Running AG on AWS EC2 — AllegroGraph Python client 105.1.0 documentation

# Running AG on AWS EC2

Federating multiple repositories located on the same server (as shown in Example 16: Federated repositories) can be useful for organizing data, but to truly explore the scalability potential of federated repositories we should look at a system consisting of multiple machines. This example will illustrate this by instantiating multiple AllegroGraph virtual machines on AWS, joining all servers in a single federated repository and issuing a simple query.

Warning

This example involves instantiating multiple AWS resources. These are not free and you will be charged by Amazon. While the cost should not exceed a few dollars, we are not responsible for any charges you might incur while running this tutorial.

To allow our script to interact with AWS we will need to install an additional dependency - boto3.

    pip install boto3

We will also need to configure credentials to allow the script to access the Amazon account that it should use. This can be done in multiple ways. One possibility is to create a file named `~/.aws/credentials` with the following contents:

    [default]
    aws_access_key_id = YOUR_KEY
    aws_secret_access_key = YOUR_SECRET

The key and key id can be obtained from the web interface of AWS.

We’re now ready to begin writing the actual script. Let’s start with some imports:

    import boto3
    import atexit
    import time

We will need the `boto3` module to interact with AWS. We also want to make sure that any resources we have provisioned will be properly discarded when the scripts exits, even if it exits because of an error. The `atexit` module provides a convenient way of doing that.

Warning

While the mechanism of releasing resources used in this tutorial is reasonably robust, it might still fail in rare circumstances (e.g. if your computer loses power). It is important to manually check your AWS account for any stray resources after executing this tutorial to avoid unnecessary costs.

Now we will set a few configuration constants:

    REGION = 'us-west-2'
    AMI = 'ami-5616d82e'
    TYPE = 't2.medium'

These describe the kind of servers that we will be provisioning, as well as the AWS region in which our resources will reside. AMI should be the image id of an AllegroGraph image appropriate for the chosen region. Image identifiers can be found here. The actual value shown above refers to the AllegroGraph 6.3.0 HVM image for the `us-west-2` region. `TYPE` is the ‘instance type’ and determines the amount of compute resources (RAM and CPU) that will be available for each of our servers. The list of instance types can be found here.

We will create a specified number of servers plus an additional one to manage the federation. The number below is the number of federated instances (i.e. it does not include the management instance).

    INSTANCE_COUNT = 2

It is desirable to limit the connections to the system that we are creating so that only your machine will be able to access it. If you have a static IP address, fill it below. If not, leave the value as it is.

    MY_IP = '0.0.0.0/0'

The next set of constants describe various aspect of the infrastructure that we are about to provision. There should be no need to adjust any values here.

    VPC_CIDR = '10.0.0.0/16'
    PUBLIC_CIDR = '10.0.0.0/24'
    PRIVATE_CIDR = '10.0.1.0/24'
    KEY_NAME = 'AG-TUTORIAL-KEYPAIR'
    PROFILE_NAME = 'agprofile'
    USER = 'ec2-user'

The first three values describe the structure of the virtual network that will contain our machines. The network will consist of two subnets - a public one which will contain the management instance and a private one which will contain all other servers. Only machines in the public subnet will be directly accessible over the Internet. `KEY_NAME` is a name that will be assigned to the keypair that we will generate and use to connect to our servers. `PROFILE_NAME` is the name for an instance profile that we will create for our AG servers. `USER` is the system user on the machines we want to connect to. Since AllegroGraph’s images are based on Amazon Linux, that username must be set to `ec2_user`.

We will now create handles for Amazon services that we want to use.

    ec2 = boto3.resource('ec2', region_name=REGION)
    ec2_client = boto3.client('ec2', region_name=REGION)
    iam = boto3.resource('iam', region_name=REGION)
    ssm = boto3.client('ssm', region_name=REGION)

These come in two variants, called `resources` and `clients`. Clients provide low-level access to the Amazon API, while resources are a high-level abstraction built over clients. Using resources is slightly easier and thus preferable, but some operations can only be performed with clients. In our case `ec2_client` and `ssm` objects are clients for the respective AWS services, while other handles are resources.

The first thing that we will create is a security role that will be assigned to our machines. This is necessary to allow the use of SSM, which we will need to execute scripts.

    ssm_role = iam.create_role(RoleName='ssm',
                               AssumeRolePolicyDocument="""{
        "Version":"2012-10-17",
        "Statement":[
           {
              "Effect":"Allow",
              "Principal":{
                 "Service": ["ssm.amazonaws.com", "ec2.amazonaws.com"]
              },
              "Action":"sts:AssumeRole"
           }]}""")
    atexit.register(ssm_role.delete)

The role created above can be assumed by EC2 instances and allows access to SSM. We have also installed an `atexit` handler to make sure that the role is deleted once we are done. We will do the same thing for every other AWS resource that we create.

