Install and configure Apptainer and Nextflow

Author: m-bull

ansible/extras.yml

@@ -48,6 +48,26 @@
         name: cuda
         tasks_from: "{{ 'runtime.yml' if appliances_mode == 'configure' else 'install.yml' }}"
 
+- name: Setup Apptainer
+  hosts: apptainer
+  gather_facts: yes
+  tags: apptainer
+  tasks:
+    - name: Install and configure Apptainer
+      include_role:
+        name: azimuth_cloud.image_utils.apptainer
+        tasks_from: "{{ 'configure.yml' if appliances_mode == 'configure' else 'main.yml' }}"
+
+- name: Setup Apptainer
+  hosts: nextflow
+  gather_facts: yes
+  tags: nextflow
+  tasks:
+    - name: Install and configure Nextflow
+      include_role:
+        name: azimuth_cloud.image_utils.nextflow
+        tasks_from: "{{ 'configure.yml' if appliances_mode == 'configure' else 'main.yml' }}"
+
 - name: Persist hostkeys across rebuilds
   # Must be after filesystems.yml (for storage)
   # and before portal.yml (where OOD login node hostkeys are scanned)

environments/.stackhpc/tofu/cluster_image.auto.tfvars.json

@@ -1,6 +1,6 @@
 {
     "cluster_image": {
-        "RL8": "openhpc-RL8-250514-1502-5a923b2c",
-        "RL9": "openhpc-RL9-250514-1502-5a923b2c"
+        "RL8": "openhpc-RL8-250204-1352-8d071ba8",
+        "RL9": "openhpc-RL9-250204-1432-8d071ba8"
     }
 }

environments/common/inventory/group_vars/all/apptainer.yml

@@ -0,0 +1,7 @@
+---
+
+# Mounting /tmp by default can break assumptions made
+# by some containers used in nf-core workflows.
+apptainer_config_overrides:
+  - directive: "mount tmp"
+    value: "no"

environments/common/inventory/group_vars/all/nextflow.yml

@@ -0,0 +1,4 @@
+---
+
+nextflow_skel_config: |
+  process.executor = 'slurm'

environments/common/inventory/group_vars/all/openhpc.yml

@@ -38,7 +38,6 @@ openhpc_packages_default:
   - ohpc-gnu12-openmpi4-perf-tools # for hpctests
   - openblas-gnu12-ohpc # for hpctests (HPL)
   # EPEL packages:
-  - apptainer
   - podman-compose
 openhpc_packages_extra: []
 openhpc_packages: "{{ (openhpc_packages_default + openhpc_packages_extra) | select | list }}"

environments/common/inventory/groups

@@ -182,3 +182,9 @@ extra_packages
 
 [gateway]
 # Add builder to this group to install gateway ansible-init playbook into image
+
+[apptainer]
+# Hosts to install and configure Apptainer on
+
+[nextflow]
+# Hosts to install and configure Nextflow on

environments/common/layouts/everything

@@ -125,3 +125,10 @@ builder
 [gateway:children]
 # Add builder to this group to install gateway ansible-init playbook into image
 builder
+
+[apptainer:children]
+login
+compute
+
+[nextflow:children]
+login

requirements.yml

@@ -48,7 +48,7 @@ collections:
     version: 0.4.0
   - name: https://github.com/azimuth-cloud/ansible-collection-image-utils
     type: git
-    version: 0.5.0
+    version: apptainer
   # stackhpc.pulp has pulp.squeezer as dependency, any version, but latest
   # requires newer ansible than can install
   - name: pulp.squeezer