hcls/namd-on-slurm/namd-slurm.yaml

# Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

---

# See instructions at
# https://github.com/GoogleCloudPlatform/hpc-toolkit/tree/main/examples#image-builderyaml-

blueprint_name: namd-slurm

vars:
  project_id:  ## Set GCP Project ID Here ##
  deployment_name: namd-slurm
  region: us-central1
  zone: us-central1-c
  custom_image:
    family: apptainer-enabled
    project: $(vars.project_id)
  disk_size: 64
  bucket_prefix: namd_bucket

# Documentation for each of the modules used below can be found at
# https://github.com/GoogleCloudPlatform/hpc-toolkit/blob/main/modules/README.md

deployment_groups:
- group: primary
  modules:
  - id: network
    source: modules/network/vpc
  - id: enable_apis
    source: community/modules/project/service-enablement
    settings:
      gcp_service_list: [
        "cloudresourcemanager.googleapis.com",
        "container.googleapis.com",
        "logging.googleapis.com",
        "compute.googleapis.com"
      ]
  - id: homefs
    source: modules/file-system/filestore
    use: [network]
    settings:
      local_mount: /home

  - id: hpc_dash
    source: modules/monitoring/dashboard
    settings:
      title: HPC


  - id: scripts_for_image
    source: modules/scripts/startup-script
    settings:
      runners:
      - type: shell
        destination: install_apptainer.sh
        content: |
          #!/bin/sh
          dnf install -y epel-release
          dnf install -y apptainer

  - id: startup
    source: modules/scripts/startup-script
    settings:
      #install_cloud_ops_agent: true
      runners:
      - type: shell
        destination: "/tmp/apptainer.sh"
        content: |
          #!/bin/sh
          dnf install -y epel-release && sudo dnf install -y apptainer-suid
  - id: startup_login
    source: modules/scripts/startup-script
    settings:
      runners:
      - type: shell
        destination: "/tmp/apptainer.sh"
        content: |
          #!/bin/sh
          dnf install -y epel-release && sudo dnf install -y apptainer-suid
      - type: data
        destination: "/tmp/namd_apoa1.job"
        content: $(file(ghpc_stage("namd_apoa1.job")))
      - type: data
        destination: "/tmp/namd_stmv.job"
        content: $(file(ghpc_stage("namd_stmv.job")))
      - type: data
        destination: "/tmp/get_data.sh"
        content: $(file(ghpc_stage("get_data.sh")))
  - id: data_bucket
    source: community/modules/file-system/cloud-storage-bucket
    settings:
      name_prefix: $(vars.bucket_prefix)
      random_suffix: true
      force_destroy: true
      local_mount: /mnt/data_bucket
      mount_options: defaults,_netdev,implicit_dirs,allow_other,dir_mode=0777,file_mode=766


- group: packer
  modules:
  - id: apptainer-enabled-image
    source: modules/packer/custom-image
    kind: packer
    use:
    - network
    - scripts_for_image
    settings:
      source_image_project_id: [schedmd-slurm-public]
      # see latest in https://github.com/GoogleCloudPlatform/slurm-gcp/blob/master/docs/images.md#published-image-family
      source_image_family: slurm-gcp-6-8-hpc-rocky-linux-8
      # You can find size of source image by using following command
      # gcloud compute images describe-from-family <source_image_family> --project schedmd-slurm-public
      disk_size: $(vars.disk_size)
      image_family: $(vars.custom_image.family)
      state_timeout: 15m

- group: cluster
  modules:
  - id: compute_nodeset
    source: community/modules/compute/schedmd-slurm-gcp-v6-nodeset
    use: [network]
    settings:
      node_count_dynamic_max: 20
      disk_size_gb: $(vars.disk_size)
      instance_image: $(vars.custom_image)
      instance_image_custom: true
      bandwidth_tier: gvnic_enabled
      allow_automatic_updates: false

  - id: compute_partition
    source: community/modules/compute/schedmd-slurm-gcp-v6-partition
    use: [compute_nodeset]
    settings:
      partition_name: compute
      is_default: true

  - id: g2_nodeset
    source: community/modules/compute/schedmd-slurm-gcp-v6-nodeset
    use: [network,startup]
    settings:
      node_count_dynamic_max: 16
      disk_size_gb: $(vars.disk_size)
      instance_image: $(vars.custom_image)
      instance_image_custom: true
      machine_type: g2-standard-48
      bandwidth_tier: gvnic_enabled
      allow_automatic_updates: false

  - id: g2_partition
    source: community/modules/compute/schedmd-slurm-gcp-v6-partition
    use:
    - g2_nodeset
    settings:
      partition_name: g2 

  - id: a2_nodeset
    source: community/modules/compute/schedmd-slurm-gcp-v6-nodeset
    use: [network,startup]
    settings:
      node_count_dynamic_max: 20
      disk_size_gb: $(vars.disk_size)
      instance_image: $(vars.custom_image)
      instance_image_custom: true
      machine_type: a2-highgpu-4g
      bandwidth_tier: gvnic_enabled
      allow_automatic_updates: false

  - id: a2_partition
    source: community/modules/compute/schedmd-slurm-gcp-v6-partition
    use:
    - a2_nodeset
    settings:
      partition_name: a2 

  - id: slurm_login
    source: community/modules/scheduler/schedmd-slurm-gcp-v6-login
    use: [network]
    settings:
      name_prefix: login
      enable_login_public_ips: true
      machine_type: n2-standard-4
      disk_size_gb: $(vars.disk_size)
      instance_image: $(vars.custom_image)
      instance_image_custom: true

  - id: slurm_controller
    source: community/modules/scheduler/schedmd-slurm-gcp-v6-controller
    use:
    - network
    - compute_partition
    - a2_partition
    - g2_partition
    - data_bucket
    - homefs
    - slurm_login
    settings:
      enable_controller_public_ips: true
      disk_size_gb: $(vars.disk_size)
      instance_image: $(vars.custom_image)
      instance_image_custom: true
      login_startup_script: $(startup_login.startup_script)