From 7d6d32104e65ead58c7a8850f062c3118052b950 Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Wed, 6 Mar 2024 09:01:44 +0100 Subject: [PATCH 01/10] Set max resources in jobs --- artifacts/k8s_galaxy.yml | 15 +++++++++++++++ templates/k8s_galaxy.yaml | 2 ++ 2 files changed, 17 insertions(+) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index c859832..7743c82 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -6,6 +6,8 @@ NAMESPACE: galaxy admin_users: "{{ galaxy_admin_users | default('admin@galaxy.com') }}" brand: "{{ galaxy_brand | default('IM Deployed Galaxy K8s Cluster') }}" + max_mem: "{{ galaxy_max_mem | default(0) }}" + max_cores: "{{ galaxy_max_cores | default(0) }}" tasks: - name: Install Git package: name=git @@ -69,6 +71,11 @@ environment: KUBECONFIG: /etc/kubernetes/admin.conf + - name: Remove GB from max_mem + set_fact: + max_mem: "{{ max_mem[:-2] | float - 0.5 }}" + when: max_mem and "GB" in max_mem + - name: Create galaxy helm chart values file copy: dest: /opt/galaxy_values.yaml @@ -84,6 +91,14 @@ galaxy: admin_users: {{ admin_users }} brand: {{ brand }} + jobs: + rules: + tpv_rules_local.yml: + destinations: + k8s: + runner: k8s + {{ 'max_cores: ' ~ max_cores if max_cores else '' }} + {{ 'max_mem: ' ~ max_mem if max_mem else '' }} - name: Deploy Galaxy command: helm install --create-namespace -n {{ NAMESPACE }} galaxy . --timeout 15m -f /opt/galaxy_values.yaml diff --git a/templates/k8s_galaxy.yaml b/templates/k8s_galaxy.yaml index 85a6194..02f3f4e 100644 --- a/templates/k8s_galaxy.yaml +++ b/templates/k8s_galaxy.yaml @@ -70,6 +70,8 @@ topology_template: inputs: galaxy_admin_users: { get_input: galaxy_admin_users } galaxy_brand: { get_input: galaxy_brand } + galaxy_max_memory: { get_input: wn_mem } + galaxy_max_cores: { get_input: wn_cpus } outputs: galaxy_endpoint: From 620c377b4e34af6babdf128928f37bcfcb4c0c8f Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Wed, 6 Mar 2024 09:52:34 +0100 Subject: [PATCH 02/10] Fix set max resources in jobs --- artifacts/k8s_galaxy.yml | 4 ++-- templates/k8s_galaxy.yaml | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 7743c82..1ba8446 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -97,8 +97,8 @@ destinations: k8s: runner: k8s - {{ 'max_cores: ' ~ max_cores if max_cores else '' }} - {{ 'max_mem: ' ~ max_mem if max_mem else '' }} + {{ 'max_cores: ' ~ max_cores if max_cores | int > 0 else '' }} + {{ 'max_mem: ' ~ max_mem if max_mem | int > 0 else '' }} - name: Deploy Galaxy command: helm install --create-namespace -n {{ NAMESPACE }} galaxy . --timeout 15m -f /opt/galaxy_values.yaml diff --git a/templates/k8s_galaxy.yaml b/templates/k8s_galaxy.yaml index 02f3f4e..2521277 100644 --- a/templates/k8s_galaxy.yaml +++ b/templates/k8s_galaxy.yaml @@ -37,8 +37,8 @@ topology_template: - valid_values: [ docker ] wn_num: type: integer - description: Number of WNs in the cluster - default: 2 + description: "Number of WNs in the cluster (Minimum recommended: 3)" + default: 3 required: yes wn_cpus: type: integer @@ -70,7 +70,7 @@ topology_template: inputs: galaxy_admin_users: { get_input: galaxy_admin_users } galaxy_brand: { get_input: galaxy_brand } - galaxy_max_memory: { get_input: wn_mem } + galaxy_max_mem: { get_input: wn_mem } galaxy_max_cores: { get_input: wn_cpus } outputs: From 32f69f3fc36493864c9ab5210dee7c7693c41a5a Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Wed, 6 Mar 2024 10:15:18 +0100 Subject: [PATCH 03/10] Fix set max resources in jobs --- artifacts/k8s_galaxy.