Getting Started with EFA and MPI

This tutorial helps you to launch an EFA and MPI-enabled instance cluster for HPC workloads. In this tutorial, you will perform the following steps:

Step 1: Prepare an EFA-Enabled Security Group

An EFA requires a security group that allows all inbound and outbound traffic to and from the security group itself.

To create an EFA-enabled security group

1. Open the Amazon EC2 console at https://console.aws.amazon.com/ec2/.

2. In the navigation pane, choose Security Groups and then choose Create Security Group.

3. In the Create Security Group window, do the following:

   1. For Security group name, enter a descriptive name for the security group, such as EFA-enabled security group.

   2. (Optional) For Description, enter a brief description of the security group.

   3. For VPC, select the VPC into which you intend to launch your EFA-enabled instances.

   4. Choose Create.

4. Select the security group that you created, and on the Description tab, copy the Group ID.

5. On the Inbound and Outbound tabs, do the following:

   1. Choose Edit.

   2. For Type, choose All traffic.

   3. For Source, choose Custom.

   4. Paste the security group ID that you copied into the field.

   5. Choose Save.

Step 2: Launch a Temporary Instance

Launch a temporary instance that you can use to install and configure the EFA software components. You use this instance to create an EFA-enabled AMI from which you can launch your EFA-enabled instances.

To launch a temporary instance

1. Open the Amazon EC2 console at https://console.aws.amazon.com/ec2/.

2. Choose Launch Instance.

3. On the Choose an AMI page, choose Select for one of the following supported AMIs: Amazon Linux, Amazon Linux 2, RHEL 7.6, RHEL 7.7, CentOS 7, Ubuntu 16.04, and Ubuntu 18.04.

4. On the Choose an Instance Type page, select one of the following supported instance types and then choose Next: Configure Instance Details: c5n.18xlarge, c5n.metal, i3en.24xlarge, i3en.metal, inf1.24xlarge, m5dn.24xlarge, m5n.24xlarge, r5dn.24xlarge, r5n.24xlarge, and p3dn.24xlarge.

5. On the Configure Instance Details page, do the following:

   1. For Elastic Fabric Adapter, choose Enable.

   2. In the Network Interfaces section, for device eth0, choose New network interface.

   3. Choose Next: Add Storage.

6. On the Add Storage page, specify the volumes to attach to the instances in addition to the volumes that are specified by the AMI (such as the root device volume). Then choose Next: Add Tags.

7. On the Add Tags page, specify a tag that you can use to identify the temporary instance, and then choose Next: Configure Security Group.

8. On the Configure Security Group page, for Assign a security group, select Select an existing security group, and then select the security group that you created in Step 1.

9. On the Review Instance Launch page, review the settings, and then choose Launch to choose a key pair and to launch your instance.

Step 3: Install the EFA Software

Install the EFA-enabled kernel, EFA drivers, Libfabric, and Open MPI stack that is required to support EFA on your temporary instance.

The steps differ depending on whether you intend to use EFA with Open MPI or with Intel MPI.

To install the EFA software

1. Connect to the instance you launched in Step 2. For more information, see Connect to Your Linux Instance.

2. To ensure that all of your software packages are up to date, perform a quick software update on your instance. This process may take a few minutes.

   • Amazon Linux, Amazon Linux 2, RHEL 7.6/7.7, CentOS 7

     $ sudo yum update -y

   • Ubuntu 16.04 and Ubuntu 18.04

     $ sudo apt-get update -y

     $ sudo apt-get upgrade -y

3. Download the EFA software installation files. To download the latest stable version, use the following command.

   $ curl -O https://s3.us-west-2.amazonaws.com/aws-efa-installer/aws-efa-installer-1.8.3.tar.gz

   You can also get the latest version by replacing the version number with latest in the preceding command.

4. The software installation files are packaged into a compressed .tar.gz file. Extract the files from the compressed .tar.gz file and navigate into the extracted directory.

   $ tar -xf aws-efa-installer-1.8.3.tar.gz

   $ cd aws-efa-installer

5. Install the EFA software.

   • If you intend to use EFA with Open MPI, you must install the EFA software with Libfabric and Open MPI, and you must skip Step 4: Install Intel MPI.

     To install the EFA software with Libfabric and Open MPI, run the following command.

     $ sudo ./efa_installer.sh -y

     Libfabric is installed in the /opt/amazon/efa directory, while Open MPI is installed in the /opt/amazon/openmpi directory.

