https://github.com/erikzenker/arch-linux-cluster

Using arch linux distro to build a full cluster system
https://github.com/erikzenker/arch-linux-cluster

Last synced: 26 days ago
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Using arch linux distro to build a full cluster system

• Host: GitHub
• URL: https://github.com/erikzenker/arch-linux-cluster
• Owner: erikzenker
• License: gpl-3.0
• Created: 2016-10-23T19:41:56.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2018-10-22T18:49:02.000Z (about 6 years ago)
• Last Synced: 2024-10-30T01:44:47.883Z (2 months ago)
• Size: 31.3 KB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        


# Arch Linux Cluster

Using arch linux distro to build a full cluster system.

## Installing the Base System

* Use antergos minimal image with base setup

* Install base software packages

  - base

  - base-devel

  - emacs-nox

  - git

  - pacaur

* Basic setup

  - Set hostname in `/etc/hostname`

## Installing SSH Server

* Install `openssh` package: `# pacman -S openssh`

* Start ssh daemon: `# systemctl enable sshd.service`

* Login: `ssh -p 22 User@HOSTNAME`

* Login node reachable from outside

* Compute nodes only reachable from login node

## Installing Network Filesystem

## Installing Batch System

## Installing Module System / Adding Further Software

### Using Nix

* Install nix `yaourt -S nix-multiuser`

  - `# mkdir -p /etc/nix`

  - `# touch /etc/nix/nix.conf`

  - `# echo "build-users-group = nixbld" > /etc/nix/nix.conf`

  - `# systemctl enable --now nix-daemon.socket` (restart shell necessary)

  - `# nix-channel --add https://nixos.org/channels/nixpkgs-unstable`

  - `# nix-channel --update`

  - `export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt`

  - Add `~/.nix-profile/bin` to `$PATH`

* Usage nix

  - Install packages: `nix-env -i PACKAGE_NAME`

  - Uninstall packages: `nix-env -e PACKAGE_NAME`

  - Search packages: `nix-env -qaP | grep PACKAGE_NAME`

  - Switch profile: `nix-env --switch-profile /nix/var/nix/profiles/my-profile`

  - create new profile: `cp -r OLD_PROFILE_PATH NEW_PROFILE_PATH`

  - List profiles: `ls /nix/var/nix/profiles/per-user/$USER`

  - List generations: `nix-env --list-generations`

  - Remove generations: `nix-env --delete-generations`

  - Switch generation: `nix-env -G GENERATION`

  - Switch to previous generaion: `nix-env --rollback`

  - List packages of current generation: `nix-env -q`

* Q&A:

  - Install nix-packets as non-root user?

    - Remove: `~/.nix-profile`

    - Run: `https://gist.github.com/erikzenker/807e9a39706e2ca1312ee052eaeaae22`

  - How to provide some kind of profile per user?

    - Provide a profiles folder: `~/profiles/`

    - Use nix file `my_profile.nix` and `nix-shell`

    - Set packages `nix-env --set PACKAGES`

  - Why takes cmake the gcc compiler from the overall default profile?

  - Cmake: the c compiler is not able to compile a simple test program

    - clang works / gcc currently not

### Using Spack

* Install spack: `git clone https://github.com/llnl/spack.git`

* Use bash: `bash`

* Usage spack

  - Install packages: `spack install PACKAGE_NAME@VERSION_NUMBER`

  - Use a particular compiler: `spack install PACKAGE_NAME@VERSION_NUMBER %COMPILER_NAME@COMPILER_VERSION`

    - to install with root `export FORCE_UNSAFE_CONFIGURE=1`

  - Show compilers: `spack compilers`  

  - Uninstall packages: `spack uninstall PACKAGE_NAME`

  - List installed packages: `spack find`

  - Search packages: `spack list PACKAGE_NAME`

  - List package versions: `spack versions PACKAGE_NAME`

  - Print package info: `spack info PACKAGE_NAME`

  - Switch prefix: `spack bootstrap NEW_PREFIX`

  

* Usage with environmental modules

  - Install the env-modules package: `pacaur -S env-modules`

  - Source init script for the particular shell: `source /etc/modules/init/bash`

  - Setup spack env for bash: `./share/spack/setup-env.sh`

  - List avail modules: `module avail`

  - Load module: `module load MODULE_NAME`

  - Unload module: `module unload MODULE_NAME`

  - List loaded modules: `module list`

  

* Known issues:

  - gcc 7.3.0/6.4.0 etc. might not be compilable by clang, or gcc 8.2.0

  

### Using Conda

### Using Linuxbrew

* Install linuxbrew: `pacaur -S linuxbrew`

* Set directory permissions

* Usage linuxbrew

  - Install packages: `brew install PACKAGE_NAME@VERSION_NUMBER`

  - Search packages: `brew search PACKAGE_NAME`

  

  

## Maintainance

* Refresh keys: `# pacman-key --refresh-keys`

* Update packets: `# pacman -Syu`

## Automatation of Node Installation

### Using Ansible

* Install ansible on control host: `# pacman -S ansible`

* Add public key of control host to ansible slaves in `authorized_keys`

* Add login and compute nodes to ansible hosts in `/etc/ansible/hosts`

  ```

  [login]

  IP:PORT

  

  [compute]

  IP:PORT

  ```

* Run playbook: `ansible-playbook -b --become-method=sudo --ask-become-pass PLAYBOOK.yml`

  * [Login node playbook yml](login_base_system.yml)

### Using Docker

## Useful Links

* [Gentoo HPC Guide](https://wiki.gentoo.org/wiki/High_Performance_Computing_on_Gentoo)

* [Slurm](https://wiki.archlinux.org/index.php/Slurm)

* [Nix Package Manager Howto](https://nixos.org/nixos/manual/index.html#sec-ad-hoc-packages)

* [Environmental Modules](http://www.admin-magazine.com/HPC/Articles/Environment-Modules)

* [Lmod: Environmental Modules Alternative](http://www.admin-magazine.com/HPC/Articles/Lmod-Alternative-Environment-Modules)

* [Ansible Documetation](https://docs.ansible.com/ansible/latest/index.html)