To make all instances that have assumed the role defined above accessible to SSM we need to connect that role to the appropriate policy document.

    ssm_arn = 'arn:aws:iam::aws:policy/service-role/AmazonEC2RoleforSSM'
    ssm_role.attach_policy(PolicyArn=ssm_arn)
    atexit.register(ssm_role.detach_policy, PolicyArn=ssm_arn)

Again, we have installed an atexit handler to undo the association. Without that we would not be able to remove the role itself.

Now we create an instance profile that we will use to launch instances using our new role.

    instance_profile = iam.create_instance_profile(
      InstanceProfileName=PROFILE_NAME
    )
    atexit.register(instance_profile.delete)

    instance_profile.add_role(RoleName=ssm_role.name)
    atexit.register(instance_profile.remove_role,
                    RoleName=ssm_role.name)

Now it is time to create the virtual network infrastructure for our system.

    vpc = ec2.create_vpc(CidrBlock=VPC_CIDR)
    atexit.register(vpc.delete)

    public_subnet = vpc.create_subnet(CidrBlock=PUBLIC_CIDR)
    atexit.register(public_subnet.delete)

    private_subnet = vpc.create_subnet(CidrBlock=PRIVATE_CIDR)
    atexit.register(private_subnet.delete)

We have two subnets - one for things that should be accessible from the Internet and one for all other machines. To make the public subnet work we need to add an Internet gateway to it.

    internet_gateway = ec2.create_internet_gateway()
    atexit.register(internet_gateway.delete)

    internet_gateway.attach_to_vpc(VpcId=vpc.vpc_id)
    atexit.register(internet_gateway.detach_from_vpc,
                    VpcId=vpc.vpc_id)

As usual, we have to install `atexit` handlers to undo all operations. This is important not only for operations that create resources, but also for those that add associations, since AWS will not allow us to remove a resource with existing associations.

Now we need to define a route table for the public subnet. The route table will basically tell our instances to use the Internet gateway that we have just created to communicate with the Internet.

    public_route_table = vpc.create_route_table()
    atexit.register(public_route_table.delete)

    public_route_table.create_route(
        DestinationCidrBlock='0.0.0.0/0',
        GatewayId=internet_gateway.internet_gateway_id)

    public_rt_assoc = public_route_table.associate_with_subnet(
        SubnetId=public_subnet.id)
    atexit.register(public_rt_assoc.delete)

Machines in the private subnet should not be accessible from the Internet, but must still be able to access external resources. To facilitate that we will create a NAT gateway in the private subnet. A NAT gateway must have a public IP address, so will get one first.

    nat_eip = ec2_client.allocate_address(Domain='vpc')
    atexit.register(ec2_client.release_address,
                    AllocationId=nat_eip['AllocationId'])

Before we actually create the gateway, we must ensure that we will be able to decommission it in a safe manner. The issue is that deleting a NAT gateway is not instantaneous and we cannot remove other resources (the VPC and subnet) until it is gone. So we will define a function that periodically checks the status of our gateway and blocks until it has been fully removed.

    def wait_for_nat_gateway_termination(nat):
        for repeat in range(40):
            time.sleep(10)
            response = ec2_client.describe_nat_gateways(
                NatGatewayIds=[nat['NatGateway']['NatGatewayId']])
            if not response.get('NatGateways', False):
                return
            if response['NatGateways'][0]['State'] in ('deleted', 'failed'):
                return
        raise Exception('NAT gateway refuses to go away')

`boto3` uses so called `waiters` to automate the process of wating for a state change of an AWS resource. Unfortunately there is no `waiter` that checks for the termination of a NAT gateway, so we had to write our own. We will use `boto3` waiters in other parts of the code.

We are now ready to create the gateway. Notce that the gateway itself must be a part of the public subent, even though it is meant to be used by the private subnet.

    nat = ec2_client.create_nat_gateway(
        AllocationId=nat_eip['AllocationId'],
        SubnetId=public_subnet.id
    )
    atexit.register(wait_for_nat_gateway_termination, nat)
    atexit.register(ec2_client.delete_nat_gateway,
                    NatGatewayId=nat['NatGateway']['NatGatewayId'])

Notice two `atexit` handlers - one issues the delete command, the other one waits for its completion. The handlers are executed in reverse registration order, so the ‘waiting’ handler is registered first. We will see this pattern again in the future.

