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This repository provides easy automation scripts for building a HPC environment in Azure. It also includes examples to build e2e environment and run some of the key HPC benchmarks and applications.

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AzureHPC

Overview

This project is aimed at simplifiying deployment and setup for HPC environments in Azure. The deployment scripts include setting up various building blocks available for Networking, Compute and Storage that are needed for an e2e setup. You can do this all with a few commands and fast as these are run in parallel.

They key motivation is:

  • Simplified Automation
  • Flexibility
  • Speed of deployment

The basis for the project is a single JSON config file and some shell scripts for installing. The key point about the config file is that you can describe network, resources and installation steps. Tags are applied to resources that determines which resources run each install step.

The azhpc_* scripts only require the azure cli and a few utilities (bash, jq and ssh).

All of this is available in the Cloud Shell. Alternatively you can run on a Linux VM on Azure or from the Windows Ubuntu Shell.

Multiple examples for building blocks commonly used, scripts for building, installing and running some applications are included here so they can be used as you build your environment and run benchmarks.

We have also made some tutorials available that you can follow to not only learn more about the framework but also to understand how you can easily set an environment up e2e for your own application.

JSON configuration file

The JSON file is composed of the following:

  • Variables dictionary
  • Setup information
  • Network dictionary
  • Storage dictionary
  • Resources dictionary
  • Install list
  • CycleCloud dictionary

Note : for the full config structure file see config.json

Variables dictionary

This allows variables to be created and used throughout the config file (see how this works here. This can be used when creating a template for others to use or just when the same value is repeated for many resources, e.g. choosing the OS image.

When creating templates for others to use the value should be <NOT-SET> so the azhpc-* commands will notify the user.

To allow a better reuse of variables across several configuration files the variable section can reference a file like this :

{
  "variables": "@variables.json"
}

The referenced file should contains variables this way :

{
    "image": "OpenLogic:CentOS:7.7:latest",
    "hpc_image": "OpenLogic:CentOS-HPC:7.7:latest",
    "location": "westeurope",
    "resource_group": "my resource group",
    "vm_type": "Standard_HB60rs",
    "vnet_resource_group": "variables.resource_group",
}

Setup information

The following properties are global :

Name Description Required Default
location The region where the resources are created yes
resource_group The resource group to put the resources yes
install_from The resource where the install script will be run no
admin_user The admin user for all resources yes
proximity_placement_group_name The proximity group name to create no
global_tags Global tags to apply to all ARM resources no

The azhpc-build command will generate an install script from the configuration file. This will be run from the install_from VM. The install_from VM must either have a public IP address or be accessible by hostname from where azhpc-build is run (i.e. run azhpc-build from a VM on the same vnet).

Network dictionary

The config file will create or reuse vnet and subnets from the config file.

Name Description Required Default
resource_group This can be used if different to the resources no
name Vnet name yes
address_prefix The address prefix (CIDR notation) yes
subnets Dictionary containing key-values for <subnet-name> and <subnet-address-prefix> yes
dns_domain Private domain name to create no
peer Dictionary of peer names to create no
routes Dictionary of route names to create no

Peer dictionary

This dictionary describes the virtual network peering to be created

Name Description Required Default
resource_group Name of the resource group containing the vnet to peer to yes
vnet_name Name of the vnet to peer to yes

Route dictionary

This dictionary describes routes to be created

Name Description Required Default
address_prefix Address space (CIDR) yes
next_hop TO DOCUMENT yes
subnet TO DOCUMENT yes

Here is an example setup with four subnets:

...
"vnet": {
    "resource_group": "vnet-resource-group",
    "name": "hpcvnet",
    "address_prefix": "10.2.0.0/20",
    "subnets": {
        "admin": "10.2.1.0/24",
        "viz": "10.2.2.0/24",
        "storage": "10.2.3.0/24",
        "compute": "10.2.4.0/22"
    }
},
...

Note: If the vnets/subnets exist it will use what it already there. In thta case the resource_group property of the vnet should be different from the one your deploy in

Storage dictionary

This dictionary desribes the storage resources to be created. Today only Azure NetApp files is supported, but additional ones will be added.