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 1ba8446..48e5bd9 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -97,8 +97,8 @@ destinations: k8s: runner: k8s - {{ 'max_cores: ' ~ max_cores if max_cores | int > 0 else '' }} - {{ 'max_mem: ' ~ max_mem if max_mem | int > 0 else '' }} + {{ 'max_cores: ' ~ max_cores if max_cores | int > 0 else '# no max_cores' }} + {{ 'max_mem: ' ~ max_mem if max_mem | int > 0 else '# no max_mem' }} - name: Deploy Galaxy command: helm install --create-namespace -n {{ NAMESPACE }} galaxy . --timeout 15m -f /opt/galaxy_values.yaml From affef585b77786ae6c0f2d4d4d1c4a7d158a98ca Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Wed, 6 Mar 2024 10:28:46 +0100 Subject: [PATCH 04/10] Fix set max resources in jobs --- artifacts/k8s_galaxy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 48e5bd9..808d0b1 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -73,7 +73,7 @@ - name: Remove GB from max_mem set_fact: - max_mem: "{{ max_mem[:-2] | float - 0.5 }}" + max_mem: "{{ max_mem[:-2] | float - 1 }}" when: max_mem and "GB" in max_mem - name: Create galaxy helm chart values file From 08d20211cd576730166cc3d34120e024380bfee0 Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Wed, 6 Mar 2024 12:42:57 +0100 Subject: [PATCH 05/10] try to pack all the pods in the same nodes --- artifacts/k8s_galaxy.yml | 51 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 808d0b1..06dfdcb 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -37,6 +37,34 @@ - when: deployed.rc == 1 block: + - name: Create galaxy helm chart values file + copy: + dest: /opt/galaxy-cvmfs-csi_values.yaml + mode: '644' + content: | + storageClassName: galaxy-cvmfs + cvmfscsi: + cache: + alien: + pvc: + storageClass: managed-nfs-storage + name: cvmfs-alien-cache + # try to pack all the pods in the same nodes + controllerplugin: + affinity: + podAffinity: + preferredDuringSchedulingIgnoredDuringExecution: + - weight: 100 + podAffinityTerm: + topologyKey: "kubernetes.io/hostname" + nodeplugin: + affinity: + podAffinity: + preferredDuringSchedulingIgnoredDuringExecution: + - weight: 100 + podAffinityTerm: + topologyKey: "kubernetes.io/hostname" + - name: Update Galaxy CVMFS CSI chart dependencies command: helm dep up args: @@ -46,7 +74,7 @@ KUBECONFIG: /etc/kubernetes/admin.conf - name: Deploy Galaxy CVMFS CSI - command: helm install --create-namespace -n {{ NAMESPACE }} galaxy-cvmfs . --wait --set storageClassName="galaxy-cvmfs" --set cvmfscsi.cache.alien.pvc.storageClass=managed-nfs-storage --set cvmfscsi.cache.alien.pvc.name="cvmfs-alien-cache" + command: helm install --create-namespace -n {{ NAMESPACE }} galaxy-cvmfs . --wait -f /opt/galaxy-cvmfs-csi_values.yaml args: chdir: /opt/galaxy-cvmfs-csi-helm/galaxy-cvmfs-csi environment: @@ -99,6 +127,27 @@ runner: k8s {{ 'max_cores: ' ~ max_cores if max_cores | int > 0 else '# no max_cores' }} {{ 'max_mem: ' ~ max_mem if max_mem | int > 0 else '# no max_mem' }} + # try to pack all the pods in the same nodes + affinity: + podAffinity: + preferredDuringSchedulingIgnoredDuringExecution: + - weight: 100 + podAffinityTerm: + topologyKey: "kubernetes.io/hostname" + postgresql: + affinity: + podAffinity: + preferredDuringSchedulingIgnoredDuringExecution: + - weight: 100 + podAffinityTerm: + topologyKey: "kubernetes.io/hostname" + rabbitmq: + affinity: + podAffinity: + preferredDuringSchedulingIgnoredDuringExecution: + - weight: 100 + podAffinityTerm: + topologyKey: "kubernetes.io/hostname" - name: Deploy Galaxy command: helm install --create-namespace -n {{ NAMESPACE }} galaxy . --timeout 15m -f /opt/galaxy_values.yaml From 07275d656031af091024a15c65ff95596a2534c0 Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Wed, 6 Mar 2024 13:33:49 +0100 Subject: [PATCH 06/10] Fix affinity --- artifacts/k8s_galaxy.