Custom Bootstrap Actions Amazon ParallelCluster 2.x and 3.x use different configuration file syntax Inclusive language Scheduler Support Amazon ParallelCluster CLI IMDS configuration update

Moving from Amazon ParallelCluster 2.x to 3.x

Custom Bootstrap Actions

With Amazon ParallelCluster 3, you can specify different custom bootstrap actions scripts for the head node and compute nodes using OnNodeStart (pre_install in Amazon ParallelCluster version 2) and OnNodeConfigured (post_install in Amazon ParallelCluster version 2) parameters in the HeadNode and Scheduling / SlurmQueues sections. For more information, see Custom bootstrap actions.

Custom bootstrap actions scripts that are developed for Amazon ParallelCluster 2 must be adapted to be used in Amazon ParallelCluster 3:

We don't recommend using /etc/parallelcluster/cfnconfig and cfn_node_type to differentiate between head and compute nodes. Instead, we recommend that you specify two different scripts in the HeadNode and Scheduling / SlurmQueues.
If you prefer to continue loading /etc/parallelcluster/cfnconfig for use in your bootstrap actions script, note the value of cfn_node_type is changed from "MasterServer" to "HeadNode" (see: Inclusive language).
On Amazon ParallelCluster 2, the first input argument to bootstrap action scripts was the S3 URL to the script and was reserved. In Amazon ParallelCluster 3, only the arguments configured in the configuration are passed to the scripts.

Warning

Using internal variables provided through the /etc/parallelcluster/cfnconfig file isn't officially supported. This file might be removed as part of a future release.

Amazon ParallelCluster 2.x and 3.x use different configuration file syntax

Amazon ParallelCluster 3.x configuration uses YAML syntax. The full reference can be found at Configuration files.

In addition to requiring a YAML file format, a number of configuration sections, settings, and parameter values have been updated in Amazon ParallelCluster 3.x. In this section, we note key changes to the Amazon ParallelCluster configuration along with side-by-side examples illustrating these differences across each version of Amazon ParallelCluster.

Example of multiple scheduler queues configuration with hyperthreading enabled and disabled

Amazon ParallelCluster 2:


[cluster default]
queue_settings = ht-enabled, ht-disabled
...

[queue ht-enabled]
compute_resource_settings = ht-enabled-i1
disable_hyperthreading = false

[queue ht-disabled]
compute_resource_settings = ht-disabled-i1
disable_hyperthreading = true

[compute_resource ht-enabled-i1]
instance_type = c5n.18xlarge
[compute_resource ht-disabled-i1]
instance_type = c5.xlarge

Amazon ParallelCluster 3:


...
Scheduling:
  Scheduler: slurm
  SlurmQueues:
    - Name: ht-enabled
      Networking:
        SubnetIds:
          - compute_subnet_id
      ComputeResources:
        - Name: ht-enabled-i1
          DisableSimultaneousMultithreading: true
          InstanceType: c5n.18xlarge     
    - Name: ht-disabled
      Networking:
        SubnetIds:
          - compute_subnet_id
      ComputeResources:
        - Name: ht-disabled-i1
          DisableSimultaneousMultithreading: false
          InstanceType: c5.xlarge

Example of new FSx for Lustre file-system configuration

Amazon ParallelCluster 2:


[cluster default]
fsx_settings = fsx
...

[fsx fsx]
shared_dir = /shared-fsx
storage_capacity = 1200
imported_file_chunk_size = 1024
import_path = s3://bucket
export_path = s3://bucket/export_dir
weekly_maintenance_start_time = 3:02:30
deployment_type = PERSISTENT_1
data_compression_type = LZ4

Amazon ParallelCluster 3:


...
SharedStorage:
  - Name: fsx
    MountDir: /shared-fsx
    StorageType: FsxLustre
    FsxLustreSettings:
      StorageCapacity: 1200
      ImportedFileChunkSize: 1024
      ImportPath: s3://bucket
      ExportPath: s3://bucket/export_dir
      WeeklyMaintenanceStartTime: "3:02:30"
      DeploymentType: PERSISTENT_1
      DataCompressionType: LZ4

Example of a cluster configuration mounting an existing FSx for Lustre file-system

Amazon ParallelCluster 2:


[cluster default]
fsx_settings = fsx
...

[fsx fsx]
shared_dir = /shared-fsx
fsx_fs_id = fsx_fs_id

Amazon ParallelCluster 3:


...
SharedStorage:
  - Name: fsx
    MountDir: /shared-fsx
    StorageType: FsxLustre
    FsxLustreSettings:
      FileSystemId: fsx_fs_id

Example of a cluster with the Intel HPC Platform Specification software stack

Amazon ParallelCluster 2:


[cluster default]
enable_intel_hpc_platform = true
...

