Configuring AWS ParallelCluster - AWS ParallelCluster

Configuring AWS ParallelCluster

After you install AWS ParallelCluster, complete the following configuration steps.

Verify that your AWS Account has a role that includes the permissions needed to run the pcluster CLI. For more information, see AWS ParallelCluster example user policies.

Set up your AWS credentials. For more information, see Configuring the AWS CLI in the AWS CLI user guide.

$ aws configure AWS Access Key ID [None]: AKIAIOSFODNN7EXAMPLE AWS Secret Access Key [None]: wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY Default region name [us-east-1]: us-east-1 Default output format [None]:

The AWS Region where the cluster is launched must have at least one Amazon EC2 key pair. For more information, see Amazon EC2 key pairs in the Amazon EC2 User Guide for Linux Instances.

$ pcluster configure --config cluster-config.yaml

The configure wizard prompts you for all of the information that's required to create your cluster. The details of the sequence differ when using AWS Batch as the scheduler compared to using Slurm.

Slurm

From the list of valid AWS Region identifiers, choose the Region where you want your cluster to run.

Note

The list of Regions shown is based on the partition of your account, and only includes Regions that are enabled for your account. For more information about enabling Regions for your account, see Managing AWS Regions in the AWS General Reference. The example shown is from the AWS Global partition. If your account is in the AWS GovCloud (US) partition, only Regions in that partition are listed (gov-us-east-1 and gov-us-west-1). Similarly, if your account is in the AWS China partition, only cn-north-1 and cn-northwest-1 are shown. For the complete list of Regions supported by AWS ParallelCluster, see Supported Regions for AWS ParallelCluster version 3.

Allowed values for AWS Region ID: 1. af-south-1 2. ap-east-1 3. ap-northeast-1 4. ap-northeast-2 5. ap-south-1 6. ap-southeast-1 7. ap-southeast-2 8. ca-central-1 9. eu-central-1 10. eu-north-1 11. eu-south-1 12. eu-west-1 13. eu-west-2 14. eu-west-3 15. me-south-1 16. sa-east-1 17. us-east-1 18. us-east-2 19. us-west-1 20. us-west-2 AWS Region ID [ap-northeast-1]:

The key pair is selected from the key pairs that are registered with Amazon EC2 in the selected Region. Choose the key pair:

Allowed values for EC2 Key Pair Name: 1. your-key-1 2. your-key-2 EC2 Key Pair Name [your-key-1]:

Choose the scheduler to use with your cluster.

Allowed values for Scheduler: 1. slurm 2. awsbatch Scheduler [slurm]:

Choose the operating system.

Allowed values for Operating System: 1. alinux2 2. centos7 3. ubuntu1804 4. ubuntu2004 Operating System [alinux2]:

Choose head node instance type:

Head node instance type [t2.micro]:

Choose the queue configuration. Note: Instance type can't be specified for multiple compute resources in the same queue.

Number of queues [1]: Name of queue 1 [queue1]: Number of compute resources for queue1 [1]: 2 Compute instance type for compute resource 1 in queue1 [t2.micro]: Maximum instance count [10]:

Enable EFA to run applications that require high levels of inter-instance communication at scale on AWS at no additional charge:

Compute instance type for compute resource 2 in queue1 [t2.micro]: c5n.18xlarge Enable EFA on c5n.18xlarge (y/n) [y]: y Maximum instance count [10]: Placement Group name []:

After the previous steps are completed, decide whether to use an existing VPC or let AWS ParallelCluster create a VPC for you. If you don't have a properly configured VPC, AWS ParallelCluster can create a new one for you. It either places both the head and compute nodes in the same public subnet, or only the head node in a public subnet with all compute nodes in a private subnet. If you let AWS ParallelCluster create a VPC, you must decide if all nodes are to be in a public subnet. For more information, see Network configurations.

If you configure your cluster to use instance types that have multiple network interfaces or a network card, see Network configurations for additional networking requirements.

It's possible to reach your quota for the number of VPCs allowed in a Region. The default quota is five VPCs for a Region. For more information about this quota and how to request an increase, see VPC and subnets in the Amazon VPC User Guide.

