fedora-sc-builder

A cjr stack for scientific computing based on Fedora and dnf. This stack is used to build images for the fedora-sc stack. It can also be used as a highly customizable standalone stack.

Description

This stack creates a non-root user with matching user id and group id as the host user, and uses dnf to install basic support for any subset of the following:

1. Languages
   • c, c++
   • Fortran
   • Python 3
   • Julia
   • R
   • Latex
2. Libraries
   • Matplotlib
   • Ray (Temporarily Disabled)
   • BLAS, LAPACK
   • OPENMPI, mpi4py
   • X11
3. Dev Environments
   • Jupyter notebook, Jupyter lab
   • Theia
   • vim, git, vim, emacs, tmux
4. Additional Software
   • spack
   • tigervnc
   • slurm
   • sshd

The configurations for Jupyter and Theia are respectively stored the directories config/jupyter and config/theia which are bound to ~/.jupyter and ~/.theia in the container.

Installation

To use use this stack with cjr simply run the command

cjr stack:pull https://github.com/container-job-runner/stack-fedora-basic.git

or manually clone the repository into your cjr stacks directory.

You can then build the stack by running

cjr stack:build stack-fedora-basic

By default this stack does not install any dependencies. To configure the software list see the following customization section.

Customization

By editing the args in config.yml and setting fields to TRUE you can enable any of the items listed above. For example, by changing the following fields in config.yml

# ---- languages -----------------------------------------------------------
LANG_C: "TRUE"
LANG_FORTRAN: "TRUE"
LANG_PYTHON3: "TRUE"
LANG_JULIA: "FALSE"
LANG_R: "FALSE"
LANG_LATEX: "FALSE"
# ---- libraries -----------------------------------------------------------
LIB_MATPLOTLIB : "TRUE"
LIB_LINALG : "FALSE"
LIB_OPENMPI: "FALSE"
LIB_X11: "FALSE"
# ---- dev enviroment ------------------------------------------------------
DEV_JUPYTER: "TRUE"
DEV_THEIA: "FALSE"
DEV_CLI: "FALSE"
# ---- additional software -------------------------------------------------
ASW_SPACK: "FALSE"
ASW_VNC: "FALSE"

the stack will contain basic language dependencies for c, c++, python, the matplotlib library and Jupyter. Note that after changing the params you will need to rebuild the stack (e.g. cjr stack:build stack-fedora-basic)

Additional dependencies can be installed by modifying the files

• build/scripts/root/install-extra.sh
• build/scripts/user/install-extra.sh

To modify the main package install process, modify the files

• build/scripts/root/install.sh
• build/scripts/user/install.sh

Profiles: This stack contains the following profiles:

• all : installs everything.
• reference: used to build official cjr fedora-sc image
• LANGUAGE-IDE where LANGUAGE can be either 'fortran', 'python', or 'julia' and IDE can be 'jupyter' or 'theia'.
• LANGUAGE where LANGUAGE can be either 'c', 'fortran', 'python', 'julia', or 'octave'

Theia Plugins: Additional plugins can be installed by adding .vsix extension files to the directory config/theia/plugins. Note that Theia does not yet support all vs code extensions correctly, especially the latest versions. Several recommended extensions and their versions are:

• Python: vscode-python, version 2020.10.332292344.
• Julia: julia-vscode, version 0.15.40.
• C/C++: vscode-cpptools, version 0.28.3.
• Fortran: Modern Fortran, version 2.2.1. (Requires vscode-cpptools)

User Settings: The container user's username, password, and sudo privileges can also be modified by adjusting the user args in config.yml