Scientific Computing

RHEL adds a few complexities on top of the “plain” Debian-based Linux distros. SELinux in particular is another layer to consider. Here are common considerations for settings up SSH and/or VNC on RHEL, CentOS or similar RHEL-derived Linux distro.

For SSH connection problems, consider adding to /etc/ssh/sshd_config:

LogLevel DEBUG

then:

systemctl restart sshd.service

then:

journalctl -f

and try to login. This will print a good amount of information streaming and helps reveal .ssh/authorized_keys permissions issues and more.

To determine if SELinux is causing an issue, as a last resort one may temporarily and carefully edit /etc/selinux/config to have

SELINUX=permissive

and reboot. Be sure to put that back to enforcing and reboot when done.

Check that firewalld is allowing the desired SSH port through.

tcpdump port 22 -n -Q inout

should show packets from the client–if not the SSH server firewall may be blocking them.

Waypipe remote desktop

In general current VNC servers are not compatible with the Wayland desktop (that replaces X11). Waypipe is a new remote desktop tool that works with Wayland. However, Waypipe requires another Linux machine with Wayland, so it doesn’t work with Windows or macOS natively. If permissible for your system, you may wish to switch the desktop to X11 instead of Wayland so that traditional VNC servers work.

X11 VNC server

If you are able to switch to X11, then you can use a traditional VNC server like TigerVNC.

Switch to X11 desktop on the server by editing /etc/gdm/custom.conf:

[daemon]
WaylandEnable=false
DefaultSession=gnome-xorg.desktop

Then reboot. Ensure you can locally logon to the X11 desktop as usual.

Install TigerVNC server:

dnf install tigervnc-server

Ensure username is specified with a display number in file: “/etc/tigervnc/vncserver.users”. You do not need or want a file ~/.vnc/xstartup or ~/.vnc/config.

Enable SELinux VNC server:

ausearch -c 'vncsession' --raw | audit2allow -M my-vncsession

semodule -X 300 -i my-vncsession.pp

Set a password for the VNC server:

vncpasswd

Then start the VNC server:

systemctl enable --now vncserver@:2

Logoff the local server, otherwise when you try to view VNC, it will just show a black screen. If you are logged on remotely and try to login locally, the local login gets a black screen. If this happens, you can logout the unwanted black-screen sessions by:

who -u

# gives PID of the local user (:1)

then:

kill <PID of local user>

Reference: RHEL Remote desktop

Linux package managers like Apt and DNF can be set to not install recommended packages by default, which can be useful for headless embedded systems or WSL. This can save 100s of MB or more, which can be important for embedded systems or WSL to save time and disk space. Saving of download/install time is often relevant to CI/CD systems. A caveat is that some expected features may be missing.

Apt

From the command line (without changing default):

apt install --no-install-recommends <package>

Create a file like “/etc/apt/apt.conf.d/95-no-install-recommends” with the following contents:

apt::install-recommends "false";

To override this setting at the command line, to install recommended packages add “–install-recommends” to the apt command line.

DNF

From the command line (without changing default):

dnf install --setopt=install_weak_deps=False <package>

Edit “/etc/dnf/dnf.conf” adding under [main]:

install_weak_deps=False

Git submodules don’t put their individual Git config file under .git/config. This Git command issued from the Git submodule directory tells the file path to the Git submodule config file:

git rev-parse --git-path config

Say a repository “alpha” has submodule “beta”. Find the Git config file location of “beta” from “alpha” like:

git -C beta rev-parse --git-path config

# OR

cd beta
git rev-parse --git-path config

NEXRAD preview PNGs are 12200 x 5400 pixels: example This takes over 650 MB of RAM to load each frame.

ImageMagick -limit option can be used to limit the amount of RAM and/or disk used by ImageMagick operations. For example, if processing images on an embedded systems like a Raspberry Pi, the limited RAM may lead to disk swapping, taking 1000x longer or failing anyway. Use combinations of -limit options to control RAM and disk usage.

magick -limit map 500MB -limit memory 500MB -limit disk 100MB in.png -scale 10% out.png

The -debug cache option show how ImageMagick is using memory for a magick command.

On Windows, Miniconda can be installed from the Command Prompt or PowerShell:

winget install --id=Anaconda.Miniconda3 -e

Update conda from Command Prompt / Terminal:

conda update conda

Setup the new shell support (PowerShell, Bash, Command Prompt, etc.) with

conda init

Reopen Terminal to see new conda environment.

If message upon opening PowerShell like:

Documents\WindowsPowerShell\profile.ps1 cannot be loaded because running scripts is disabled on this system.

Consider ExecutionPolicy like:

Set-ExecutionPolicy -ExecutionPolicy RemoteSigned

By design, CTest WILL_FAIL test property does not handle segmentation faults and other unexpected terminations. That is, a failing test will also show as failed in CTest, when the desire may have been to show an intended failure as success via WILL_FAIL. A simple workaround for this is to make a wrapper call for the intentionally segfaulting executable and catch that result, as in example project.

Visual Studio Code can compare folders via Extension Compare Folders. In Unix-like shells, an alias can be used to ease command line use:

alias vsdiff="COMPARE_FOLDERS=DIFF code"

Then, to compare two folders, use:

vsdiff folder1 folder2

vsdiff allows applying changes from the left to the right. To “swap sides” click the left-right arrow in the top right corner.

Git submodules can switch remotes. This is useful when making a pull request for a project that relies on another pull request submodule. Verify the change in the top project’s “.gitmodules” file.

Example: suppose the directory “subdir” is a Git submodule. In this command, do not put “./subdir” or “subdir/”, just “subdir” by itself. Suppose you also wish to change the branch to “feat1” in the submodule.

git submodule set-url -- subdir https://github.invalid/username/new

git submodule sync

git -C subdir pull

git -C subdir switch feat1

Whether using Clang / LLVM or Homebrew GNU GCC compiler, GNU ld is not supported on macOS. Only the Apple macOS Xcode ld is supported. The ld linker in Xcode 15 breaks numerous projects, including OpenMPI < 4.1.6. The workaround is to use the classic linker, which is still supported in Xcode 15.

Set in ~/.zshrc

export LDFLAGS="$LDFLAGS -Wl,-ld_classic"

or specify on the program command line like:

LDFLAGS="$LDFLAGS -Wl,-ld_classic" make

Note that for CMake, LDFLAGS environment variable is read only on the first CMake configure and cached.

It’s straightforward to detect if running inside WSL or if WSL is available.

These functions use only Python standard library modules. Other languages are demonstrated as well for checking WSL.