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The following provides instructions on how to log on to the Sage Scientific Compute workspace using your Synapse credentials, and how to use the products provided in the AWS Service Catalog to setup or modify EC2 instances and S3 buckets.

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Access to Sage Scientific Compute workspace is organized by communities. Community membership is defined by a Synapse Team and managed by its community manager. Each community also has a defined entry point URL, as shown below:

For Sage Bionetworks employees, access is granted during employee on boarding. For other groups, the community manager will add your Synapse account to the list of allowed users for the compute workspace.

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Note: You can add additional custom tags when provisioning resources however there are 3 reserved tags that you should avoid adding: Department, Project, and OwnerEmail. The owner email tag is automatically set to <Synapse Username>@synapse.org

Notifications

Please skip the Notifications pane. SNS notifications are not operational at this time.

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The AWS SSM allows direct access to private instances from your own computer terminal. To setup access with the AWS SSM we need to create a special Synapse personal access token (PAT) that will work with the Sage Service Catalog. This is special PAT that can only be created using this workflow, creating a PAT from the Synapse personal token manager web page will NOT work.

1. Request a Synapse PAT by visiting https://sc.sageit.org/personalaccesstoken , for Sage employees, or https://ad.strides.sc.sageit.org/personalaccesstoken for AMP-AD members. (You may need to login to Synapse.) If you have already created a PAT through this mechanism and are repeating the process you must first visit the token management page in Synapse and delete the existing one with the same name.

2. After logging into Synapse a file containing the PAT, which is a long character string (i.e. eyJ0eXAiOiJ...Z8t9Eg), is returned to you. Save the file to your local machine and note the location where you saved it to then close the browser session.

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• If you encounter errors try running the AWS start-session command with the --debug option.

• If you use an invalid personal access token you will get an error similar to this

  Code Block
  ➜ aws ssm start-session --profile service-catalog \ --target i-0fd5c9ff0ef675ceb Expecting value: line 1 column 1 (char 0)

  To check whether your token is valid run the following command

  Code Block
  ➜ curl -I --location-trusted \ -H Authorization:"Bearer ${SYNAPSE_PAT}" https://sc.sageit.org/ststoken

  If the HTTP response status is 2xx then the PAT is valid. If the PAT is invalid the response will be 4xx

• If you continue to have similar errors to Expecting value: line X column X (char X) then it could mean that your synapse_creds.sh file is invalid. Try verifying your synapse_creds.sh script independently of the AWS command by executing just the script. A successful execution should return a valid json and look something like this

  Code Block
  ➜ ~/synapse_creds.sh "https://sc.sageit.org" "eyJ0eXAiO...2GLQg" {"SessionToken":"FwoGZXIvYXdzEN7//////////wEaDP2imuwAK+...13GnBrJc9SlOW6uY=","Version":1,"AccessKeyId":"XXXXXXX","SecretAccessKey":"XXXXXXXXXXXXXXXX","Expiration":"2021-07-21T22:02:17Z"}

• Another problem could be that your ~/.aws/config file is invalid. For debugging we recommend backing up your current config file and creating a new one with just one service-catalog profile in it and then try re-running the start-session command.

• If you get a message similar to “.. AccessDeniedException when calling the TerminateSession operation..”. I it could mean that the AWS SSM session plugin was not install correctly. Please verify that it was successfully installed.

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1. Setup profile for SSM access

2. Run an application on the EC2 (i.e. docker run -p 80:80 httpd)

   Code Block

   [ec2-user@ip-10-49-26-50 ~]$ docker run -p 80:80 httpd Unable to find image 'httpd:latest' locally latest: Pulling from library/httpd 33847f680f63: Pull complete d74938eee980: Pull complete 963cfdce5a0c: Pull complete 8d5a3cca778c: Pull complete e06a573b193b: Pull complete Digest: sha256:71a3a8e0572f18a6ce71b9bac7298d07e151e4a1b562d399779b86fef7cf580c Status: Downloaded newer image for httpd:latest AH00558: httpd: Could not reliably determine the server's fully qualified domain name, using 172.17.0.2. Set the 'ServerName' directive globally to suppress this message AH00558: httpd: Could not reliably determine the server's fully qualified domain name, using 172.17.0.2. Set the 'ServerName' directive globally to suppress this message [Thu Jul 22 23:54:12.106344 2021] [mpm_event:notice] [pid 1:tid 140706544895104] AH00489: Apache/2.4.48 (Unix) configured -- resuming normal operations [Thu Jul 22 23:54:12.107307 2021] [core:notice] [pid 1:tid 140706544895104] AH00094: Command line: 'httpd -D FOREGROUND'

3. To provide access to that app an SC user can use the port forwarding feature to gain access to the app by running the AWS SSM CLI command

   Code Block
   aws ssm start-session --profile service-catalog \ --target i-0fd5c9ff0ef675ceb \ --document-name AWS-StartPortForwardingSession \ --parameters '{"portNumber":["80"],"localPortNumber":["9090"]}'

4. Now you should be able to access that app on your local machine at http://localhost:9090 

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Using the update action allows you to change parameters or update to a new version of the product. WARNING: changes to configuration parameters usually result in a recreation (“replacement”) of the instance, any data saved on the instance will be lost, and the nature of the update by Amazon is difficult to predict. We recommend that you save any important data to S3, provision a new instance and terminate the original.

Terminate

The terminate action deletes the instance permanently.

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