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Created on Jun 30, 2019

Introduction

In this document we will demonstrate a deployment procedure of RDMA accelerated applications running in Docker containers over NVIDIA end-to-end 100 Gb/s InfiniBand (IB) solution.

We use Ubuntu 16.04.6 LTS as host OS and install latest Docker CE (how-to install guide). We show how to update and install the NVIDIA software and hardware components on host and on Docker container.

For network communication each Docker has 2 devices:

  1. Linux bridge device for IP connectivity. Bridge is connected to host IPoIB interface
  2. Manually mapped InfiniBand uverbs device for RDMA traffic


This guide for Docker deployment with no K8s orchestration. For K8s deployment please proceed to this link: https://docs.mellanox.com/label/SOL/k8s

References

Setup Overview

Equipment

Server Logical Design

Docker Network Diagram

Server Wiring

In our reference we'll wire 1st port to InfiniBand switch and will not use a 2nd port.

Network Configuration

The will use in our install setup 4 servers.

Each servers will connected to the SB7700 switch by a 100Gb/s IB copper cable. The switch port connectivity in our case is as follow:

  • 1st -4th ports – connected to Host servers

Server names with network configuration provided below

Server type Server name IP and NICs
Internal network External network
Server 01clx-mld-41ib0: 12.12.12.41eno1: From DHCP (reserved)
Server 02clx-mld-42ib0: 12.12.12.42eno1: From DHCP (reserved)
Server 03clx-mld-43ib0: 12.12.12.43eno1: From DHCP (reserved)
Server 04clx-mld-44ib0: 12.12.12.44eno1: From DHCP (reserved)

Deployment Guide

Prerequisites

Update Ubuntu Software Packages

To update/upgrade Ubuntu software packages, run the commands below.

Server Console
sudo apt-get update # Fetches the list of available update
sudo apt-get upgrade -y # Strictly upgrades the current packages

Enable the Subnet Manager(SM) on the IB Switch

Refer to the MLNX-OS User Manual to become familiar with switch software (located at support.mellanox.com ).
Before starting to use of the NVIDIA switch, we recommend that you upgrade the switch to the latest MLNX-OS version.

There are three options to select the best place to locate the SM:

  1. Enabling the SM on one of the managed switches. This is a very convenient and quick operation and make InfiniBand ‘plug & play’ easily.
  2. Run /etc/init.d/opensmd on one or more servers. It is recommended to run the SM on a server in case there are 648 nodes or more.
  3. Use Unified Fabric Management (UFM®) Appliance dedicated server. UFM offers much more than the SM.
    |UFM needs more compute power than the existing switches have, but does not require an expensive server.
    It does represent additional cost for the dedicated server.

We'll explain options 1 and 2 only

Option 1: Configuring the SM on a Switch MLNX-OS® all NVIDIA switch systems.
To enable the SM on one of the managed switches follow the next steps.

  1. Login to the switch and enter to config mode:

    Switch Console
    NVIDIA MLNX-OS Switch Management 
    
    switch login: admin 
    Password: 
    Last login: Wed Aug 12 23:39:01 on ttyS0 
    
    MNVIDIASwitch 
    
    switch [standalone: master] > enable 
    switch [standalone: master] # conf t 
    switch [standalone: master] (config)#
  2. Run the command:

    Switch Console
    switch [standalone: master] (config)#ib sm 
    switch [standalone: master] (config)#
  3. Check if the SM is running. Run:

    Switch Console
    switch [standalone: master] (config)#show ib sm 
    enable 
    switch [standalone: master] (config)#

To save the configuration (permanently), run:

Switch Console
switch (config) # configuration write


Option 2: Configuring the SM on a Server ( Skip this procedure if you enable SM on switch)

To start up OpenSM on a server, simply run opensm from the command line on your management node by typing:

Server Console
opensm

Or:

Start OpenSM automatically on the head node by editing the /etc/opensm/opensm.conf file.

