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Merge pull request #98 from RLOpenCatalyst/topic-release
1.12.1 build updates to RG
2 parents 5d7126a + ff63b97 commit 087cf7a

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Lines changed: 189 additions & 7 deletions

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‎cft-templates/fsx-for-lustre.yaml‎

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AWSTemplateFormatVersion: 2010-09-09
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Description: Sets up an FSX for Lustre filesystem with PERSISTENT_1 deployment type using SSD storage.
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Parameters:
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StorageCapacity:
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Description: >-
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The storage capacity of the file system that you're creating.
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The valid values are 1200 GiB, 2400 GiB, and increments of 2400 GiB.
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Default: 1200
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Type: Number
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ImportPath:
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Description: The path to the Amazon S3 bucket (including the optional prefix) that you're using as the data repository for your Amazon FSx for Lustre file system
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Default: NONE
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Type: String
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AllowedPattern: ^[^\u0000\u0085\u2028\u2029\r\n]{3,4357}$
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ExportPath:
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Description: The path in the Amazon S3 bucket where the root of your Amazon FSx file system is exported.
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Default: NONE
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Type: String
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AllowedPattern: ^[^\u0000\u0085\u2028\u2029\r\n]{3,4357}$
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VpcId:
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Description: The ID of the VPC that the file system will be accessible from
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Type: AWS::EC2::VPC::Id
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SubnetId:
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Description: The ID of the subnet that the file system will be accessible from. Make sure the subnet is part of the VPC selected above.
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Type: AWS::EC2::Subnet::Id
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KmsKeyId:
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Description: The ID of the AWS Key Management Service (AWS KMS) key used to encrypt Amazon FSx file system data.
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Default: NONE
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Type: String
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AutoImportPolicy:
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Description: Choose how Amazon FSx keeps your file and directory listings up to date as you add or modify objects in your linked S3 bucket
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Type: String
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Default: NONE
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AllowedValues: [NONE, NEW, NEW_CHANGED, NEW_CHANGED_DELETED]
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DataCompressionType:
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Description: Sets the data compression configuration for the file system.
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Type: String
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Default: NONE
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AllowedValues: [NONE, LZ4]
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PerUnitStorageThroughput:
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Description: The amount of read and write throughput for each 1 tebibyte (TiB) of file system storage capacity.
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Type: Number
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Default: 50
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AllowedValues: [50, 100, 200]
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ResearcherName:
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Type: String
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Description: Researcher name that will be added as tag to the resources
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ProjectId:
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Type: String
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Description: Project Id that will be added as tag to the resources
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Namespace:
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Type: String
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Description: An environment name that will be prefixed to resource names
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Conditions:
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KMSKeyNotProvided: !Equals [!Ref KmsKeyId, 'NONE']
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ImportPathNotProvided: !Equals [!Ref ImportPath, 'NONE']
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ExportPathNotProvided: !Equals [!Ref ExportPath, 'NONE']
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Resources:
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FSXSecurityGroup:
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Type: AWS::EC2::SecurityGroup
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Properties:
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VpcId: !Ref VpcId
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SecurityGroupIngress:
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- CidrIp: "0.0.0.0/0"
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FromPort: 988
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ToPort: 988
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IpProtocol: tcp
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- CidrIp: "0.0.0.0/0"
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FromPort: 1021
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ToPort: 1023
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IpProtocol: tcp
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GroupDescription: FSX Security Group
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FileSystem:
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Type: AWS::FSx::FileSystem
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Properties:
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FileSystemType: LUSTRE
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FileSystemTypeVersion: 2.12
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KmsKeyId: !If [KMSKeyNotProvided, !Ref 'AWS::NoValue', !Ref KmsKeyId]
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LustreConfiguration:
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AutoImportPolicy: !If [ImportPathNotProvided, !Ref 'AWS::NoValue', !Ref AutoImportPolicy]
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CopyTagsToBackups: True
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DataCompressionType: !Ref DataCompressionType
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DeploymentType: PERSISTENT_1
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ImportPath: !If [ImportPathNotProvided, !Ref 'AWS::NoValue', !Ref ImportPath]
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ExportPath: !If [ExportPathNotProvided, !Ref 'AWS::NoValue', !Ref ExportPath]
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PerUnitStorageThroughput: !Ref PerUnitStorageThroughput
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SecurityGroupIds: [!GetAtt FSXSecurityGroup.GroupId]
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StorageCapacity: !Ref StorageCapacity
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StorageType: SSD
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SubnetIds:
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- !Ref SubnetId
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Tags:
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- Key: cost_resource
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Value: !Sub ${AWS::StackName}
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- Key: researcher_name
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Value: !Ref ResearcherName
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- Key: project_name
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Value: !Ref ProjectId
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- Key: Name
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Value: !Join ['-', [Ref: Namespace, 'file-system']]
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Outputs:
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FileSystemId:
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Value: !Ref FileSystem

