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DeepOps Virtual

Set up a virtual cluster with DeepOps. Useful for...

  1. Learning how to deploy DeepOps on limited hardware
  2. Testing new features in DeepOps
  3. Tailoring DeepOps in a local environment before deploying it to the production cluster

Requirements

Hardware Requirements

The host machine should have enough resources to fulfill the minimum VM needs...

Total: 8 vCPU, 22 GB RAM, 96 GB Storage

  • virtual-login01: 2 vCPU, 2GB RAM and 32GB Storage
  • virtual-mgmt01: 4 vCPU, 4GB RAM and 32GB Storage
  • virtual-gpu01: 2 vCPU, 16GB RAM and 32GB Storage

If deploying kubeflow or another resource-intensive application in this environment, more vCPU, RAM, and storage resources must be allocated to virtual-mgmt01 especially.

Operating System Requirements

  • Ubuntu 18.04 (or greater)
  • CentOS 7.6 (or greater)

Running DeepOps virtually assumes that the host machine's OS is an approved OS. If this is not the case, the scripts used in the steps below may be modified to work with a different OS.

Also, using VMs and optionally GPU passthrough assumes that the host machine has been configured to enable virtualization in the BIOS. For instructions on how to accomplish this, refer to the sections at the bottom of this README: Enabling virtualization and GPU passthrough.

Start the Virtual Cluster

  1. From the main deepops directory, run the setup script.

    This will install Ansible and other software on the provisioning machine which will be used to deploy all other software to the cluster. For more information on Ansible and why we use it, consult the Ansible Guide.

    ./scripts/setup.sh

  2. In the virtual directory, startup vagrant. This will start 3 VMs by default.

    # NOTE: The default VM OS is Ubuntu. If you wish the VMs to spawn CentOS,
#       configure the DEEPOPS_VAGRANT_FILE variable accordingly...
#       export DEEPOPS_VAGRANT_FILE=$(pwd)/Vagrantfile-centos
# NOTE: virtual-gpu01 requires GPU passthrough, by default it is not enabled
# NOTE: 3 VMs are started by default: virtual-mgmt01, virtual-login01, virtual-gpu01
# NOTE: 6 VMs are started if the environment variable DEEPOPS_FULL_INSTALL is set:
#       virtual-mgmt01, virtual-mgmt02, virtual-mgmt03, virtual-login01, virtual-gpu01, virtual-gpu02

cd virtual
./vagrant_startup.sh

  3. Start the cluster.

    # NOTE: Only Kubernetes is deployed by default. To also deploy Slurm,
#       configure the DEEPOPS_ENABLE_SLURM variable accordingly...
#       export DEEPOPS_ENABLE_SLURM=1

./cluster_up.sh

    This script will run the ansible playbooks to deploy DeepOps to the Vagrant VMs and should complete without errors.

  4. Set up the Kubernetes environment.

    As part of cluster_up.sh, a fresh kubectl executable and the Kubernetes cluster's admin.conf are downloaded. To use these so commands may be run locally, a convenient script may be sourced...

    source k8s_environment.sh

    Optionally, kubectl can permanently be added to the PATH and admin.conf can be copied to ~/.kube/config, which results in a more permanent solution.

Using the Virtual Cluster

Kubernetes

Consult the Kubernetes Usage Guide for examples of how to use Kubernetes.

Connecting to the VMs

Connect to any of the VM nodes directly via vagrant ssh...

# NOTE: Must be in the `deepops/virtual` directory

vagrant ssh virtual-gpu01

Destroy the Virtual Cluster

To destroy the cluster and shutdown the VMs, run the vagrant_shutdown.sh script...

./vagrant_shutdown.sh

Check that there are no running VMs using virsh list...

$ virsh list --all
 Id    Name                           State
----------------------------------------------------

Configure GPU Passthrough

If the host machine has a GPU and is configured for GPU passthrough, it is possible to configure the virtual-gpu01 VM to use the GPU.

Run lspci to discover the appropriate bus...

