Merge pull request #187 from spatel-gfb/master

Updated Code to Handle few things
aws-samples · Mar 30, 2022 · c2f5856 · c2f5856
2 parents 1675a2d + 846d63a
commit c2f5856
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Showing 3 changed files with 31 additions and 67 deletions.
diff --git 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<AWS::EC2::Subnet::Id>
@@ -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
@@ -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
@@ -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