‎cft-templates/pcluster.yaml‎

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- HeadNodeInstanceType
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- VpcId
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- HeadNodeSubnetId
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- FileSystemId
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- Label:
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default: Scheduler Configuration
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Parameters:
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CustomAMI:
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Type: String
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Description: Enter the AMI Id of a custom AMI if you wish to use a non-default AMI. e.g. ami-12345678. The AMI Id entered should exist in this project account and region
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Default: default
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FileSystemId:
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Type: String
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Description: Enter the File System Id of the FSx for Lustre file system which you want to use. e.g. fs-12345678. Leave this field to default if you do not want to use FSx for Lustre
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Default: default
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- dynamodb:*
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- route53:*
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- ssm:*
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- fsx:*
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Resource: "*"
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InstanceSecurityGroup:
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Type: AWS::EC2::SecurityGroup
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trap '/opt/aws/bin/cfn-signal --exit-code 1 --resource EC2Instance --region ${AWS::Region} --stack ${AWS::StackName}' ERR
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sudo yum update -y --security
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cd /home/ec2-user/parallel-update
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sudo -u ec2-user ./Provision-pcluster.sh ${Scheduler} ${AWS::Region} ${HeadNodeInstanceType} ${HeadNodeSubnetId} ${KeyPair} ${WorkerNodeInstanceType} ${ComputeEnvMinvCpus} ${ComputeEnvMaxvCpus} ${WorkerNodeSubnetId} ${ComputeEnvDesiredvCpus} ${SpotBidPercentage} ${AWS::StackName} ${CustomAMI}
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sudo -u ec2-user ./Provision-pcluster.sh ${Scheduler} ${AWS::Region} ${HeadNodeInstanceType} ${HeadNodeSubnetId} ${KeyPair} ${WorkerNodeInstanceType} ${ComputeEnvMinvCpus} ${ComputeEnvMaxvCpus} ${WorkerNodeSubnetId} ${ComputeEnvDesiredvCpus} ${SpotBidPercentage} ${AWS::StackName} ${CustomAMI} ${FileSystemId}
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/opt/aws/bin/cfn-signal --exit-code 0 --resource EC2Instance --region ${AWS::Region} --stack ${AWS::StackName}
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sleep 10
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aws ec2 stop-instances --instance-ids `wget -qO- http://instance-data/latest/meta-data/instance-id`
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Outputs:

‎config/access-policy.json‎

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"iam:GetRolePolicy",
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"iam:GetPolicy",
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"iam:ListPolicyVersions",
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"iam:CreateServiceLinkedRole",
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"batch:*",
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"sts:AssumeRole",
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"sts:GetFederationToken",
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"imagebuilder:UntagResource",
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"cognito-idp:DeleteUserPool",
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"codebuild:DeleteProject",
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"route53:*"
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"route53:*",
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"fsx:*"
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],
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"Resource": [
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"*"

‎config/settings-config.json‎

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}
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],
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"action": [
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{
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"action": "Share",
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"imageUrl": "../../assets/images/share@2x.png"
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},
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{
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"action": "Unshare",
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"imageUrl": "../../assets/images/unshare@2x.png"
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}
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],
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"action": [
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{
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"action": "Share",
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"imageUrl": "../../assets/images/share@2x.png"
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},
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{
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"action": "Upload",
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"imageUrl": "../../assets/images/cloud-computing@2x.png"

‎dump/standardcatalogitems.json‎

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},
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{
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"Key": "DetailsLink",
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"Value": "https://researchgateway.readthedocs.io/en/latest/linux.html"
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"Value": "https://researchgateway.readthedocs.io/en/latest/DockerEC2linux.html"
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},
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{
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"Key": "Service",
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},
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{
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"Key": "DetailsLink",
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"Value": "https://researchgateway.readthedocs.io/en/latest/linux.html"
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"Value": "https://researchgateway.readthedocs.io/en/latest/MySql.html"
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},
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{
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"Key": "Service",
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},
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{
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"Key" : "DetailsLink",
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"Value" : "https://researchgateway.readthedocs.io/en/latest/linux.html"
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"Value" : "https://researchgateway.readthedocs.io/en/latest/ubuntu.html"
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},
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{
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"Key" : "Service",
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},
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{
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"Key": "DetailsLink",
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"Value": "https://gatk.broadinstitute.org/hc/en-us/categories/360002302312"
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"Value": "https://researchgateway.readthedocs.io/en/latest/cromwell.html"
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},
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{
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"Key": "TypeOfProduct",
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},
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{
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"Key" : "DetailsLink",
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"Value" : "https://docs.aws.amazon.com/parallelcluster/latest/ug/install-v3-virtual-environment.html"
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"Value" : "https://researchgateway.readthedocs.io/en/latest/PCluster.html"
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},
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{
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"Key" : "TypeOfProduct",
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}
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}
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},
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{
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"_id": {
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"$oid": "60504955135663522b880cfe"
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},
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"name": "FSx For Lustre",
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"description": "Sets up an FSX for Lustre filesystem with PERSISTENT_1 deployment type using SSD storage",
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"fileName": "fsx-for-lustre.yaml",
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"tags": [
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{
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"Key": "EstimatedTimeToProvision",
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"Value": "20 Minutes"
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},
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{
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"Key": "DetailsLink",
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"Value": "https://docs.aws.amazon.com/fsx/latest/LustreGuide/what-is.html"
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},
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{
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"Key": "Service",
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"Value": "FSXForLustre"
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},
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{
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"Key": "TypeOfProduct",
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"Value": "Research"
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}
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],
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"owner": "RL",
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"portfolio": "RGPortfolio",
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"availableRegions": [],
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"assignedOU": [],
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"metaData": {
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"pre_provisioning": [
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{
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"code": "CFT_PARAMS",
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"params": [
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{
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"name": "ProjectId",
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"type": "RL::SC::PARAM::HD"
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},
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{
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"name": "ResearcherName",
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"type": "RL::SC::PARAM::HD"
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},
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{
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"name": "Namespace",
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"type": "RL::SC::PARAM::HD"
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}
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]
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}
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],
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"post_provisioning": [],
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"checks_before_assigning_product": [],
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"checks_after_assigning_product": [],
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"permission_required": {},
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"cost_resource": true
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}
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}
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]

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