diff --git a/src/templates/cromwell/cromwell-resources.template.yaml b/src/templates/cromwell/cromwell-resources.template.yaml index 4ecbe569b..abe5965df 100644 --- a/src/templates/cromwell/cromwell-resources.template.yaml +++ b/src/templates/cromwell/cromwell-resources.template.yaml @@ -141,7 +141,7 @@ Parameters: Description: >- URL to a pre-built cromwell-*.jar file. Example: https://mycicdserver.com/build/cromwell-XX-SNAP.jar. If this is specifed, CromwellVersion is ignored. - Default: "https://github.com/henriqueribeiro/cromwell/releases/download/78-AWS/cromwell-78-600df43-AWS.jar" + Default: "https://github.com/henriqueribeiro/cromwell/releases/download/78-AWS/cromwell-78-AWS.jar" DBSubnetIDs: Type: List @@ -265,7 +265,16 @@ Resources: - "batch:ListJobs" - "batch:DescribeComputeEnvironments" - "ecs:DescribeContainerInstances" + - "imagebuilder:GetComponent" + - "imagebuilder:GetContainerRecipe" - "ecr:GetAuthorizationToken" + - "ecr:BatchGetImage" + - "ecr:InitiateLayerUpload" + - "ecr:UploadLayerPart" + - "ecr:CompleteLayerUpload" + - "ecr:BatchCheckLayerAvailability" + - "ecr:GetDownloadUrlForLayer" + - "ecr:PutImage" - PolicyName: !Sub CromwellServer-S3-Access-${AWS::Region} PolicyDocument: @@ -498,7 +507,7 @@ Resources: url = "jdbc:mysql://${DBAddress}/cromwell?rewriteBatchedStatements=true&useSSL=false" user = "${DBUsername}" password = "${DBPassword}" - connectionTimeout = 5000 + connectionTimeout = 30000 } } @@ -585,7 +594,7 @@ Resources: url = "jdbc:mysql://${DBAddress}/cromwell?rewriteBatchedStatements=true&useSSL=false" user = "${DBUsername}" password = "${DBPassword}" - connectionTimeout = 5000 + connectionTimeout = 30000 } } @@ -684,7 +693,7 @@ Resources: user=ec2-user ; setuid to this UNIX account to run the program redirect_stderr=true ; redirect proc stderr to stdout (default false) stdout_logfile=/home/ec2-user/cromwell-server.log ; stdout log path, NONE for none; default AUTO - + "/etc/nginx/nginx.conf": mode: "000644" content: | diff --git a/src/templates/gwfcore/gwfcore-batch.template.yaml b/src/templates/gwfcore/gwfcore-batch.template.yaml index 125c0a8ee..55ced4756 100644 --- a/src/templates/gwfcore/gwfcore-batch.template.yaml +++ b/src/templates/gwfcore/gwfcore-batch.template.yaml @@ -24,6 +24,7 @@ Metadata: - SpotFleetRoleArn - FSxSubnetId - BatchSpotBidPercentage + - BatchComputeInstanceTypes ParameterLabels: LaunchTemplateId: default: Launch Template ID @@ -49,6 +50,8 @@ Metadata: default: The FSx subnet Id. BatchSpotBidPercentage: default: The % of the On-demand EC2 price the SPOT instances should be bid at. + BatchComputeInstanceTypes: + default: The list of instance types to be used for EC2 instances using Batch Compute Environments. Parameters: Namespace: @@ -81,7 +84,7 @@ Parameters: DefaultCEMaxvCpus: Type: Number Description: Maximum number of CPUs in the default compute environment. Should be >= than MinCpus - Default: 100 + Default: 1000 MinValue: 0 BatchServiceRoleArn: Type: String @@ -100,6 +103,9 @@ Parameters: Type: Number Description: The maximum percentage that an EC2 Spot Instance price can be when compared with the On-Demand price for that instance type before instances are launched. Default: 100 + BatchComputeInstanceTypes: + Type: String + Description: The list of instance types to be used for EC2 instances using Batch Compute Environments. Mappings: TagMap: @@ -168,43 +174,7 @@ Resources: LaunchTemplateId: !Ref