Scientific Computing

Extracting zstd archive with tar

Zstd is a modern performant file archiving standard widely used to replace .zip, gzip, etc. With modern “tar” extract .zst like:

tar -xf arc.zst

If needed for older tar, specify the program “tar” should use to extract .zst:

tar --use-compress-program=zstd -xf arc.zst

Matlab can extract .zst files.

For very old “tar” one may get:

zstd: error 25 : Write error : Broken pipe (cannot write compressed block) tar: Error opening archive: Child process exited with status 25

In this case, use a two-step process to extract the .zst file fully:

zstd -d myfile.zst   # creates tar file "myfile"
tar -xf myfile       # extract the original file/directory hierarchy

Matlab curl instead of websave

Matlab websave or ftp might not work in cases where a plain “curl” or “wget” command works. A symptom of this issue is HTML is downloaded instead of the intended binary file. Websites such as Dropbox recognize the HTTP User Agent of curl and Wget and mutate the web server response to be automation-friendly. Since Matlab is much less commonly used than Python, curl, Wget, etc. this user agent-dependent behavior results. We recommend understanding why Matlab websave doesn’t work, or use the low-level Matlab HTTP Interface.

To use curl from Matlab, recognize this may require unique setup for each system, despite that curl is included (preinstalled) in modern operating systems including Windows.

The extra quotes around “url” allow for arbitrary characters to be used in the URL that can confuse shells like zsh. The “-L” option to curl allows redirects.

function curlsave(filename, url)

cmd = "curl -L -o " + filename + " '" + url + "'";

assert(system(cmd) == 0, "download failed: " + url)

end

Linux systems with multiple curl versions installed may need to set an environment variable to prioritize. Set the filename as appropriate for computer (ensure the file exists).

LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libcurl.so.4 matlab

This can help errors like

curl: (48) An unknown option was passed in to libcurl

Even this doesn’t always work, so we recommend understanding why Matlab websave doesn’t work, or use the low-level Matlab HTTP Interface.

CMake generate Fortran from template

CMake configure_file can serve to generate source code files including Fortran. For templates beyond a few lines of code, it may be useful to read the template from a file. This requires setting CMake directory property CMAKE_CONFIGURE_DEPENDS to have CMake regenerate the file if the template file changes as in the example below.

file(READ my_template.in.f90 template_code)
configure_file(example.in.f90 example.f90 @ONLY)

set_property(DIRECTORY PROPERTY CMAKE_CONFIGURE_DEPENDS my_template.in.f90)

#example use
add_executable(main ${CMAKE_CURRENT_BINARY_DIR}/example.f90)

iftop config file

iftop is a handy utility on macOS, Linux and other Unices for a live Terminal graph of network data flow to particular addresses. On computers with many network interfaces, including virtual interfaces such as on macOS, it is handy to set a default interface in a config file. iftop uses the file ~/.iftoprc.

For example, on macOS you may be interested in interface “en1”. To help determine the desired interface, use ifconfig or ip a to find the interface with the public IP address. Then create ~/.iftoprc containing like:

interface: en1

where “en1” is your desired interface determined as per above.

Red Hat firewalld port add

RHEL uses firewalld to provide network firewall. firewalld has the concept of runtime vs. permanent rules, which help avoid getting the firewall into an unusable state. Permanent rules become live at next restart/reboot, while runtime rules disappear at restart/reboot.

Suppose one wishes to put the SSH server on a non-default port 12345 to mitigate auth log clutter. First configure the SSH server in /etc/ssh/sshd_config, then restart SSH and verify the SSH configuration is working by adding the port to firewalld (here, 12345):

firewall-cmd --add-port=12345/tcp

If this works, make the firewalld rule permanent:

firewall-cmd --permanent --add-port=12345/tcp

SELinux will also need an updated policy to allow the SSH port change, like:

semanage port -a -t ssh_port_t -p tcp 12345

CMake expanduser tilde ~

To have the most reliable path operations in CMake, it’s typically best to resolve paths to the full expanded path. Note: there are a few CMake functions that desire relative paths, but those are clearly spelled out in the docs.

expanduser.cmake for CMake expands the ~ tilde character to the user home directory on all operating systems, including Windows.

Related:

List all CMake tests with CTest

As a CMake project grows, increasing complexity can make it hard to discern what tests are to be run and their properties. Perhaps the project logic is unexpectedly omitting necessary tests. The CI system or human can verify the list of tests by:

ctest -N

For machine parsing and human-readable verbose details including fixtures and labels, output JSON:

ctest --show-only=json-v1

To ensure an accurate test list, the project must first be configured and built as usual:

cmake -B build

cmake --build build

ctest --test-dir build -N

CMake file separator

In many cases, using the Unix-type slash file separator / will work even on Windows. Trying to manually specify backslash Windows file separator \ can cause problems in CMake and many other languages. Thus in CMake and other languages like Python, we always use / as path separator, and only transform to backslash for the rare cases it’s needed.

Transform to Unix file separator:

cmake_path(CONVERT "path\in\file.txt" TO_CMAKE_PATH_LIST out)

That switches backslash \ file separators to Unix slash / file separators. This becomes relevant if manually adjusting Include paths by appending to lib_INCLUDE_DIRS or similar. If backslashes sneak through, unexpected build-time errors can result, and even configure-time errors with “check_source_compiles()” and similar. As the docs note, put quotes "${mypath}" around the variable expansion to ensure CMake doesn’t mangle the path.

Transform to native file separator is generally more rarely used. CMake can transform paths to native file separator, with the caveat that this can cause unpredictable Windows-specific backslash problems, as with any program.

Related: CMake expanduser ~