Development

Optional

VS Code with the following extensions:
GitHub CLI

Development Cycle Overview

Branch
Develop
- cargo build
- Develop:
  - tests
  - implementation
- Document:
  - mdbook build
    - output: automesh/book/build
  - mdbook serve --open
    - interactive mode
    - On the local machine, with Firefox, open the index.html file, e.g.,
      - file:///Users/chovey/autotwin/automesh/book/build/index.html
- Test:
  - cargo test
  - cargo run // test without required input and output flags
  - cargo run --release -- -i tests/input/f.npy -o foo.exo
  - cargo run -- --help
- Pre-commit:
  - pre-commit run --all-files
- Clean:
  - cargo clean
- cargo doc --open
Test
- maturin develop --release --features python
Merge Request

Environment Modules

The automesh application can be installed as a service on a High-Performance Computing (HPC) system with the following steps:

Install and Compile Application

automesh must be available and installed to a file location that is accessible by all compute nodes and users who need it.

Location: Choose a central directory such as /opt/hpc/ or /sw/ for the automesh binaries, libraries, and associated files. For example, let's assume the install path is /opt/hpc/apps/automesh/0.3.7.
Compilation: Compile automesh and all its dependencies statically if possible, or ensure all shared libraries (.so files) are also included in the installation directory structure.

The module file, a small script usually written in Tcl or Lua, provides the module load functionality. It tells the shell what changes to make to the user's environment when the module is loaded.

Location: Module files are placed in a specific directory structure that is scanned by the Environment Modules software (e.g., Lmod or Tcl-based modules). A common path would be /opt/hpc/modules/automesh/0.3.7.

A typical module file would be something like this:

#%Module
# Define the application name and version
set name automesh
set version 0.3.7

# 1. Prerequisite check (e.g., automesh needs a specific compiler)
# If your app needs a specific compiler, you can ensure it's loaded first:
# prereq gcc/11.2

# 2. Update the PATH variable
# This is the most critical step, allowing the user to run 'automesh' command
prepend-path PATH /opt/hpc/apps/$name/$version/bin

# 3. Update the LD_LIBRARY_PATH variable
# Allows the application to find shared libraries if not statically linked
prepend-path LD_LIBRARY_PATH /opt/hpc/apps/$name/$version/lib

# 4. Define other environment variables (optional)
# For configuration files, data paths, etc.
setenv MYAPP_HOME /opt/hpc/apps/$name/$version

# 5. Provide a short description (optional)
module-whatis "Loads $name $version, a high-performance compute application."

System Configuration

Finally, an HPC administrator needs to ensure that the directory containing the new module file is known to the module system. The administrator must add the root of your module directory (e.g., /opt/hpc/modules) to the central module configuration, typically via a command such as:

module use /opt/hpc/modules

This is usually done in a global system profile script so it is active for all users.

End User

Users can discover and load automesh:

Check for the module: module avail automesh
Load the service: module load automesh/0.3.7 (or module load automesh if it is the default)
Run the program: automesh --version

References

As of Oct 2024, cmake is required for hdf5-metno-src v0.9.2, used for writing Exodus II files. On macOS with brew, install with brew install cmake instead of the GUI installer. ↩

automesh