl CURLOPT_LOW_SPEED_TIME to fail much earlier than a TIMEOUT option would when the connection speed is extremely slow. However, some systems intentionally block downloads, but do so in a way that fools the underlying curl library into not tripping INACTIVITY_TIMEOUT. Rather than try to figure out a direct fix in curl for this apparently longstanding problem, we instead decide to implement a CMake configure-time internet connectivity detection.

When a CTest test is comprised of a CMake script, this test can be setup as a FIXTURES_SETUP to avoid calling it repeatedly for each test, instead just once for a set of tests.

The key technique here is the URL connectivitycheck.gstatic.com/generate_204 that is used by Android devices to check connectivity. Any similar URL with zero or tiny download size would also be suitable.