   • If you intend to use EFA with Intel MPI only, you can install the EFA software without Libfabric and Open MPI. In this case, Intel MPI uses its embedded Libfabric. If you choose to do this, you must complete Step 4: Install Intel MPI.

     To install the EFA software without Libfabric and Open MPI, run the following command.

     $ sudo ./efa_installer.sh -y --minimal

6. Log out of the instance and then log back in.

7. Confirm that the EFA software components were successfully installed.

   $ fi_info -p efa

   The command should return information about the Libfabric EFA interfaces. The following example shows the command output.

   provider: efa
       fabric: EFA-fe80::94:3dff:fe89:1b70
       domain: efa_0-rdm
       version: 2.0
       type: FI_EP_RDM
       protocol: FI_PROTO_EFA
   provider: efa
       fabric: EFA-fe80::94:3dff:fe89:1b70
       domain: efa_0-dgrm
       version: 2.0
       type: FI_EP_DGRAM
       protocol: FI_PROTO_EFA
   provider: efa;ofi_rxd
       fabric: EFA-fe80::94:3dff:fe89:1b70
       domain: efa_0-dgrm
       version: 1.0
       type: FI_EP_RDM
       protocol: FI_PROTO_RXD

Step 4: Disable Ptrace Protection

To improve your HPC application's performance, Libfabric uses the instance's local memory for interprocess communications when the processes are running on the same instance.

The shared memory feature uses Cross Memory Attach (CMA), which is not supported with ptrace protection. If you are using a Linux distribution that has ptrace protection enabled by default, such as Ubuntu, you must disable it. If your Linux distribution does not have ptrace protection enabled by default, skip this step.

To disable ptrace protection

Do one of the following:

• To temporarily disable ptrace protection for testing purposes, run the following command.

  $ sudo sysctl -w kernel.yama.ptrace_scope=0

• To permanently disable ptrace protection, add kernel.yama.ptrace_scope = 0 to /etc/sysctl.d/10-ptrace.conf and reboot the instance.

Step 5: (Optional) Install Intel MPI

Important

If you intend to use Open MPI, skip this step. Perform this step only if you intend to use Intel MPI.

Intel MPI requires an additional installation and environment variable configuration.

Prerequisites

Ensure that the user performing the following steps has sudo permissions.

To install Intel MPI

1. To download the Intel MPI installation files, see the Intel Developer Zone website.

   You must register before you can download the installation files. After you have registered, do the following:

   1. For Product, choose Intel MPI Library for Linux.

   2. For Version, choose 2019 Update 6, and then choose Full Product.

2. The installation files are packaged into a compressed .tar.gz file. Extract the files from the compressed .tar.gz file and navigate into the extracted directory.

   $ tar -xf file_name.tgz

   $ cd directory_name

3. Open silent.cfg using your preferred text editor. In line 10, change ACCEPT_EULA=decline to ACCEPT_EULA=accept. Save the changes and close the file.

4. Run the installation script.

   $ sudo ./install.sh -s silent.cfg

   Intel MPI is installed in the /opt/intel/impi/ directory by default.

5. Add the Intel MPI environment variables to the corresponding shell startup scripts to ensure that they are set each time that the instance starts. Do one of the following depending on your shell.

   • For bash, add the following environment variable to /home/username/.bashrc and /home/username/.bash_profile.

     source /opt/intel/compilers_and_libraries/linux/mpi/intel64/bin/mpivars.sh

   • For csh and tcsh, add the following environment variable to /home/username/.cshrc.

     source /opt/intel/compilers_and_libraries/linux/mpi/intel64/bin/mpivars.csh

6. Log out of the instance and then log back in.

7. Run the following command to confirm that Intel MPI was successfully installed.

   $ which mpicc

   Ensure that the returned path includes the /opt/intel/ subdirectory.

Note

If you no longer want to use Intel MPI, remove the environment variables from the shell startup scripts.

Step 6: Install Your HPC Application

Install the HPC application on the temporary instance. The installation procedure varies depending on the specific HPC application. For more information about installing software on your Linux instance, see Managing Software on Your Linux Instance.

Note

You might need to refer to your HPC application’s documentation for installation instructions.

Step 7: Create an EFA-Enabled AMI

After you have installed the required software components, you create an AMI that you can reuse to launch your EFA-enabled instances.

To create an AMI from your temporary instance

1. Open the Amazon EC2 console at https://console.aws.amazon.com/ec2/.

2. In the navigation pane, choose Instances.

3. Select the instance that you created in Step 1 and choose Actions, Image, Create Image.

4. In the Create Image window, do the following:

   1. For Image name, enter a descriptive name for the AMI.

   2. (Optional) For Image description, enter a brief description of the AMI.