$ lspci -nnk | grep NVIDIA
07:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:15fc] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]
07:00.1 Audio device [0403]: NVIDIA Corporation Device [10de:0fb1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]
08:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:15fc] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]
08:00.1 Audio device [0403]: NVIDIA Corporation Device [10de:0fb1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]
0e:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:15fc] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]
0e:00.1 Audio device [0403]: NVIDIA Corporation Device [10de:0fb1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]
0f:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:15fc] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]
0f:00.1 Audio device [0403]: NVIDIA Corporation Device [10de:0fb1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1195]

In this example, the GPU at 08:00.0 is chosen.

In the Vagrantfile there is a "magic string" #BUS-GPU01 that is utilized in Jenkins automation. This can be updated manually.

Uncomment the #BUS-GPU01 v.pci configuration and update it with a mapping to the bus discovered with lspci...

v.pci :bus => '0x08', :slot => '0x00', :function => '0x0'

Note that more than one GPU may be passed through by adding additional v.pci lines.

Next, shutdown the virtual cluster (if it is running) and startup vagrant + run cluster up again...

./vagrant_shutdown.sh
./vagrant_startup.sh
./cluster_up.sh

Other Customization

The default Vagrantfiles create VMs that are very minimal in terms of resources to maximize where a virtual DeepOps cluster can be run. To run resource-intensive Kubernetes applications such as Kubeflow, it's necessary to increase some of the settings.

Specify the cluster Operating System

By default, all virtual nodes will deploy with Ubuntu 18.04. This can be changed by overriding the environment variables DEEPOPS_VAGRANT_OS and DEEPOPS_OS_VERSION. Supported OS versions are Ubuntu 18.04, Ubuntu 20.04, CentOS 7, and CentOS 8.

export DEEPOPS_VAGRANT_OS=centos
export DEEPOPS_OS_VERSION=8

Increase CPUs, memory, and GPUs

In the Vagrantfile of choice (Vagrantfile-<os_type>), make the following modifications...

  1. Increase the memory and cpus for the virtual-mgmt01 VM. Suggested - v.memory = 16384, v.cpus = 8.
  2. Comment out the virtual-login01 VM. Unless you are running slurm, this is not necessary and just takes up resources.
  3. Increase the cpus for the virtual-gpu01 VM. Suggested - v.cpus = 8.
  4. If more GPUs are available, pass all of them through using the instructions in the section above.

NOTE: The amount of CPUs and memory on the host system will vary. Change the amounts above accordingly to values that make sense.

Increase Disk Space

  1. Add v.machine_virtual_size = 100 to the Vagrantfile (Vagrantfile-<os_type>). This parameter should go under each libvirt section per node. The units are GBs, so in this case 100 GB are allocated per node.
  2. vagrant ssh to each machine (ex: vagrant ssh virtual-gpu01) and do the following...
# run fdisk
sudo fdisk /dev/sda
# d, 3, n, p, 3, enter, enter, no, p, w
# resize
sudo resize2fs /dev/sda3
# double-check that the disk size increased
df -h /

Larger Clusters

The default configuration deploys a single management node and a single GPU node. To run multi-node Deep Learning jobs or to test our Kubernetes HA it's necessary to deploy multiple nodes.

  1. If using GPUs, ensure that 2 GPUs are available.
  2. If using GPUS, update the GPU BUS address for virtual-gpu01 and virtual-gpu02 in the "full" Vagrantfile of choice (Vagrantfile-<os_type>-full).
  3. Run export DEEPOPS_FULL_INSTALL=true.
  4. Continue with the standard installation steps.

Enabling Virtualization and GPU Passthrough

On many machines, virtualization and GPU passthrough are not enabled by default. Follow these directions so that a virtual DeepOps cluster can start on your host machine with GPU access on the VMs.

BIOS and Bootloader Changes

To support KVM, we need GPU pass through. To enable GPU pass through, we need to enable VFIO support in BIOS and Bootloader.

BIOS Changes

  • Enable BIOS settings: Intel VT-d and Intel VT-x
  • Enable BIOS support for large-BAR1 GPUs: 'MMIO above 4G' or 'Above 4G encoding', etc.

DGX-2 SBIOS

  • VT-x: enable
  • VT-d: enable
  • MMIO above 4G: enable
  • Intel AMT: disable

DGX-1/1V SBIOS

  • VT-x: Intel RC Setup -> Processor Configuration -> VMX
  • VT-d: Intel RC Setup -> IIO Configuration -> VT-d
  • MMIO above 4G: Advanced -> PCI Subsystem Setting -> Above 4G Encoding

DGX Station SBIOS

  • VT-x:
  • VT-d:
  • MMIO above 4G: verify virtualization support is enabled in the BIOS, by looking for vmx for Intel or svm for AMD processors...
$ grep -oE 'svm|vmx' /proc/cpuinfo | uniq
vmx

Bootloader Changes

  1. Add components necessary to load VFIO (Virtual Function I/O). VFIO is required to pass full devices through to a virtual machine, so that Ubuntu loads everything it needs. Edit and add the following to /etc/modules file:
pci_stub
vfio
vfio_iommu_type1
vfio_pci
kvm
kvm_intel
  1. Next, need Ubuntu to load IOMMU properly. Edit /etc/default/grub and modify "GRUB_CMDLINE_LINUX_DEFAULT", by adding "intel_iommu=on" to enable IOMMU. May also need to add "vfio_iommu_type1.allow_unsafe_interrupts=1" if interrupt remapping should be enabled. Post these changes, the GRUB command line should look like this:
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash intel_iommu=on vfio_iommu_type1.allow_unsafe_interrupts=1
iommu=pt"
  1. Enable the vfio-pci driver on boot:
$ echo vfio-pci | sudo tee /etc/modules-load.d/vfio-pci.conf
  1. Run sudo update-grub to update GRUB with the new settings and reboot the system.

Blacklist the GPU Devices

We do not want the host running DGX Base OS to use the GPU Devices. Instead we want Guest VMs to get full access to the NVIDIA GPU devices. Hence, in the DGX Base OS on the host, blacklist them by adding their IDs to the initramfs.

  1. Run the command lspci -nn | grep NVIDIA to get the list of PCI-IDs
08:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
0a:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
10:00.0 Bridge [0680]: NVIDIA Corporation Device [10de:1ac1] (rev a1)
11:00.0 Bridge [0680]: NVIDIA Corporation Device [10de:1ac1] (rev a1)
12:00.0 Bridge [0680]: NVIDIA Corporation Device [10de:1ac1] (rev a1)
18:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
1a:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
89:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
8b:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
92:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
94:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
  1. Edit /etc/modprobe.d/vfio.conf and add this line:
options vfio-pci ids=10de:1db1,10de:1ac1

NOTE: First entry is for Volta and the latter for NVSwitch

  1. Rebuild the initramfs by running sudo update-initramfs -u and reboot the system.

  2. After the system reboots, verify GPU devices and NVSwitches are claimed by vfio_pci driver by running dmesg | grep vfio_pci...

[   15.668150] vfio_pci: add [10de:1db1[ffff:ffff]] class 0x000000/00000000
[   15.736099] vfio_pci: add [10de:1ac1[ffff:ffff]] class 0x000000/00000000

$ lspci -nnk -d 10de:1ac1
10:00.0 Bridge [0680]: NVIDIA Corporation Device [10de:1ac1] (rev a1)
	Kernel driver in use: vfio-pci
11:00.0 Bridge [0680]: NVIDIA Corporation Device [10de:1ac1] (rev a1)
	Kernel driver in use: vfio-pci
12:00.0 Bridge [0680]: NVIDIA Corporation Device [10de:1ac1] (rev a1)
	Kernel driver in use: vfio-pci

If the Kernel driver in use is not vfio-pci and instead the nvidia driver, it may be necessary to blacklist the nvidia driver or instruct it to load vfio-pci beforehand...

$ cat /etc/modprobe.d/nvidia.conf
softdep nvidia_384 pre: vfio-pci

One more check...

$ lspci -nnk -d 10de:1db1
08:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia
0a:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia
18:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia
1a:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia
89:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia
8b:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia
92:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia
94:00.0 3D controller [0302]: NVIDIA Corporation Device [10de:1db1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1212]
	Kernel driver in use: vfio-pci
	Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia_vgpu_vfio, nvidia