Create a configuration file by running:

Server Console
opensm –config /etc/opensm/opensm.conf

Edit /etc/opensm/opensm.conf file with the following line:

Server Console
onboot=yes

Upon initial installation, OpenSM is configured and running with a default routing algorithm. When running a multi-tier fat-tree cluster, it is recommended to change the following options to create the most efficient routing algorithm delivering the highest performance:

Server Console
–routing_engine=updn

For full details on other configurable attributes of OpenSM, see the “OpenSM – Subnet Manager” chapter of the NVIDIA OFED for Linux User Manual.

Installation NVIDIA OFED for Ubuntu on a Host

This chapter describes how to install and test the NVIDIA OFED for Linux package on a single host machine with NVIDIA ConnectX®-5 adapter card installed. For more information click on NVIDIA OFED for Linux User Manual.

Downloading NVIDIA OFED

  1. Verify that the system has a NVIDIA network adapter (HCA/NIC) installed.

    Server Console
    lspci -v | grep Mellanox

    The following example shows a system with an installed NVIDIA HCA:

  2. Download the ISO image according to you OS to your host.
    The image’s name has the format
    MLNX_OFED_LINUX-<ver>-<OS label><CPUarch>.iso. You can download it from:
    http://www.mellanox.com > Products > Software > InfiniBand/VPI Drivers > Mellanox OFED Linux (MLNX_OFED) > Download.

  3. Use the MD5SUM utility to confirm the downloaded file’s integrity. Run the following command and compare the result to the value provided on the download page.

    Server Console
    md5sum MLNX_OFED_LINUX-<ver>-<OS label>.tgz

Installing NVIDIA OFED

MLNX_OFED is installed by running the mlnxofedinstall script. The installation script, performs the following:

  • Discovers the currently installed kernel
  • Uninstalls any software stacks that are part of the standard operating system distribution or another vendor's commercial stack
  • Installs the MLNX_OFED_LINUX binary RPMs (if they are available for the current kernel)
  • Identifies the currently installed InfiniBand and Ethernet network adapters and automatically upgrades the firmware

The installation script removes all previously installed NVIDIA OFED packages and re-installs from scratch. You will be prompted to acknowledge the deletion of the old packages.

  1. Log into the installation machine as root.
  2. Copy the downloaded tgz to /tmp

    Server Console
    cd /tmp
    tar -xzvf MLNX_OFED_LINUX-4.5-1.0.1.0-ubuntu16.04-x86_64.tgz
    cd MLNX_OFED_LINUX-4.5-1.0.1.0-ubuntu16.04-x86_64/
  3. Run the installation script.

    Server Console
    ./mlnxofedinstall
  4. Reboot after the installation finished successfully.

    Server Console
    /etc/init.d/openibd restart
    reboot

    By default both ConnectX®-5 VPI ports are initialized as InfiniBand ports.

  5. Check the ports’ mode is InfiniBand 

    Server Console
    ibv_devinfo

  6. If you see the following - You need to change the interfaces port type to InfiniBand
     
    Change the interfaces port type to InfiniBand mode ConnectX®-5 ports can be individually configured to work as InfiniBand or Ethernet ports.
    Change the mode to InfiniBand. Use the mlxconfig script after the driver is loaded.
    * LINK_TYPE_P1=1 is a InfiniBand mode
    a. Start mst and see ports names

    Server Console
    mst start
    mst status

    b. Change the mode of both ports to InfiniBand:

    Server Console
    mlxconfig -d /dev/mst/mt4121_pciconf0 s LINK_TYPE_P1=1 
    Server Console Output
    Port 1 set to IB mode
    Server Console
    reboot


    c. Queries InfiniBand devices and prints about them information that is available for use from user-space.

    Server Console
    ibv_devinfo
  7. Run the ibdev2netdev utility to see all the associations between the Ethernet devices and the IB devices/ports.

    Server Console
    ibdev2netdev
    
    ifconfig ib0 12.12.12.41 netmask 255.255.255.0
  8. Insert to the /etc/network/interfaces file the lines below after the following lines:

    Server Console
    vim /etc/network/interfaces

    Example:

    Sample
    auto eno1 
    iface eno1 inet dhcp 
    
    auto ib0 
    iface ib0 inet static 
    address 12.12.12.41 
    netmask 255.255.255.0
  9. Check the network configuration is set correctly.

    Server Console
    ifconfig -a

Docker installing and configured

Uninstall old versions

To uninstall old versions, we recommend run following command:

Server Console
sudo apt-get remove docker docker-engine docker.io

It’s OK if apt-get reports that none of these packages are installed.

The contents of /var/lib/docker/, including images, containers, volumes, and networks, are preserved.

Install Docker CE

For Ubuntu 16.04 and higher, the Linux kernel includes support for OverlayFS, and Docker CE will use the overlay2 storage driver by default.

Install using the repository

Before you install Docker CE for the first time on a new host machine, you need to set up the Docker repository. Afterward, you can install and update Docker from the repository.

Set Up the repository

  1. Update the apt package index:

    Server Console
    sudo apt-get update
  2. Install packages to allow apt to use a repository over HTTPS:

    Server Console
    sudo apt-get install apt-transport-https ca-certificates curl software-properties-common
  3. Add Docker’s official GPG key:

    Server Console
    sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

    Verify that the key fingerprint is 9DC8 5822 9FC7 DD38 854A E2D8 8D81 803C 0EBF CD88.

    Server Console
    sudo apt-key fingerprint 0EBFCD88
    Server Console
    pub 4096R/0EBFCD88 2017-02-22 
    Key fingerprint = 9DC8 5822 9FC7 DD38 854A E2D8 8D81 803C 0EBF CD88 
    uid Docker Release (CE deb) <docker@docker.com> 
    sub 4096R/F273FCD8 2017-02-22

Install Docker CE

Install the latest version of Docker CE, or go to the next step to install a specific version. Any existing installation of Docker is replaced.

Server Console
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"
sudo apt-get update
sudo apt-get install docker-ce

Customize the docker0 bridge

The recommended way to configure the Docker daemon is to use the daemon.json file, which is located in /etc/docker/ on Linux. If the file does not exist, create it. You can specify one or more of the following settings to configure the default bridge network

Server Console
{ 
"bip": "172.16.41.1/24",
"fixed-cidr": "172.16.41.0/24",
"mtu": 1500, 
"dns": ["8.8.8.8","8.8.4.4"] 
}


The same options are presented as flags to dockerd , with an explanation for each:

  • --bip=CIDR : supply a specific IP address and netmask for the docker0 bridge, using standard CIDR notation. For example: 172.16.41.1/16.
  • --fixed-cidr=CIDR : restrict the IP range from the docker0 subnet, using standard CIDR notation. For example: 172.16.41.0/16 .
  • --mtu=BYTES: override the maximum packet length on docker0 . For example: 1500.
  • --dns=[] : The DNS servers to use. For example: --dns=8.8.8.8,8.8.4.4.

Restart Docker after making changes to the daemon.json file.

Server Console
sudo /etc/init.d/docker restart


Set communicating to the outside world

Check ip forwarding in kernel:

Server Console
sysctl net.ipv4.conf.all.forwarding
Server Console Output
net.ipv4.conf.all.forwarding = 1

If disabled

Server Console
sysctl net.ipv4.conf.all.forwarding
Server Console Output
net.ipv4.conf.all.forwarding = 0

please enable and check again:

Server Console Output
sysctl net.ipv4.conf.all.forwarding=1

For security reasons, Docker configures the iptables rules to prevent containers from forwarding traffic from outside the host machine, on Linux hosts. Docker sets the default policy of the FORWARD chain to DROP.