Important

VPCs created by AWS ParallelCluster do not enable VPC Flow Logs by default. VPC Flow Logs enable you to capture information about the IP traffic going to and from network interfaces in your VPCs. For more information, see VPC Flow Logs in the Amazon VPC User Guide.

Automate VPC creation? (y/n) [n]: y Allowed values for Availability Zone: 1. us-east-1a 2. us-east-1b 3. us-east-1c 4. us-east-1d 5. us-east-1e 6. us-east-1f Availability Zone [us-east-1a]: Allowed values for Network Configuration: 1. Head node in a public subnet and compute fleet in a private subnet 2. Head node and compute fleet in the same public subnet Network Configuration [Head node in a public subnet and compute fleet in a private subnet]: 1 Beginning VPC creation. Please do not leave the terminal until the creation is finalized

If you don't create a new VPC, you must select an existing VPC.

If you choose to have AWS ParallelCluster create the VPC, make a note of the VPC ID so you can use the AWS CLI to delete it later.

Automate VPC creation? (y/n) [n]: n Allowed values for VPC ID: # id name number_of_subnets --- --------------------- --------------------------------- ------------------- 1 vpc-0b4ad9c4678d3c7ad ParallelClusterVPC-20200118031893 2 2 vpc-0e87c753286f37eef ParallelClusterVPC-20191118233938 5 VPC ID [vpc-0b4ad9c4678d3c7ad]: 1

After the VPC has been selected, decide whether to use existing subnets or create new ones.

Automate Subnet creation? (y/n) [y]: y
Creating CloudFormation stack... Do not leave the terminal until the process has finished
AWS Batch

From the list of valid AWS Region identifiers, choose the Region where you want your cluster to run.

Note

The list of Regions shown is based on the partition of your account. It only includes Regions that are enabled for your account. For more information about enabling Regions for your account, see Managing AWS Regions in the AWS General Reference. The example shown is from the AWS Global partition. If your account is in the AWS GovCloud (US) partition, only Regions in that partition are listed (gov-us-east-1 and gov-us-west-1). Similarly, if your account is in the AWS China partition, only cn-north-1 and cn-northwest-1 are shown. For the complete list of Regions supported by AWS ParallelCluster, see Supported Regions for AWS ParallelCluster version 3.

Allowed values for AWS Region ID: 1. af-south-1 2. ap-east-1 3. ap-northeast-1 4. ap-northeast-2 5. ap-south-1 6. ap-southeast-1 7. ap-southeast-2 8. ca-central-1 9. eu-central-1 10. eu-north-1 11. eu-south-1 12. eu-west-1 13. eu-west-2 14. eu-west-3 15. me-south-1 16. sa-east-1 17. us-east-1 18. us-east-2 19. us-west-1 20. us-west-2 AWS Region ID [us-east-1]:

The key pair is selected from the key pairs registered with Amazon EC2 in the selected Region. Choose the key pair:

Allowed values for EC2 Key Pair Name: 1. your-key-1 2. your-key-2 EC2 Key Pair Name [your-key-1]:

Choose the scheduler to use with your cluster.

Allowed values for Scheduler: 1. slurm 2. awsbatch Scheduler [slurm]: 2

When awsbatch is selected as the scheduler, alinux2 is used as the operating system. The head node instance type is entered:

Head node instance type [t2.micro]:

Choose the queue configuration. The AWS Batch scheduler only contains a single queue. The maximum size of the cluster of compute nodes is entered. This is measured in vCPUs.

Number of queues [1]: Name of queue 1 [queue1]: Maximum vCPU [10]:

Decide whether to use existing VPCs or let AWS ParallelCluster create VPCs for you. If you don't have a properly configured VPC, AWS ParallelCluster can create a new one. It either uses both the head and compute nodes in the same public subnet, or only the head node in a public subnet with all nodes in a private subnet. It's possible to reach your quota on the number of VPCs allowed in a Region. The default number of VPCs is five. For more information about this quota and how to request an increase, see VPC and subnets in the Amazon VPC User Guide.

Important

VPCs created by AWS ParallelCluster do not enable VPC Flow Logs by default. VPC Flow Logs enable you to capture information about the IP traffic going to and from network interfaces in your VPCs. For more information, see VPC Flow Logs in the Amazon VPC User Guide.

If you let AWS ParallelCluster create a VPC, make sure that you decide whether all nodes are to be in a public subnet.