LaunchTemplateId Version: $Latest InstanceRole: !Ref Ec2InstanceProfileArn - InstanceTypes: - - c4.large - - m4.large - - r4.large - - c4.xlarge - - m4.xlarge - - r4.xlarge - - c4.2xlarge - - m4.2xlarge - - r4.2xlarge - - c4.4xlarge - - m4.4xlarge - - r4.4xlarge - - c5.large - - m5.large - - r5.large - - c5.xlarge - - m5.xlarge - - r5.xlarge - - c5.2xlarge - - m5.2xlarge - - r5.2xlarge - - c5.4xlarge - - m5.4xlarge - - r5.4xlarge - - c5n.large - - m5n.large - - r5n.large - - c5n.xlarge - - m5n.xlarge - - r5n.xlarge - - c5n.2xlarge - - m5n.2xlarge - - r5n.2xlarge - - c5n.4xlarge - - m5n.4xlarge - - r5n.4xlarge + InstanceTypes: !Split [",", !Ref BatchComputeInstanceTypes ] MinvCpus: !Ref DefaultCEMinvCpus MaxvCpus: !Ref DefaultCEMaxvCpus SecurityGroupIds: @@ -231,31 +201,7 @@ Resources: LaunchTemplateId: !Ref LaunchTemplateId Version: $Latest InstanceRole: !Ref Ec2InstanceProfileArn - InstanceTypes: - - c5.large - - m5.large - - r5.large - - c5.xlarge - - m5.xlarge - - r5.xlarge - - c5.2xlarge - - m5.2xlarge - - r5.2xlarge - - c5.4xlarge - - m5.4xlarge - - r5.4xlarge - - c5n.large - - m5n.large - - r5n.large - - c5n.xlarge - - m5n.xlarge - - r5n.xlarge - - c5n.2xlarge - - m5n.2xlarge - - r5n.2xlarge - - c5n.4xlarge - - m5n.4xlarge - - r5n.4xlarge + InstanceTypes: !Split [",", !Ref BatchComputeInstanceTypes ] MinvCpus: !Ref PriorityCEMinvCpus MaxvCpus: !Ref PriorityCEMaxvCpus SecurityGroupIds: diff --git a/src/templates/gwfcore/gwfcore-root.template.yaml b/src/templates/gwfcore/gwfcore-root.template.yaml index b1d41bb17..7a274640a 100644 --- a/src/templates/gwfcore/gwfcore-root.template.yaml +++ b/src/templates/gwfcore/gwfcore-root.template.yaml @@ -30,6 +30,7 @@ Metadata: - FSxPerUnitStorageThroughput - FSxStorageType - BatchSpotBidPercentage + - BatchComputeInstanceTypes - Label: default: Distribution Configuration Parameters: @@ -78,6 +79,8 @@ Metadata: default: The type of FS needed i.e. SSD or HDD or SCRATCH BatchSpotBidPercentage: default: The maximum percentage that an EC2 Spot Instance price can be when compared with the On-Demand price for that instance type before instances are launched. + BatchComputeInstanceTypes: + default: The list of instance types to be used for EC2 instances using Batch Compute Environments. Parameters: Namespace: @@ -193,6 +196,11 @@ Parameters: Description: The maximum percentage that an EC2 Spot Instance price can be when compared with the On-Demand price for that instance type before instances are launched. Default: 100 + BatchComputeInstanceTypes: + Type: String + Description: The list of instance types to be used for EC2 instances using Batch Compute Environments. + Default: "c4.large,m4.large,r4.large,c4.xlarge,m4.xlarge,r4.xlarge,c4.2xlarge,m4.2xlarge,r4.2xlarge,c4.4xlarge,m4.4xlarge,r4.4xlarge,c5.large,m5.large,r5.large,c5.xlarge,m5.xlarge,r5.xlarge,c5.2xlarge,m5.2xlarge,r5.2xlarge,c5.4xlarge,m5.4xlarge,r5.4xlarge,c5n.large,m5n.large,r5n.large,c5n.xlarge,m5n.xlarge,r5n.xlarge,c5n.2xlarge,m5n.2xlarge,r5n.2xlarge,c5n.4xlarge,m5n.4xlarge,r5n.4xlarge" + Conditions: NoNamespace: !Equals [ !Ref Namespace, "" ] EfsCondition: !Equals [ !Ref CreateEFS, "Yes"] @@ -306,6 +314,7 @@ Resources: SpotFleetRoleArn: !Sub ${IamStack.Outputs.BatchSpotFleetRoleArn} FSxSubnetId: !Ref FSxSubnetId BatchSpotBidPercentage: !Ref BatchSpotBidPercentage + BatchComputeInstanceTypes: !Ref BatchComputeInstanceTypes FSxSGIngressTCP: Condition: FsxCondition