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 06dfdcb..00f30d9 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -134,6 +134,12 @@ - weight: 100 podAffinityTerm: topologyKey: "kubernetes.io/hostname" + labelSelector: + matchExpressions: + - key: app.kubernetes.io/instance + operator: In + values: + - galaxy postgresql: affinity: podAffinity: @@ -141,6 +147,12 @@ - weight: 100 podAffinityTerm: topologyKey: "kubernetes.io/hostname" + labelSelector: + matchExpressions: + - key: app.kubernetes.io/instance + operator: In + values: + - galaxy rabbitmq: affinity: podAffinity: @@ -148,6 +160,12 @@ - weight: 100 podAffinityTerm: topologyKey: "kubernetes.io/hostname" + labelSelector: + matchExpressions: + - key: app.kubernetes.io/instance + operator: In + values: + - galaxy - name: Deploy Galaxy command: helm install --create-namespace -n {{ NAMESPACE }} galaxy . --timeout 15m -f /opt/galaxy_values.yaml From a7f83e92ce46ec7946ea1fb2fe2f92acd5ac670c Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Thu, 7 Mar 2024 07:53:25 +0100 Subject: [PATCH 07/10] Split install --- artifacts/k8s_galaxy.yml | 174 ++++++++++++++++++++------------------- 1 file changed, 90 insertions(+), 84 deletions(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 00f30d9..e0687d8 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -4,27 +4,84 @@ connection: local vars: NAMESPACE: galaxy + AFFINITY: + affinity: + podAffinity: + preferredDuringSchedulingIgnoredDuringExecution: + - weight: 100 + podAffinityTerm: + topologyKey: "kubernetes.io/hostname" + labelSelector: + matchExpressions: + - key: app.kubernetes.io/instance + operator: In + values: + - galaxy + - postgres-operator + - rabbitmq-operator admin_users: "{{ galaxy_admin_users | default('admin@galaxy.com') }}" brand: "{{ galaxy_brand | default('IM Deployed Galaxy K8s Cluster') }}" max_mem: "{{ galaxy_max_mem | default(0) }}" max_cores: "{{ galaxy_max_cores | default(0) }}" tasks: - - name: Install Git - package: name=git - - - name: Clone galaxy-cvmfs-csi-helm git repo - git: - repo: https://github.com/CloudVE/galaxy-cvmfs-csi-helm - dest: /opt/galaxy-cvmfs-csi-helm - update: false - version: "master" - - - name: Clone galaxy-helm git repo - git: - repo: https://github.com/galaxyproject/galaxy-helm - dest: /opt/galaxy-helm - update: false - version: "master" + + - name: "Check if postgres-operator is already deployed" + command: helm status postgres-operator -n {{ NAMESPACE }} + register: deployed + failed_when: deployed.rc != 0 and deployed.rc != 1 + changed_when: false + environment: + KUBECONFIG: /etc/kubernetes/admin.conf + + - when: deployed.rc == 1 + block: + + - name: Create postgres-operator helm chart values file + copy: + dest: /opt/postgres_values.yaml + mode: '644' + content: "{{ AFFINITY | to_nice_yaml }}" + + - name: Add helm repo postgres-operator-charts + command: helm repo add postgres-operator-charts https://opensource.zalando.com/postgres-operator/charts/postgres-operator + environment: + KUBECONFIG: /etc/kubernetes/admin.conf + + - name: Deploy postgres-operator + command: helm install -n {{ NAMESPACE }} --create-namespace postgres-operator postgres-operator-charts/postgres-operator --version 1.9.0 -f /opt/postgres_values.yaml --wait + environment: + KUBECONFIG: /etc/kubernetes/admin.conf + + - name: "Check if rabbitmq-operator is already deployed" + command: helm status rabbitmq-operator -n {{ NAMESPACE }} + register: deployed + failed_when: deployed.rc != 0 and deployed.rc != 1 + changed_when: false + environment: + KUBECONFIG: /etc/kubernetes/admin.conf + + - when: deployed.rc == 1 + block: + + - name: Create rabbitmq-operator helm chart values file + copy: + dest: /opt/rabbitmq_values.yaml + mode: '644' + content: | + clusterOperator: + {{ AFFINITY | to_nice_yaml(indent=2) }} + msgTopologyOperator: + {{ AFFINITY | to_nice_yaml(indent=2) }} + + - name: Add helm repo bitnami + command: helm repo add bitnami https://charts.bitnami.com/bitnami + environment: + KUBECONFIG: /etc/kubernetes/admin.conf + + - name: Deploy postgres-operator + command: helm install -n {{ NAMESPACE }} --create-namespace rabbitmq-operator bitnami/rabbitmq-cluster-operator --version 2.6.12 -f /opt/rabbitmq_values.yaml + environment: + KUBECONFIG: /etc/kubernetes/admin.conf - name: "Check if galaxy-cvmfs is already deployed" command: helm status galaxy-cvmfs -n {{ NAMESPACE }} @@ -51,32 +108,17 @@ name: cvmfs-alien-cache # try to pack all the pods in the same nodes controllerplugin: - affinity: - podAffinity: - preferredDuringSchedulingIgnoredDuringExecution: - - weight: 100 - podAffinityTerm: - topologyKey: "kubernetes.io/hostname" + {{ AFFINITY | to_nice_yaml(indent=2) }} nodeplugin: - affinity: - podAffinity: - preferredDuringSchedulingIgnoredDuringExecution: - - weight: 100 - podAffinityTerm: - topologyKey: "kubernetes.io/hostname" - - - name: Update Galaxy CVMFS CSI chart dependencies - command: helm dep up - args: - chdir: /opt/galaxy-cvmfs-csi-helm/galaxy-cvmfs-csi - creates: /opt/galaxy-cvmfs-csi-helm/galaxy-cvmfs-csi/charts + {{ AFFINITY | to_nice_yaml(indent=2) }} + + - name: Add helm repo galaxy + command: helm repo add galaxy https://raw.githubusercontent.com/CloudVE/helm-charts/master/ environment: KUBECONFIG: /etc/kubernetes/admin.conf - name: Deploy Galaxy CVMFS CSI - command: helm install --create-namespace -n {{ NAMESPACE }} galaxy-cvmfs . --wait -f /opt/galaxy-cvmfs-csi_values.yaml - args: - chdir: /opt/galaxy-cvmfs-csi-helm/galaxy-cvmfs-csi + command: helm install --create-namespace -n {{ NAMESPACE }} galaxy-cvmfs galaxy/galaxy-cvmfs-csi --wait -f /opt/galaxy-cvmfs-csi_values.yaml --version 2.2.0 environment: KUBECONFIG: /etc/kubernetes/admin.conf @@ -91,14 +133,6 @@ - when: deployed.rc == 1 block: - - name: Update Galaxy chart dependencies - command: helm dep up - args: - chdir: /opt/galaxy-helm/galaxy - creates: /opt/galaxy-helm/galaxy/charts - environment: - KUBECONFIG: /etc/kubernetes/admin.conf - - name: Remove GB from max_mem set_fact: max_mem: "{{ max_mem[:-2] | float - 1 }}" @@ -114,6 +148,10 @@ cvmfs: deploy: false storageClassName: galaxy-cvmfs + postgresql: + deploy: false + rabbitmq: + deploy: false configs: galaxy.yml: galaxy: @@ -128,47 +166,15 @@ {{ 'max_cores: ' ~ max_cores if max_cores | int > 0 else '# no max_cores' }} {{ 'max_mem: ' ~ max_mem if max_mem | int > 0 else '# no max_mem' }} # try to pack all the pods in the same nodes - affinity: - podAffinity: - preferredDuringSchedulingIgnoredDuringExecution: - - weight: 100 - podAffinityTerm: - topologyKey: "kubernetes.io/hostname" - labelSelector: - matchExpressions: - - key: app.kubernetes.io/instance - operator: In - values: - - galaxy - postgresql: - affinity: - podAffinity: - preferredDuringSchedulingIgnoredDuringExecution: - - weight: 100 - podAffinityTerm: - topologyKey: "kubernetes.io/hostname" - labelSelector: - matchExpressions: - - key: app.kubernetes.io/instance - operator: In - values: - - galaxy - rabbitmq: - affinity: - podAffinity: - preferredDuringSchedulingIgnoredDuringExecution: - - weight: 100 - podAffinityTerm: - topologyKey: "kubernetes.io/hostname" - labelSelector: - matchExpressions: - - key: app.kubernetes.io/instance - operator: In - values: - - galaxy + {{ AFFINITY | to_nice_yaml(indent=2) }} + + - name: Add helm repo galaxy + command: helm repo add galaxy https://raw.githubusercontent.com/CloudVE/helm-charts/master/ + environment: + KUBECONFIG: /etc/kubernetes/admin.conf - name: Deploy Galaxy - command: helm install --create-namespace -n {{ NAMESPACE }} galaxy . --timeout 15m -f /opt/galaxy_values.yaml + command: helm install --create-namespace -n {{ NAMESPACE }} galaxy galaxy/galaxy --timeout 15m -f /opt/galaxy_values.yaml --version 5.9.0 args: chdir: /opt/galaxy-helm/galaxy environment: From 5a5b2a5cf6d9833300724ab16edc3ebb0b696b0b Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Thu, 7 Mar 2024 08:30:09 +0100 Subject: [PATCH 08/10] Fix errors --- artifacts/k8s_galaxy.yml | 42 +++++++++++++++++++--------------------- 1 file changed, 20 insertions(+), 22 deletions(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index e0687d8..2ebc6a7 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -8,17 +8,17 @@ affinity: podAffinity: preferredDuringSchedulingIgnoredDuringExecution: - - weight: 100 - podAffinityTerm: - topologyKey: "kubernetes.io/hostname" - labelSelector: - matchExpressions: - - key: app.kubernetes.io/instance - operator: In - values: - - galaxy - - postgres-operator - - rabbitmq-operator + - weight: 100 + podAffinityTerm: + topologyKey: "kubernetes.io/hostname" + labelSelector: + matchExpressions: + - key: app.kubernetes.io/instance + operator: In + values: + - galaxy + - postgres-operator + - rabbitmq-operator admin_users: "{{ galaxy_admin_users | default('admin@galaxy.com') }}" brand: "{{ galaxy_brand | default('IM Deployed Galaxy K8s Cluster') }}" max_mem: "{{ galaxy_max_mem | default(0) }}" @@ -40,7 +40,7 @@ copy: dest: /opt/postgres_values.yaml mode: '644' - content: "{{ AFFINITY | to_nice_yaml }}" + content: "{{ AFFINITY | to_yaml }}" - name: Add helm repo postgres-operator-charts command: helm repo add postgres-operator-charts https://opensource.zalando.com/postgres-operator/charts/postgres-operator @@ -48,7 +48,7 @@ KUBECONFIG: /etc/kubernetes/admin.conf - name: Deploy postgres-operator - command: helm install -n {{ NAMESPACE }} --create-namespace postgres-operator postgres-operator-charts/postgres-operator --version 1.9.0 -f /opt/postgres_values.yaml --wait + command: helm install -n {{ NAMESPACE }} --create-namespace postgres-operator postgres-operator-charts/postgres-operator --version 1.9.0 -f /opt/postgres_values.yaml --wait environment: KUBECONFIG: /etc/kubernetes/admin.conf @@ -69,17 +69,17 @@ mode: '644' content: | clusterOperator: - {{ AFFINITY | to_nice_yaml(indent=2) }} + {{ AFFINITY | to_yaml(indent=4) }} msgTopologyOperator: - {{ AFFINITY | to_nice_yaml(indent=2) }} + {{ AFFINITY | to_yaml(indent=4) }} - name: Add helm