   3. Choose Create Image and then choose Close.

5. In the navigation pane, choose AMIs.

6. Locate the AMI you created in the list. Wait for the Status to transition from pending to available before continuing to the next step.

Step 8: Launch EFA-Enabled Instances into a Cluster Placement Group

Launch your EFA-enabled instances into a cluster placement group using the EFA-enabled AMI that you created in Step 6, and the EFA-enabled security group that you created in Step 1.

Note

It is not an absolute requirement to launch your EFA-enabled instances into a cluster placement group. However, we do recommend running your EFA-enabled instances in a cluster placement group as it launches the instances into a low-latency group in a single Availability Zone.

To launch your EFA-enabled instances into a cluster placement group

1. Open the Amazon EC2 console at https://console.aws.amazon.com/ec2/.

2. Choose Launch Instance.

3. On the Choose an AMI page, choose My AMIs, find the AMI that you created in Step 6, and then choose Select.

4. On the Choose an Instance Type page, select one of the following supported instance types and then choose Next: Configure Instance Details: c5n.18xlarge, c5n.metal, i3en.24xlarge, i3en.metal, inf1.24xlarge, m5dn.24xlarge, m5n.24xlarge, r5dn.24xlarge, r5n.24xlarge, and p3dn.24xlarge.

5. On the Configure Instance Details page, do the following:

   1. For Number of instances, enter the number of EFA-enabled instances that you want to launch.

   2. For Network and Subnet, select the VPC and subnet into which to launch the instances.

   3. For Placement group, select Add instance to placement group.

   4. For Placement group name, select Add to a new placement group, enter a descriptive name for the placement group, and then for Placement group strategy, select cluster.

   5. For EFA, choose Enable.

   6. In the Network Interfaces section, for device eth0, choose New network interface. You can optionally specify a primary IPv4 address and one or more secondary IPv4 addresses. If you're launching the instance into a subnet that has an associated IPv6 CIDR block, you can optionally specify a primary IPv6 address and one or more secondary IPv6 addresses.

   7. Choose Next: Add Storage.

6. On the Add Storage page, specify the volumes to attach to the instances in addition to the volumes specified by the AMI (such as the root device volume), and then choose Next: Add Tags.

7. On the Add Tags page, specify tags for the instances, such as a user-friendly name, and then choose Next: Configure Security Group.

8. On the Configure Security Group page, for Assign a security group, select Select an existing security group, and then select the security group that you created in Step 1.

9. Choose Review and Launch.

10. On the Review Instance Launch page, review the settings, and then choose Launch to choose a key pair and to launch your instances.

Step 9: Terminate the Temporary Instance

At this point, you no longer need the temporary instance that you launched in Step 1. You can terminate the instance to stop incurring charges for it.

To terminate the temporary instance

1. Open the Amazon EC2 console at https://console.aws.amazon.com/ec2/.

2. In the navigation pane, choose Instances.

3. Select the temporary instance that you created in Step 1 and then choose Actions, Instance State, Terminate, Yes, Terminate.

Step 10: Enable Passwordless SSH

To enable your applications to run across all of the instances in your cluster, you must enable passwordless SSH access from the leader node to the member nodes. The leader node is the instance from which you run your applications. The remaining instances in the cluster are the member nodes.

To enable passwordless SSH between the instances in the cluster

1. Select one instance in the cluster as the leader node, and connect to it.

2. Disable strictHostKeyChecking and enable ForwardAgent on the leader node. Open ~/.ssh/config using your preferred text editor and add the following.

   Host *
       ForwardAgent yes
   Host *
       StrictHostKeyChecking no

3. Generate an RSA key pair.

   $ ssh-keygen -t rsa -N "" -f /home/ubuntu/.ssh/id_rsa

   The key pair is created in the $HOME/.ssh/ directory.

4. Change the permissions of the private key on the leader node.

   $ chmod 600 ~/.ssh/id_rsa

5. Open ~/.ssh/id_rsa.pub using your preferred text editor and copy the key.

6. For each member node in the cluster, do the following:

   1. Connect to the instance.

   2. Open ~/.ssh/authorized_keys using your preferred text editor and add the public key that you copied earlier.

7. To test that the passwordless SSH is functioning as expected, connect to your leader node and run the following command.

   $ ssh member_node_private_ip

   You should connect to the member node without being prompted for a key or password.