Custom Bootstrap actions AWS ParallelCluster 2.x and 3.x use different configuration file syntax Inclusive language Scheduler support AWS ParallelCluster CLI IMDS configuration update

Moving from AWS ParallelCluster 2.x to 3.x

The following sections describe what happens when you move from AWS ParallelCluster 2.x to 3.x, including the changes from one version to the other.

Custom Bootstrap actions

With AWS ParallelCluster 3, you can specify different custom bootstrap actions scripts for the head node and compute nodes using OnNodeStart (pre_install in AWS ParallelCluster version 2) and OnNodeConfigured (post_install in AWS 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 AWS ParallelCluster 2 must be adapted to be used in AWS 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 AWS ParallelCluster 2, the first input argument to bootstrap action scripts was the S3 URL to the script and was reserved. In AWS 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.

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

AWS 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 AWS ParallelCluster 3.x. In this section, we note key changes to the AWS ParallelCluster configuration along with side-by-side examples illustrating these differences across each version of AWS ParallelCluster.

Example of multiple scheduler queues configuration with hyperthreading enabled and disabled

AWS 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

AWS 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

AWS ParallelCluster 2:


[cluster default]
fsx_settings = fsx
...

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

AWS ParallelCluster 3:


...
SharedStorage:
  - Name: fsx
    MountDir: /shared-fsx
    StorageType: FsxLustre
    FsxLustreSettings:
      StorageCapacity: 1200
      ImportedFileChunkSize: 1024
      ImportPath: s3://amzn-s3-demo-bucket
      ExportPath: s3://amzn-s3-demo-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

AWS ParallelCluster 2:


[cluster default]
fsx_settings = fsx
...

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

AWS 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

AWS ParallelCluster 2:


[cluster default]
enable_intel_hpc_platform = true
...

AWS 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

AWS 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
...

AWS 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 AWS 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 AWS ParallelCluster 3, you can have different IAM settings for head and compute nodes and even specify different IAM settings for each compute queue.
For AWS 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

AWS ParallelCluster 2:


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

AWS ParallelCluster 3:


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

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

AWS ParallelCluster 2:


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

AWS ParallelCluster 3:


...
HeadNode:
  ...
  Iam:
    S3Access:
      - BucketName: amzn-s3-demo-bucket
        KeyName: read_only/
        EnableWriteAccess: False
      - BucketName: amzn-s3-demo-bucket
        KeyName: read_and_write/
        EnableWriteAccess: True
Scheduling:
  Scheduler: slurm
  SlurmQueues:
    - Name: queue1
      ...
      Iam:
        S3Access:
          - BucketName: amzn-s3-demo-bucket
            KeyName: read_only/
            EnableWriteAccess: False
          - BucketName: amzn-s3-demo-bucket
            KeyName: read_and_write/
            EnableWriteAccess: True

Inclusive language

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

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

Scheduler support

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

The AWS 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 AWS ParallelCluster on the head node. You can still use these AWS Batch commands from the cluster's head node. However, if you wish to use AWS Batch commands from a location other than the head node, you must first install the aws-parallelcluster-awsbatch-cli PyPI package.

AWS ParallelCluster CLI

The AWS ParallelCluster command line interface (CLI) has been changed. The new syntax is described in AWS 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 AWS ParallelCluster 3 as compared to AWS ParallelCluster 2. For more information, see pcluster configure.

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

Creating a new cluster

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

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

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

The following is an example configuration file.


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

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

Listing clusters

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

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


# AWS ParallelCluster v2
$ pcluster list -r REGION

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

Starting and Stopping a cluster

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

Starting a compute fleet:


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

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

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

Stopping a compute fleet:


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

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

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

Connecting to a cluster

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

Connecting to a cluster:


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

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

IMDS configuration update

Starting with version 3.0.0, AWS 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.

Warning Javascript is disabled or is unavailable in your browser.

To use the Amazon Web Services Documentation, Javascript must be enabled. Please refer to your browser's Help pages for instructions.

Document Conventions

Best practices

Using AWS ParallelCluster