repo bitnami command: helm repo add bitnami https://charts.bitnami.com/bitnami environment: KUBECONFIG: /etc/kubernetes/admin.conf - - name: Deploy postgres-operator - command: helm install -n {{ NAMESPACE }} --create-namespace rabbitmq-operator bitnami/rabbitmq-cluster-operator --version 2.6.12 -f /opt/rabbitmq_values.yaml + - name: Deploy rabbitmq-operator + command: helm install -n {{ NAMESPACE }} --create-namespace rabbitmq-operator bitnami/rabbitmq-cluster-operator --version 2.6.12 -f /opt/rabbitmq_values.yaml environment: KUBECONFIG: /etc/kubernetes/admin.conf @@ -108,9 +108,9 @@ name: cvmfs-alien-cache # try to pack all the pods in the same nodes controllerplugin: - {{ AFFINITY | to_nice_yaml(indent=2) }} + {{ AFFINITY | to_yaml(indent=4) }} nodeplugin: - {{ AFFINITY | to_nice_yaml(indent=2) }} + {{ AFFINITY | to_yaml(indent=4) }} - name: Add helm repo galaxy command: helm repo add galaxy https://raw.githubusercontent.com/CloudVE/helm-charts/master/ @@ -166,7 +166,7 @@ {{ 'max_cores: ' ~ max_cores if max_cores | int > 0 else '# no max_cores' }} {{ 'max_mem: ' ~ max_mem if max_mem | int > 0 else '# no max_mem' }} # try to pack all the pods in the same nodes - {{ AFFINITY | to_nice_yaml(indent=2) }} + {{ AFFINITY | to_yaml }} - name: Add helm repo galaxy command: helm repo add galaxy https://raw.githubusercontent.com/CloudVE/helm-charts/master/ @@ -175,8 +175,6 @@ - name: Deploy Galaxy command: helm install --create-namespace -n {{ NAMESPACE }} galaxy galaxy/galaxy --timeout 15m -f /opt/galaxy_values.yaml --version 5.9.0 - args: - chdir: /opt/galaxy-helm/galaxy environment: KUBECONFIG: /etc/kubernetes/admin.conf From f6b726126ad0f10f9cb4b999dc359cf2196185db Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Thu, 7 Mar 2024 09:01:25 +0100 Subject: [PATCH 09/10] Fix errors --- artifacts/k8s_galaxy.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 2ebc6a7..13a0d43 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -163,7 +163,7 @@ destinations: k8s: runner: k8s - {{ 'max_cores: ' ~ max_cores if max_cores | int > 0 else '# no max_cores' }} + {{ 'max_cores: ' ~ (max_cores | int - 1) if max_cores | int > 0 else '# no max_cores' }} {{ 'max_mem: ' ~ max_mem if max_mem | int > 0 else '# no max_mem' }} # try to pack all the pods in the same nodes {{ AFFINITY | to_yaml }} @@ -174,9 +174,10 @@ KUBECONFIG: /etc/kubernetes/admin.conf - name: Deploy Galaxy - command: helm install --create-namespace -n {{ NAMESPACE }} galaxy galaxy/galaxy --timeout 15m -f /opt/galaxy_values.yaml --version 5.9.0 + command: helm install --create-namespace -n {{ NAMESPACE }} galaxy galaxy/galaxy --timeout 10m -f /opt/galaxy_values.yaml --version 5.9.0 environment: KUBECONFIG: /etc/kubernetes/admin.conf + ignore_errors: yes - name: Wait pods to be ready pause: From 079b90f83305546306356caef9941f69b6fef96e Mon Sep 17 00:00:00 2001 From: Miguel Caballer Date: Thu, 7 Mar 2024 09:06:23 +0100 Subject: [PATCH 10/10] Fix errors --- artifacts/k8s_galaxy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/artifacts/k8s_galaxy.yml b/artifacts/k8s_galaxy.yml index 13a0d43..ccff10a 100644 --- a/artifacts/k8s_galaxy.yml +++ b/artifacts/k8s_galaxy.yml @@ -177,7 +177,7 @@ command: helm install --create-namespace -n {{ NAMESPACE }} galaxy galaxy/galaxy --timeout 10m -f /opt/galaxy_values.yaml --version 5.9.0 environment: KUBECONFIG: /etc/kubernetes/admin.conf - ignore_errors: yes + ignore_errors: true - name: Wait pods to be ready pause: