Get started with EFA and MPI - Amazon Elastic Compute Cloud

Get 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. The following procedure allows all inbound and outbound traffic for testing purposes only. For other scenarios, see Security group rules for different use cases.

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 security group.

  4. Select the security group that you created, and on the Details tab, copy the Security group ID.

  5. With the security group still selected, choose Actions, Edit inbound rules, and then do the following:

    1. Choose Add rule.

    2. For Type, choose All traffic.

    3. For Source type, choose Custom and paste the security group ID that you copied into the field.

    4. Choose Add rule.

    5. For Type, choose SSH.

    6. For Source type, choose Anywhere-IPv4.

    7. Choose Save rules.

  6. With the security group still selected, choose Actions, Edit outbound rules, and then do the following:

    1. Choose Add rule.

    2. For Type, choose All traffic.

    3. For Destination type, choose Custom and paste the security group ID that you copied into the field.

    4. Choose Save rules.

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.

New console

To launch a temporary instance

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

  2. In the navigation panel, choose Instances, and then choose Launch Instances to open the new launch instance wizard.

  3. (Optional) In the Name and tags section, provide a name for the instance, such as EFA-instance. The name is assigned to the instance as a resource tag (Name=EFA-instance).

  4. In the Application and OS Images section, select a supported AMI.

  5. In the Instance type section, select a supported instance type.

  6. In the Key pair section, select the key pair to use for the instance.

  7. In the Network settings section, choose Edit, and then do the following:

    1. For Subnet, choose the subnet in which to launch the instance. If you do not select a subnet, you can't enable the instance for EFA.

    2. For Firewall (security groups), choose Select existing security group, and then select the security group that you created in the previous step.

    3. Expand the Advanced network configuration section, and for Elastic Fabric Adapter, select Enable.

  8. In the Storage section, configure the volumes as needed.

  9. In the Summary panel on the right, choose Launch instance.

Old console

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 supported AMIs.

  4. On the Choose an Instance Type page, select one of the supported instance types and then choose Next: Configure Instance Details.

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

    1. For Subnet, choose the subnet in which to launch the instance. If you do not select a subnet, you can't enable the instance for EFA.

    2. For Elastic Fabric Adapter, choose Enable.

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

    4. 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, with Intel MPI, or with Open MPI and Intel MPI.

To install the EFA software

  1. Connect to the instance you launched. 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 2, RHEL 7/8, and CentOS 7

      $ sudo yum update -y
    • Ubuntu 18.04 and 20.04

      $ sudo apt-get update
      $ sudo apt-get upgrade -y
    • SUSE Linux Enterprise

      $ sudo zypper update -y
  3. Download the EFA software installation files. The software installation files are packaged into a compressed tarball (.tar.gz) file. To download the latest stable version, use the following command.

    $ curl -O https://efa-installer.amazonaws.com/aws-efa-installer-1.17.2.tar.gz

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

  4. (Optional) Verify the authenticity and integrity of the EFA tarball (.tar.gz) file. We recommend that you do this to verify the identity of the software publisher and to check that the file has not been altered or corrupted since it was published. If you do not want to verify the tarball file, skip this step.

    Note

    Alternatively, if you prefer to verify the tarball file by using an MD5 or SHA256 checksum instead, see Verify the EFA installer using a checksum.

    1. Download the public GPG key and import it into your keyring.

      $ wget https://efa-installer.amazonaws.com/aws-efa-installer.key && gpg --import aws-efa-installer.key

      The command should return a key value. Make a note of the key value, because you need it in the next step.

    2. Verify the GPG key's fingerprint. Run the following command and specify the key value from the previous step.

      $ gpg --fingerprint key_value

      The command should return a fingerprint that is identical to 4E90 91BC BB97 A96B 26B1 5E59 A054 80B1 DD2D 3CCC. If the fingerprint does not match, don't run the EFA installation script, and contact AWS Support.

    3. Download the signature file and verify the signature of the EFA tarball file.

      $ wget https://efa-installer.amazonaws.com/aws-efa-installer-1.17.2.tar.gz.sig && gpg --verify ./aws-efa-installer-1.17.2.tar.gz.sig

      The following shows example output.

      gpg: Signature made Wed 29 Jul 2020 12:50:13 AM UTC using RSA key ID DD2D3CCC gpg: Good signature from "Amazon EC2 EFA <ec2-efa-maintainers@amazon.com>" gpg: WARNING: This key is not certified with a trusted signature! gpg: There is no indication that the signature belongs to the owner. Primary key fingerprint: 4E90 91BC BB97 A96B 26B1 5E59 A054 80B1 DD2D 3CCC

      If the result includes Good signature, and the fingerprint matches the fingerprint returned in the previous step, proceed to the next step. If not, don't run the EFA installation script, and contact AWS Support.

  5. Extract the files from the compressed .tar.gz file and navigate into the extracted directory.

    $ tar -xf aws-efa-installer-1.17.2.tar.gz && cd aws-efa-installer
  6. Install the EFA software. Do one of the following depending on your use case.

    Note

    If you are using a SUSE Linux operating system, you must additionally specify the --skip-kmod option to prevent kmod installation. By default, SUSE Linux does not allow out-of-tree kernel modules. As a result, EFA and NVIDIA GPUDirect support is currently not supported with SUSE Linux.

    • Open MPI and Intel MPI

      If you intend to use an EFA with Open MPI and Intel MPI, you must install the EFA software with Libfabric and Open MPI, and you must complete Step 5: (Optional) 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.

    • Open MPI only

      If you intend to use EFA with Open MPI only, you must install the EFA software with Libfabric and Open MPI, and you can skip Step 5: (Optional) 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.

    • Intel MPI only

      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 5: (Optional) Install Intel MPI.

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

      $ sudo ./efa_installer.sh -y --minimal
  7. If the EFA installer prompts you to reboot the instance, do so and then reconnect to the instance. Otherwise, log out of the instance and then log back in to complete the installation.

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

    $ fi_info -p efa -t FI_EP_RDM

    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

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 only 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 script, do the following

    1. Visit the Intel website.

    2. In the Intel MPI Library section of the webpage, choose the link for the Intel MPI Library for Linux Offline installer.

  2. Run the installation script that you downloaded in the previous step.

    $ sudo bash installation_script_name.sh
  3. In the installer, choose Accept & install.

  4. Read the Intel Improvement Program, choose the appropriate option, and then choose Begin Installation.

  5. When the installation completes, choose Close.

  6. By default, Intel MPI uses its embedded (internal) Libfabric. You can configure Intel MPI to use the Libfabric that ships with the EFA installer instead. Typically, the EFA installer ships with a later version of Libfabric than Intel MPI. In some cases, the Libfabric that ships with the EFA installer is more performant than that of Intel MPI. To configure Intel MPI to use the Libfabric that ships with the EFA installer, do one of the following depending on your shell.

    bash shells

    For bash shells, add the following statement to /home/username/.bashrc and /home/username/.bash_profile.

    export I_MPI_OFI_LIBRARY_INTERNAL=0
    csh and tcsh shells

    For csh and tcsh shells, add the following statement to /home/username/.cshrc.

    setenv I_MPI_OFI_LIBRARY_INTERNAL 0
  7. Add the following source command to your shell script to source the vars.sh script from the installation directory to set up the compiler environment each time the instance starts. Do one of the following depending on your shell.

    bash shells

    For bash shells, add the following statement to /home/username/.bashrc and /home/username/.bash_profile.

    source /opt/intel/oneapi/mpi/latest/env/vars.sh
    csh and tcsh shells

    For csh and tcsh shells, add the following statement to /home/username/.cshrc.

    source /opt/intel/oneapi/mpi/latest/env/vars.csh
  8. By default, if EFA is not available due to a misconfiguration, Intel MPI defaults to the TCP/IP network stack, which might result in slower application performance. You can prevent this by setting I_MPI_OFI_PROVIDER to efa. This causes Intel MPI to fail with the following error if EFA is not available:

    Abort (XXXXXX) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init: OtherMPI error, MPIR_Init_thread (XXX)........: MPID_Init (XXXX)..............: MPIDI_OFI_mpi_init_hook (XXXX): open_fabric (XXXX)............: find_provider (XXXX)..........: OFI fi_getinfo() failed (ofi_init.c:2684:find_provider:

    Do one of the following depending on your shell.

    bash shells

    For bash shells, add the following statement to /home/username/.bashrc and /home/username/.bash_profile.

    export I_MPI_OFI_PROVIDER=efa
    csh and tcsh shells

    For csh and tcsh shells, add the following statement to /home/username/.cshrc.

    setenv I_MPI_OFI_PROVIDER efa
  9. By default, Intel MPI doesn't print debugging information. You can specify different verbosity levels to control the debugging information. Possible values (in order of the amount of detail they provide) are: 0 (default), 1, 2, 3, 4, 5. Level 1 and higher prints the libfabric version and libfabric provider. Use libfabric version to check whether Intel MPI is using the internal Libfabric or the Libfabric that ships with the EFA installer. If it's using the internal Libfabric, the version is suffixed with impi. Use libfabric provider to check with Intel MPI is using EFA or the TCP/IP network. If it's using EFA, the value is efa. If it's using TCP/IP, the value is tcp;ofi_rxm.

    To enable debugging information, do one of the following depending on your shell.

    bash shells

    For bash shells, add the following statement to /home/username/.bashrc and /home/username/.bash_profile.

    export I_MPI_DEBUG=value
    csh and tcsh shells

    For csh and tcsh shells, add the following statement to /home/username/.cshrc.

    setenv I_MPI_DEBUG value
  10. By default, Intel MPI uses the operating system’s shared memory (shm) for intra-node communication, and it uses Libfabric (ofi) only for inter-node communication. Generally, this configuration provides the best performance. However, in some cases the Intel MPI shm fabric can cause certain applications to hang indefinitely.

    To resolve this issue, you can force Intel MPI to use Libfabric for both intra-node and inter-node communication. To do this, do one of the following depending on your shell.

    bash shells

    For bash shells, add the following statement to /home/username/.bashrc and /home/username/.bash_profile.

    export I_MPI_FABRICS=ofi
    csh and tcsh shells

    For csh and tcsh shells, add the following statement to /home/username/.cshrc.

    setenv I_MPI_FABRICS ofi
    Note

    The EFA Libfabric provider uses the operating system's shared memory for intra-node communication. This means that setting I_MPI_FABRICS to ofi yields similar performance to the default shm:ofi configuration.

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

  12. 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, see Manage software on your Amazon 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 temporary instance that you created and choose Actions, Image, Create image.

  4. For Create image, 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 purpose of the AMI.

    3. Choose Create image.

  5. In the navigation pane, choose AMIs.

  6. Locate the AMI tht you created in the list. Wait for the status to change 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 7, 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 placementgroup. 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 ensure that capacity is available as you scale your cluster’s instances, you can create a Capacity Reservation for your cluster placement group. For more information, see Capacity Reservations in cluster placement groups.

New console

To launch a temporary instance

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

  2. In the navigation panel, choose Instances, and then choose Launch Instances to open the new launch instance wizard.

  3. (Optional) In the Name and tags section, provide a name for the instance, such as EFA-instance. The name is assigned to the instance as a resource tag (Name=EFA-instance).

  4. In the Application and OS Images section, choose My AMIs, and then select the AMI that you created in the previous step.

  5. In the Instance type section, select a supported instance type.

  6. In the Key pair section, select the key pair to use for the instance.

  7. In the Network settings section, choose Edit, and then do the following:

    1. For Subnet, choose the subnet in which to launch the instance. If you do not select a subnet, you can't enable the instance for EFA.

    2. For Firewall (security groups), choose Select existing security group, and then select the security group that you created in the previous step.

    3. Expand the Advanced network configuration section, and for Elastic Fabric Adapter, select Enable.

  8. (Optional) In the Storage section, configure the volumes as needed.

  9. In the Advanced details section, for Placement group name, select the cluster placement group into which to launch the instances. If you need to create a new cluster placement group, choose Create new placement group.

  10. In the Summary panel on the right, for Number of instances, enter the number of EFA-enabled instances that you want to launch, and then choose Launch instance.

Old console

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 7, and then choose Select.

  4. On the Choose an Instance Type page, select one of the supported instance types and then choose Next: Configure Instance Details.

  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. 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 and then choose Actions, Instance state, Terminate instance.

  4. When prompted for confirmation, choose 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 ~/.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 chmod 600 ~/.ssh/config
  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.