Now we will wait until the NAT gateway is functional This might take a while. Fortunately this time we can take advantage of a `boto3` waiter:

    ec2_client.get_waiter('nat_gateway_available').wait(
        NatGatewayIds=[nat['NatGateway']['NatGatewayId']])

Now we need a route table for the private subnet

    private_route_table = vpc.create_route_table()
    atexit.register(private_route_table.delete)

    private_route_table.create_route(
        DestinationCidrBlock='0.0.0.0/0',
        NatGatewayId=nat['NatGateway']['NatGatewayId'])

    private_rt_assoc = private_route_table.associate_with_subnet(
        SubnetId=private_subnet.id)
    atexit.register(private_rt_assoc.delete)

The next pair of resources to create will be the security groups. These determine what is allowed to connect to what over the network. We will want different rules for private and public subnets.

    public_security_group = vpc.create_security_group(
        GroupName="ag-http-global",
        Description="Allow SSH + HTTP connections to AG")
    atexit.register(public_security_group.delete)

    public_ip_permissions = [{
        'IpProtocol': 'TCP',
        'FromPort': 10035,
        'ToPort': 10035,
        'IpRanges': [{'CidrIp': MY_IP}]
    }, {
        'IpProtocol': 'TCP',
        'FromPort': 16000,
        'ToPort': 17000,
        'IpRanges': [{'CidrIp': MY_IP}]
    }, {
        'IpProtocol': 'TCP',
        'FromPort': 22,
        'ToPort': 22,
        'IpRanges': [{'CidrIp': MY_IP}]
    }]

    public_security_group.authorize_ingress(
        IpPermissions=public_ip_permissions)

We allow SSH connections and HTTP connections to AG (both the frontend (`10035`) and the session ports (`16000-17000`)) from the address we defined above. Note that if you have not changed the default value of `MY_IP` the the system will be accessible from anywhere, which is a security risk.

Private instances shall accept all connections, but only from machines within our virtual network.

    private_security_group = vpc.create_security_group(
        GroupName="all-internal",
        Description="Allow all access from our network")
    atexit.register(private_security_group.delete)

    private_ip_permissions = [{
        'IpProtocol': '-1',
        'UserIdGroupPairs': [{'GroupId': private_security_group.id},
                             {'GroupId': public_security_group.id}]
    }]

    private_security_group.authorize_ingress(
        IpPermissions=private_ip_permissions)

Now it is time to generate a keypair. This is simply the SSH key that we will use to control access to our machines.

    key_pair = ec2.create_key_pair(KeyName=KEY_NAME)
    atexit.register(key_pair.delete)

As mentioned above, we will want to use SSM to execute scripts on our servers. To do that we have to ensure that an SSM agent is installed on each machine. We can do this with the following script.

    user_data = """#!/bin/bash
        cd /tmp
        sudo yum install -y https://s3.amazonaws.com/ec2-downloads-windows/SSMAgent/latest/linux_amd64/amazon-ssm-agent.rpm
        sudo start amazon-ssm-agent"""

The script itself will be executed with cloud-init.

Now it is finally time to create our machines. Let us start with the management node.

    public_instance = ec2.create_instances(
        ImageId=AMI, InstanceType=TYPE,
        UserData=user_data,
        MinCount=1, MaxCount=1,
        KeyName=KEY_NAME,
        SecurityGroupIds=[
            public_security_group.id,
        ],
        IamInstanceProfile={
            "Arn": instance_profile.arn
        },
        SubnetId=public_subnet.id)[0]
    atexit.register(
        ec2_client.get_waiter('instance_terminated').wait,
        InstanceIds=[public_instance.id])
    atexit.register(public_instance.terminate)

We pass our SSM installation script in the `UserData` parameter. Notice how the `atexit` handlers wait for the instance to be fully deleted before proceeding to shutdown other systems.

Instances in the private subnet can be created in a similar way.

    private_instances = ec2.create_instances(
        ImageId=AMI, InstanceType=TYPE,
        MinCount=INSTANCE_COUNT, MaxCount=INSTANCE_COUNT,
        UserData=user_data,
        KeyName=KEY_NAME,
        SecurityGroupIds=[
            private_security_group.id,
        ],
        IamInstanceProfile={
            "Arn": instance_profile.arn
        },
        SubnetId=private_subnet.id)
    private_ids = [i.id for i in private_instances]
    all_ids = [public_instance.id] + private_ids
    atexit.register(
        ec2_client.get_waiter('instance_terminated').wait,
        InstanceIds=private_ids)
    for instance in private_instances:
        atexit.register(instance.terminate)

We gather the ids of all our instances in two lists. Now let us wait until all our instances are operational.

    ec2_client.get_waiter('instance_status_ok').wait(
        InstanceIds=all_ids)

We will need one more public IP address, to be used by the management instance that we need to connect to.