Amazon ParallelCluster 3:


...
AdditionalPackages:
  IntelSoftware:
    IntelHpcPlatform: true

Notes:

The installation of Intel HPC Platform Specification software is subject to the terms and conditions of the applicable Intel End User License Agreement.

Example of custom IAM configurations including: instance profile, instance role, additional policies for instances and the role for the lambda functions associated with the cluster

Amazon ParallelCluster 2:


[cluster default]
additional_iam_policies = arn:aws:iam::aws:policy/AmazonS3ReadOnlyAccess,arn:aws:iam::aws:policy/AmazonDynamoDBReadOnlyAccess
ec2_iam_role = ec2_iam_role
iam_lambda_role = lambda_iam_role
...

Amazon ParallelCluster 3:


...
Iam:
  Roles:
    CustomLambdaResources: lambda_iam_role
HeadNode:
  ...
  Iam:
    InstanceRole: ec2_iam_role
Scheduling:
  Scheduler: slurm
  SlurmQueues:
    - Name: queue1
      ...
      Iam:
        InstanceProfile: iam_instance_profile
    - Name: queue2
      ...
      Iam:
        AdditionalIamPolicies:
          - Policy: arn:aws:iam::aws:policy/AmazonS3ReadOnlyAccess
          - Policy: arn:aws:iam::aws:policy/AmazonDynamoDBReadOnlyAccess

Notes:

For Amazon ParallelCluster 2, the IAM settings are applied to all the instances of a cluster and additional_iam_policies can't be used in conjunction with ec2_iam_role.
For Amazon ParallelCluster 3, you can have different IAM settings for head and compute nodes and even specify different IAM settings for each compute queue.
For Amazon ParallelCluster 3, you can use an IAM instance profile as an alternative to an IAM role. InstanceProfile, InstanceRole or AdditionalIamPolicies can't be configured together.

Example of custom bootstrap actions

Amazon ParallelCluster 2:


[cluster default]
s3_read_resource = arn:aws:s3:::bucket_name/*
pre_install = s3://bucket_name/scripts/pre_install.sh
pre_install_args = 'R curl wget'
post_install = s3://bucket_name/scripts/post_install.sh
post_install_args = "R curl wget"
...

Amazon ParallelCluster 3:


...
HeadNode:
  ...
  CustomActions:
    OnNodeStart:
      Script: s3://bucket_name/scripts/pre_install.sh
      Args:
        - R
        - curl
        - wget
    OnNodeConfigured:
      Script: s3://bucket_name/scripts/post_install.sh
      Args: ['R', 'curl', 'wget']
  Iam:
    S3Access:
      - BucketName: bucket_name
Scheduling:
  Scheduler: slurm
  SlurmQueues:
    - Name: queue1
      ...
      CustomActions:
        OnNodeStart:
          Script: s3://bucket_name/scripts/pre_install.sh
          Args: ['R', 'curl', 'wget']
        OnNodeConfigured:
          Script: s3://bucket_name/scripts/post_install.sh
          Args: ['R', 'curl', 'wget']
      Iam:
        S3Access:
          - BucketName: bucket_name

Example of a cluster with read and write access to the S3 bucket resources

Amazon ParallelCluster 2:


[cluster default]
s3_read_resource = arn:aws:s3:::bucket/read_only/*
s3_read_write_resource = arn:aws:s3:::bucket/read_and_write/*
...

Amazon ParallelCluster 3:


...
HeadNode:
  ...
  Iam:
    S3Access:
      - BucketName: bucket_name
        KeyName: read_only/
        EnableWriteAccess: False
      - BucketName: bucket_name
        KeyName: read_and_write/
        EnableWriteAccess: True
Scheduling:
  Scheduler: slurm
  SlurmQueues:
    - Name: queue1
      ...
      Iam:
        S3Access:
          - BucketName: bucket_name
            KeyName: read_only/
            EnableWriteAccess: False
          - BucketName: bucket_name
            KeyName: read_and_write/
            EnableWriteAccess: True

Inclusive language

Amazon ParallelCluster 3 uses the words "head node" in places where "master" was used in Amazon ParallelCluster 2. This includes the following:

Variable exported in the Amazon Batch job environment changed: from MASTER_IP to PCLUSTER_HEAD_NODE_IP.
All Amazon CloudFormation outputs changed from Master* to HeadNode*.
All NodeType and tags changed from Master to HeadNode.

