hpc-slurm-gromacs.yaml

# Copyright 2022 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.

---

blueprint_name: hpc-slurm-gromacs

vars:
  project_id:  ## Set GCP Project ID Here ##
  deployment_name: hpc-slurm-gromacs
  region: us-central1
  zone: us-central1-c

# 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

  # Private Service Access (PSA) requires the compute.networkAdmin role which is
  # included in the Owner role, but not Editor.
  # PSA is a best practice for Filestore instances, but can be optionally
  # removed by deleting the private_service_access module and any references to
  # the module by Filestore modules.
  # https://cloud.google.com/vpc/docs/configure-private-services-access#permissions
  - id: private_service_access
    source: community/modules/network/private-service-access
    use: [network]

  ## Filesystems
  - id: appsfs
    source: modules/file-system/filestore
    use: [network, private_service_access]
    settings:
      local_mount: /sw

  - id: homefs
    source: modules/file-system/filestore
    use: [network, private_service_access]
    settings:
      local_mount: /home

  ## Install Scripts
  - id: spack-setup
    source: community/modules/scripts/spack-setup
    settings:
      install_dir: /sw/spack
      spack_ref: v0.20.0

  - id: spack-execute
    source: community/modules/scripts/spack-execute
    use: [spack-setup]
    settings:
      log_file: /var/log/spack.log
      data_files:
      - destination: /tmp/projections-config.yaml
        content: |
          modules:
            default:
              tcl:
                hash_length: 0
                all:
                  conflict:
                    - '{name}'
                projections:
                  all: '{name}/{version}-{compiler.name}-{compiler.version}'
      commands: |
        ## Un-comment and update mirror_url to install from spack cache
        ## if ! spack mirror list | grep -q gcs_cache; then
        ##   spack mirror add --scope site gcs_cache gs://optionally_set_spack_cache_bucket
        ## fi
        ## spack buildcache keys --install --trust

        spack config --scope defaults add config:build_stage:/sw/spack/spack-stage
        spack config --scope defaults add -f /tmp/projections-config.yaml

        spack install gcc@13.1.0 target=x86_64
        spack load gcc@13.1.0 target=x86_64
        spack compiler find --scope site

        spack install intel-oneapi-mpi@2021.9.0%gcc@13.1.0
        spack install gromacs@2020.6 %gcc@13.1.0 ^intel-oneapi-mpi@2021.9.0

  - id: script
    source: modules/scripts/startup-script
    settings:
      runners:
      - $(spack-execute.spack_runner)

  - id: compute_nodeset
    source: community/modules/compute/schedmd-slurm-gcp-v6-nodeset
    use: [network]
    settings:
      node_count_dynamic_max: 20
      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: slurm_login
    source: community/modules/scheduler/schedmd-slurm-gcp-v6-login
    use: [network]
    settings:
      enable_login_public_ips: true

  - id: slurm_controller
    source: community/modules/scheduler/schedmd-slurm-gcp-v6-controller
    use:
    - network
    - compute_partition
    - slurm_login
    - homefs
    - appsfs
    settings:
      enable_controller_public_ips: true
      login_startup_script: $(script.startup_script)
      login_startup_scripts_timeout: 21600