To override this default behavior you can manually change the default policy:

Server Console
sudo iptables -P FORWARD ACCEPT

Add IP route with specific subnet

Add routing for containers network on another hosts:

Server Console
sudo ip route add 172.16.42.0/24 via 12.12.12.42
sudo ip route add 172.16.43.0/24 via 12.12.12.43
sudo ip route add 172.16.44.0/24 via 12.12.12.44

A quick check

Give your environment a quick test run to make sure you’re all set up:

Server Console
docker run hello-world

Create or pull a base image and run Container

Docker can build images automatically by reading the instructions from a Dockerfile.

A Dockerfile is a text document that contains all the commands a user could call on the command line to assemble an image.

Dockerfile

  1. Create an empty directory.
  2. Change directories (cd) into the new directory, create a file called Dockerfile, copy-and-paste the following content into that file, and save it.
    Take note of the comments that explain each statement in your new Dockerfile.
Dockerfile
FROM ubuntu16.04

# Set MOFED version, OS version and platform
ENV MOFED_VERSION 4.5-1.0.1.0
ENV OS_VERSION ubuntu16.04
ENV PLATFORM x86_64

RUN apt-get update
RUN apt-get -y install apt-utils
RUN apt-get install -y --allow-downgrades --allow-change-held-packages --no-install-recommends \
        build-essential cmake tcsh tcl tk \
        make git curl vim wget ca-certificates \
        iputils-ping net-tools ethtool \
        perl lsb-release python-libxml2 \
        iproute2 pciutils libnl-route-3-200 \
        kmod libnuma1 lsof openssh-server \
        swig libelf1 automake libglib2.0-0 \
        autoconf graphviz chrpath flex libnl-3-200 m4 \
        debhelper autotools-dev gfortran libltdl-dev && \
        rm -rf /rm -rf /var/lib/apt/lists/*

# Download and install NVIDIA OFED 4.5-1.0.1.0 for Ubuntu 16.04

RUN wget --quiet http://content.mellanox.com/ofed/MLNX_OFED-${MOFED_VER}/MLNX_OFED_LINUX-${MOFED_VER}-${OS_VER}-${PLATFORM}.tgz &&
    tar -xvf MLNX_OFED_LINUX-${MOFED_VER}-${OS_VER}-${PLATFORM}.tgz && \
    MLNX_OFED_LINUX-${MOFED_VER}-${OS_VER}-${PLATFORM}/mlnxofedinstall --user-space-only --without-fw-update -q && \
    cd .. && \
    rm -rf ${MOFED_DIR} && \
    rm -rf *.tgz

# Allow OpenSSH to talk to containers without asking for confirmation
RUN cat /etc/ssh/ssh_config | grep -v StrictHostKeyChecking > /etc/ssh/ssh_config.new && \
    echo "    StrictHostKeyChecking no" >> /etc/ssh/ssh_config.new && \
    mv /etc/ssh/ssh_config.new /etc/ssh/ssh_config

Docker Image and run a container

  1. Now run the build command. This creates a Docker image, which we’re going to tag using -t so it has a friendly name.

    Server Console
    docker build -t myofed451image .
  2. Where is your built image? It’s in your machine’s local Docker image registry:

    Server Console
    docker images
  3. Run a Docker Container in privileged / not privileged mode from the remote repository by:

    Server Console
    docker run -it --privileged --name=mnlx-verbs-prvlg --name=my-verbs-nonprvlg myofed451image bash

    OR

    Server Console
    docker run -it --cap-add=IPC_LOCK --device=/dev/infiniband/uverbs1 --name=my-verbs-nonprvlg myofed451image bash

Benchmark

Check the NVIDIA OFED version and uverbs:

Docker Console
ofed_info -s 
Docker Console Output
MLNX_OFED_LINUX-4.5-1.0.1.0
Docker Console
ls /dev/infiniband/uverbs1

Run Bandwidth stress over IB in container.:

Server

ib_write_bw -a -d mlx5_1 &

Client

ib_write_bw -a -F $server_IP -d mlx5_1 --report_gbits

In this way you can run Bandwidth stress over IB between containers.


Done!

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