Scheduler Support

Amazon ParallelCluster 3.x doesn't support Son of Grid Engine (SGE) and Torque schedulers.

The Amazon Batch commands awsbhosts, awsbkill, awsbout, awsbqueues, awsbstat, and awsbsub are distributed as a separate aws-parallelcluster-awsbatch-cli PyPI package. This package is installed by Amazon ParallelCluster on the head node. You can still use these Amazon Batch commands from the cluster's head node. However, if you wish to use Amazon Batch commands from a location other than the head node, you must first install the aws-parallelcluster-awsbatch-cli PyPI package.

Amazon ParallelCluster CLI

The Amazon ParallelCluster command line interface (CLI) has been changed. The new syntax is described in Amazon ParallelCluster CLI commands. The output format for the CLI is a JSON string.

Configuring a new cluster

The pcluster configure command includes different parameters in Amazon ParallelCluster 3 as compared to Amazon ParallelCluster 2. For more information, see pcluster configure.

Note also that the configuration file syntax has changed from Amazon ParallelCluster 2. For a full reference of the cluster configuration settings, see Cluster configuration file.

Creating a new cluster

Amazon ParallelCluster 2's pcluster create command has been replaced by the pcluster create-cluster command.

Note the default behavior in Amazon ParallelCluster 2.x, without the -nw option, is to wait on cluster creation events, while Amazon ParallelCluster 3.x command returns immediately. The progress of the cluster creation can be monitored using pcluster describe-cluster.

An Amazon ParallelCluster 3 configuration file contains a single cluster definition, so the -t parameter is no more needed.

The following is an example configuration file.


# Amazon ParallelCluster v2
$ pcluster create \
    -r REGION \
    -c V2_CONFIG_FILE \
    -nw \
    -t CLUSTER_TEMPLATE \
    CLUSTER_NAME

# Amazon ParallelCluster v3
$ pcluster create-cluster \
    --region REGION \
    --cluster-configuration V3_CONFIG_FILE \
    --cluster-name CLUSTER_NAME

Listing clusters

The pcluster list Amazon ParallelCluster 2.x command must be replaced with pcluster list-clusters command.

Note: You need Amazon ParallelCluster v2 CLI to list clusters created with 2.x versions of Amazon ParallelCluster. See Install Amazon ParallelCluster in a virtual environment (recommended) for how to install multiple versions of Amazon ParallelCluster using virtual environments.


# Amazon ParallelCluster v2
$ pcluster list -r REGION

# Amazon ParallelCluster v3
$ pcluster list-clusters --region REGION

Starting and Stopping a cluster

The pcluster start and pcluster stop Amazon ParallelCluster 2.x commands must be replaced with pcluster update-compute-fleet commands.

Starting a compute fleet:


# Amazon ParallelCluster v2
$ pcluster start \
    -r REGION \
    CLUSTER_NAME

# Amazon ParallelCluster v3 - Slurm fleets
$ pcluster update-compute-fleet \
    --region REGION \
    --cluster-name CLUSTER_NAME \
    --status START_REQUESTED

# Amazon ParallelCluster v3 - Amazon Batch fleets
$ pcluster update-compute-fleet \
    --region REGION \
    --cluster-name CLUSTER_NAME \
    --status ENABLED

Stopping a compute fleet:


# Amazon ParallelCluster v2
$ pcluster stop \
    -r REGION \
    CLUSTER_NAME

# Amazon ParallelCluster v3 - Slurm fleets
$ pcluster update-compute-fleet \
    --region REGION \
    --cluster-name CLUSTER_NAME \
    --status STOP_REQUESTED

# Amazon ParallelCluster v3 - Amazon Batch fleets
$ pcluster update-compute-fleet \
    --region REGION \
    --cluster-name CLUSTER_NAME \
    --status DISABLED

Connecting to a cluster

The pcluster ssh Amazon ParallelCluster 2.x command has different parameters names in Amazon ParallelCluster 3.x. See pcluster ssh.

Connecting to a cluster:


# Amazon ParallelCluster v2
$ pcluster ssh \
    -r REGION \
    CLUSTER_NAME \
    -i ~/.ssh/id_rsa

# Amazon ParallelCluster v3
$ pcluster ssh \
    --region REGION \
    --cluster-name CLUSTER_NAME \
    -i ~/.ssh/id_rsa

IMDS configuration update

Starting with version 3.0.0, Amazon ParallelCluster introduced support for restricting access to the head node’s IMDS (and the instance profile credentials) to a subset of superusers, by default. For more information, see Imds properties.

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Best practices

Supported Regions for Amazon ParallelCluster