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dleThe 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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  • Department: your department within Sage Bionetworks.

  • Project: the project that this instance will be used for. Please make a request to #sageit if your project is not in the list.

  • CostCenter: bill the product to this cost center code. If the appropriate cost center code is not in the list then select “Other / 000001” and create a custom “CostCenterOther” tag. Set the tag to a value from our official list of cost centers codes. Example:

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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, CostCenter 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.

Note: At this point you can verify that the PAT for the Service Catalog was successfully created by viewing the Synapse token management page. When the PAT expires you will need to repeat these steps to create a new PAT. The PAT should look something like this

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  1. Use the ssm start-session command to connect to the instance

    Code Block
    aws ssm start-session --profile service-catalog \
                      --target i-0fd5c9ff0ef675ceb \
                      --document-name AWS-StartInteractiveCommand \
                      --parameters command="sudo su - ec2-user"

  2. Copy the public portion of your ssh key (on your local computer) to the instance’s ~/.ssh/authorizedkeysauthorized_keys file.

  3. Set the permission of the authorized_keys file to 600 (i.e. chmod 600 ~/.ssh/authorizedkeysauthorized_keys)

  4. Add the following to your local machine’s ~/.ssh/config file

    Code Block
    # SSH over Session Manager
host i-* mi-*
    ProxyCommand sh -c "aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'"

  5. From your local machine, execute the ssh command to access the instance

    Code Block
    ➜ AWS_PROFILE=service-catalog ssh -i ~/.ssh/id_rsa ec2-user@i-0fd5c9ff0ef675ceb
Last login: Thu Jun 17 21:25:56 2021

       __|  __|_  )
       _|  (     /   Amazon Linux 2 AMI
      ___|\___|___|

https://aws.amazon.com/amazon-linux-2/
[ec2-user@ip-10-41-23-76 ~]$

  6. From your local machine, execute the scp command to copy files directly to the instance

    Code Block
    ➜ AWS_PROFILE=service-catalog scp -i ~/.ssh/id_rsa README.md ec2-user@i-07eeb59282fafe244:~/.
README.md                                             100%  814     9.2KB/s   00:00

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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. To provide access to that app in the Windows Command Prompt use this syntax:

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

  5. 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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  • The “Environment” parameters are required fields. You can replace the default values, however please do not leave these fields empty. Also pay special attention to the formatting that’s required for the values. The deployment will fail if the formatting isn’t correct.

  • There is an AWS bug that prevents disabling the scheduled job after it has been enabled. The workaround is to either (1) Terminate the job and create a new one or (2) Set the rate to some distant time in the future (i.e. 3650 days).

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Secrets are stored in the AWS secrets manager and exposed to the job as environment variables. The logs above print out the environment variables from the job. Take note of the “SCHEDULED_JOB_SECRETS” parameter in the logs. The secrets that are passed into this product are exposed as environment variables in the logs by the “printenv” command. Please make sure to never expose secrets in this way. DO NOT PRINT ENVIRONMENT VARIABLES.

Accessing Scheduled Job Secrets

Job secrets can be access a number of different ways. The first way is simply to get it from the docker container environment variable SCHEDULED_JOB_SECRETS.

Environment variable example:

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