Slurm Refactoring and Improvements

Overview

After the initial Slurm deployment (documented in chapter 032), the cluster faced performance and reliability challenges that required significant refactoring. The monolithic setup role was taking 10+ minutes to execute and had idempotency issues, while memory configuration mismatches caused node validation failures.

It's my fault - it's because of my laziness. So this chapter is essentially me saying "yeah, I did a shitty thing, and so now I have to fix it."

Problems Identified

Performance Issues

Setup Duration: The original goldentooth.setup_slurm role took over 10 minutes
Non-idempotent: Re-running the role would repeat expensive operations
Monolithic Design: Single role handled everything from basic Slurm to complex HPC software stacks

Node Validation Failures

Memory Mismatch: karstark and lipps nodes (4GB Pi 4s) were configured with 4096MB but only had ~3797MB available
Invalid State: These nodes showed as "inval" in sinfo output
Authentication Issues: MUNGE key synchronization problems across nodes

Configuration Management

Static Memory Values: All nodes hardcoded to 4096MB regardless of actual capacity
Limited Flexibility: Single configuration approach didn't account for hardware variations

Refactoring Solution

Modular Role Architecture

Split the monolithic role into focused components:

Core Components (`goldentooth.setup_slurm_core`)

Purpose: Essential Slurm and MUNGE setup only
Duration: Reduced from 10+ minutes to ~50 seconds
Scope: Package installation, basic configuration, service management
Features: MUNGE key synchronization, systemd PID file fixes

Specialized Modules

goldentooth.setup_lmod: Environment module system
goldentooth.setup_hpc_software: HPC software stack (OpenMPI, Singularity, Conda)
goldentooth.setup_slurm_modules: Module files for installed software

Dynamic Memory Detection

Replaced static memory configuration with dynamic detection:

# Before: Static configuration
NodeName=DEFAULT CPUs=4 RealMemory=4096 Sockets=1 CoresPerSocket=4 ThreadsPerCore=1 State=UNKNOWN

# After: Dynamic per-node configuration
NodeName=DEFAULT CPUs=4 Sockets=1 CoresPerSocket=4 ThreadsPerCore=1 State=UNKNOWN
{% for slurm_compute_name in groups['slurm_compute'] %}
NodeName={{ slurm_compute_name }} NodeAddr={{ hostvars[slurm_compute_name].ipv4_address }} RealMemory={{ hostvars[slurm_compute_name].ansible_memtotal_mb }}
{% endfor %}

Node Exclusion Strategy

For nodes with insufficient memory (karstark, lipps):

Inventory Update: Removed from slurm_compute group
Service Cleanup: Stopped and disabled slurmd/munge services
Package Removal: Uninstalled Slurm packages to prevent conflicts

Implementation Details

MUNGE Key Synchronization

Added permanent solution to MUNGE authentication issues:

- name: 'Synchronize MUNGE keys across cluster'
  block:
    - name: 'Retrieve MUNGE key from first controller'
      ansible.builtin.slurp:
        src: '/etc/munge/munge.key'
      register: 'controller_munge_key'
      run_once: true
      delegate_to: "{{ groups['slurm_controller'] | first }}"

    - name: 'Distribute MUNGE key to all nodes'
      ansible.builtin.copy:
        content: "{{ controller_munge_key.content | b64decode }}"
        dest: '/etc/munge/munge.key'
        owner: 'munge'
        group: 'munge'
        mode: '0400'
        backup: yes
      when: inventory_hostname != groups['slurm_controller'] | first
      notify: 'Restart MUNGE'

SystemD Integration Fixes

Resolved PID file path mismatches:

- name: 'Fix slurmctld pidfile path mismatch'
  ansible.builtin.copy:
    content: |
      [Service]
      PIDFile=/var/run/slurm/slurmctld.pid
    dest: '/etc/systemd/system/slurmctld.service.d/override.conf'
    mode: '0644'
  when: inventory_hostname in groups['slurm_controller']
  notify: 'Reload systemd and restart slurmctld'

NFS Permission Resolution

Fixed directory permissions that prevented slurm user access:

# Fixed root directory permissions on NFS server
chmod 755 /mnt/usb1  # Was 700, preventing slurm user access

Results

Performance Improvements

Setup Time: Reduced from 10+ minutes to ~50 seconds for core functionality
Idempotency: Role can be safely re-run without expensive operations
Modularity: Users can choose which components to install

Cluster Health

Node Status: 9 nodes operational and idle
Authentication: MUNGE working consistently across all nodes
Resource Detection: Accurate memory reporting per node

Final Cluster State

general*     up   infinite      9   idle bettley,cargyll,dalt,erenford,fenn,gardener,harlton,inchfield,jast
debug        up   infinite      9   idle bettley,cargyll,dalt,erenford,fenn,gardener,harlton,inchfield,jast

Goldentooth