Automate VPC creation? (y/n) [n]: y Allowed values for Availability Zone: 1. us-east-1a 2. us-east-1b 3. us-east-1c 4. us-east-1d 5. us-east-1e 6. us-east-1f Availability Zone [us-east-1a]: Allowed values for Network Configuration: 1. Head node in a public subnet and compute fleet in a private subnet 2. Head node and compute fleet in the same public subnet Network Configuration [Head node in a public subnet and compute fleet in a private subnet]: *1* Beginning VPC creation. Please do not leave the terminal until the creation is finalized

If you don't create a new VPC, you must select an existing VPC.

If you choose to have AWS ParallelCluster create the VPC, make a note of the VPC ID so you can use the AWS CLI or AWS Management Console to delete it later.

Automate VPC creation? (y/n) [n]: n Allowed values for VPC ID: # id name number_of_subnets --- --------------------- --------------------------------- ------------------- 1 vpc-0b4ad9c4678d3c7ad ParallelClusterVPC-20200118031893 2 2 vpc-0e87c753286f37eef ParallelClusterVPC-20191118233938 5 VPC ID [vpc-0b4ad9c4678d3c7ad]: 1

After the VPC has been selected, make sure that you decide whether to use existing subnets or create new ones.

Automate Subnet creation? (y/n) [y]: y
Creating CloudFormation stack... Do not leave the terminal until the process has finished

When you have completed the preceding steps, a simple cluster launches into a VPC. The VPC uses an existing subnet that supports public IP addresses. The route table for the subnet is 0.0.0.0/0 => igw-xxxxxx. Note the following conditions:

  • The VPC must have DNS Resolution = yes and DNS Hostnames = yes.

  • The VPC must also have DHCP options with the correct domain-name for the Region. The default DHCP Option Set already specifies the required AmazonProvidedDNS. If specifying more than one domain name server, see DHCP options sets in the Amazon VPC User Guide. When using private subnets, use a NAT gateway or an internal proxy to enable web access for compute nodes. For more information, see Network configurations.

When all settings contain valid values, you can launch the cluster by running the create command.

$ pcluster create-cluster --cluster-name test-cluster --cluster-configuration cluster-config.yaml { "cluster": { "clusterName": "test-cluster", "cloudformationStackStatus": "CREATE_IN_PROGRESS", "cloudformationStackArn": "arn:aws:cloudformation:eu-west-1:xxx:stack/test-cluster/abcdef0-f678-890a-5abc-021345abcdef", "region": "eu-west-1", "version": "3.3.1", "clusterStatus": "CREATE_IN_PROGRESS" }, "validationMessages": [] }

Follow cluster progress:

$ pcluster describe-cluster --cluster-name test-cluster

or

$ pcluster list-clusters --query 'clusters[?clusterName==`test-cluster`]'

After the cluster reaches the "clusterStatus": "CREATE_COMPLETE" status, you can connect to it by using your normal SSH client settings. For more information about connecting to Amazon EC2 instances, see the EC2 User Guide in the Amazon EC2 User Guide for Linux Instances. Or you can connect the cluster through

$ pcluster ssh --cluster-name test-cluster -i ~/path/to/keyfile.pem

To delete the cluster, run the following command.

$ pcluster delete-cluster --region us-east-1 --cluster-name test-cluster

After the cluster is deleted, you can delete the network resources in the VPC by deleting the CloudFormation networking stack. The stack's name starts with "parallelclusternetworking-" and contains the creation time in "YYYYMMDDHHMMSS" format. You can list the stacks using the list-stacks command.

$ aws --region us-east-1 cloudformation list-stacks \ --stack-status-filter "CREATE_COMPLETE" \ --query "StackSummaries[].StackName" | \ grep -e "parallelclusternetworking-" "parallelclusternetworking-pubpriv-20191029205804"

The stack can be deleted using the delete-stack command.

$ aws --region us-east-1 cloudformation delete-stack \ --stack-name parallelclusternetworking-pubpriv-20191029205804

The VPC that pcluster configure creates for you isn't created in the CloudFormation networking stack. You can delete that VPC manually in the console or by using the AWS CLI.

$ aws --region us-east-1 ec2 delete-vpc --vpc-id vpc-0b4ad9c4678d3c7ad