    eip = ec2_client.allocate_address(Domain='vpc')
    atexit.register(ec2_client.release_address,
                    AllocationId=eip['AllocationId'])

    eip_assoc = ec2_client.associate_address(
        AllocationId=eip['AllocationId'],
        InstanceId=public_instance.id)

    atexit.register(ec2_client.disassociate_address,
                    AssociationId=eip_assoc['AssociationId'])

We have installed the SSM agent on our machines, but it takes a moment for it to become operational. We will define yet another wait function to suspend the execution until then.

    def wait_for_ssm_agents(instance_ids):
       for repeat in range(40):
           time.sleep(10)
           response = ssm.describe_instance_information(
               InstanceInformationFilterList=[{
                   'key': 'InstanceIds',
                   'valueSet': instance_ids
               }])
           num_responses = len(response.get(
               'InstanceInformationList', []))
           if num_responses != len(instance_ids):
               # It is normal for an instance to not show up
               # even if requested explicitly.
               continue
           for instance in response.get('InstanceInformationList'):
               if instance['PingStatus'] != 'Online':
                   break
           else:
               return
       raise Exception('Timed out waiting for SSM agents to activate.')

    wait_for_ssm_agents(all_ids)

We will need one more function to wait for an SSM command to complete its execution (unfortunately there is no built-in waiter for this in `boto3`).

    def wait_for_ssm_command(command):
        for repeat in range(40):
            time.sleep(10)
            response = ssm.list_commands(
                CommandId=command['Command']['CommandId'])
            if not response.get('Commands', False):
                return
            if response['Commands'][0]['Status'] in \
                    ('Success', 'Cancelled', 'Failed', 'TimedOut'):
                return
        raise Exception(
            'Timed out waiting for an SSM command to finish.')

Before we proceed, we should wait until all AG servers have started (at this point we know that the machines are up, but it takes a moment for AG itself to start processing requests). In a production system we would probably achieve this by using a dedicated monitoring solution or some other advanced mechanism, but to keep this tutorial simple we will just use SSM commands to poll the AG port until it starts responding.

    wait_for_ag = [
      'until curl -f http://127.0.0.1:10035/version; do sleep 2; done'
    ]
    cmd = ssm.send_command(
        InstanceIds=all_ids,
        DocumentName='AWS-RunShellScript',
        Parameters={'commands': wait_for_ag},
        TimeoutSeconds=120)
    wait_for_ssm_command(cmd)

We will now use SSM to send a script that will load sample data into our instances. To keep things simple we will add just a single triple per instance. That triple will include the index of the instance (a number between `0` and `INSTANCE_COUNT - 1`).

    script = [
        'ID=$(curl http://169.254.169.254/latest/meta-data/ami-launch-index)',
        'curl -X PUT -u test:xyzzy http://127.0.0.1:10035/repositories/r',
        ' '.join(['curl -X PUT -u test:xyzzy http://127.0.0.1:10035/repositories/r/statement',
                  '--data-urlencode "subj=<ex://instance${ID}>"',
                  '--data-urlencode "pred=<ex://id>"',
                  '--data-urlencode "obj=\\"${ID}\\"^^<http://www.w3.org/2001/XMLSchema#integer>"'])
    ]

    cmd = ssm.send_command(InstanceIds=private_ids,
                           DocumentName='AWS-RunShellScript',
                           Parameters={'commands': script})
    wait_for_ssm_command(cmd)

Note that the waiter functions defined above are not particularly robust in their error handling. In a production system consisting of a larger number of instances a more elaborate mechanism for error detection and handling (retries) would have to be implemented.

Now we are ready to create the federation by connecting to the management machine. Notice that we use the default credentials for the AllegroGraph AMI.

    from franz.openrdf.sail.allegrographserver import AllegroGraphServer

    server = AllegroGraphServer(host=eip['PublicIp'],
                                user='test', password='xyzzy')
    conn = server.openSession(
        '+'.join('<http://test:xyzzy@%s/repositories/r>'
                     % i.private_ip_address
                 for i in private_instances))

And now we can issue a query:

    from franz.openrdf.query.query import QueryLanguage

    query = conn.prepareTupleQuery(QueryLanguage.SPARQL, """
        SELECT (AVG(?o) as ?avg) { ?s ?p ?o }""")
    query.evaluate(output=True)

This should print the average instance id, which should equal `(INSTANCE_COUNT - 1) / 2`.

    -------
    | avg |
    =======
    | 0.5 |
    -------

That is all - the script is now done and will start tearing down the whole infrastructure.

Warning

Remember to check your AWS account for any leftover resources after running the tutorial to avoid unnecessary costs.