Name Description Required Default
type Type of storage - can be anf, storageaccount yes
sku Only for type=storageaccount can be Standard_LRS, Standard_GRS, Standard_RAGRS, Standard_ZRS, Premium_LRS, Premium_ZRS, Standard_GZRS, Standard_RAGZRS yes
containers Only for type=storageaccount. Array of containers name to create no
subnet Subnet name in which to inject ANF NICs yes
joindomain Domain name to join to no
ad_server Domain Server to connect to no
ad_username User to use to join the domain no
ad_password Domain password to join to no
pools Dictionary of ANF pools to create yes

Pools dictionary

This dictionary describes the ANF pools to be created

Name Description Required Default
service_level Service Level - can be Ultra, Premium, or Standard yes
size Total pool size in TB. From 4 to 100 yes
volumes Dictionary of ANF volumes in that pool yes
ANF Volumes dictionary

This dictionary describes the ANF volumes in a pool to be created

Name Description Required Default
size Total volume size in TB. From 4 to 100 yes
type Volume type (nfs or cifs) yes nfs
mount Mount end point to export yes

Resources dictionary

This dictionary describes the resources for the project.

Name Description Required Default
type The resource type, either "vm" or "vmss" is currently supported yes
accelerated_networking Boolean flag for whether to use accelerated networking no False
availability_set Name of the availability set and it is created if not existing (vm only) no
availability_zones List of integer where the resource need to be created. Can be 1, 2 or 3 no
data_disks Array of data disk size in GB no
dns_name The dns name to use. If this is not set, then the resource name with a uuid will be used (vm only) no uuid
fault_domain_count FD count to use (vmss only) no
image For a public image use format OpenLogic:CentOS:7.7:latest - For a custom image use the imageID of a managed image yes
instances Number of VMs or VMSS instances to create yes
low_priority Boolean flag to se Spot Instance (Eviction = Delete) no False
managed_identity Managed Identity property to use no
nsg_allow Enabled pre-defined NSG rules ssh, rdp, http, https, zcentral or grafana (vm only) no ssh/rdp
nsg_source_ip Set source IP filter for NSG Allow rule. Default is allow all no *
ephemeral_os_disk Set whether to use the ephermal disk for the operation system no False
ephemeral_os_disk_placement Specifies the ephemeral disk placement. Possible values are: CacheDisk, ResourceDisk no CacheDisk
os_disk_size OS Disk size in GB. This is only needed if you want to use a non default size or increase the OS disk size no
os_storage_sku OS Storage SKU. Premium_LRS, StandardSSD_LRS or Standard_LRS no Premium_LRS
os_storage_sku OS Storage SKU. Premium_LRS, StandardSSD_LRS or Standard_LRS no Premium_LRS
overprovision Allows a VMSS to provision additional VMs incase some don't start quickly no True
custom_data File (@file) or URL indicating the location of the cloud-init script no None
proximity_placement_group Boolean flag for wether to include the resource in the proximity placement group with the name specified in the global section no False
public_ip Boolean flag for wether to use a public IP (vm only) no False
resource_tags Tags to be assigned to the resources no
single_placement_group Used to place all VMs in a single VMSS in the same IB security group no True
subnet Subnet name to create the resource in yes
storage_cache Datadisk storage cache mode. Can be None, ReadWrite or ReadOnly no ReadWrite
storage_sku Data Disk Storage SKU. Premium_LRS, StandardSSD_LRS or Standard_LRS or UltraSSD_LRS (which needs availability_zones to be defined) no Premium_LRS
vm_type VM Size for example Standard_D16s_v3 yes
tags Array of tags used to specify which scripts need to be applied on the resource no

NOTE : When using UltraSSD_LRS then an Availability Set must be used

Managed Identity property

Name Description Required Default
role MSI role : reader, contributor, or owner yes
scope MSI Scope resource_group yes

Install array

This describes the steps to install after all the resources have been provisioned. An install script is created from the list which is run on the install_from VM. Each step is a dictionary containing the following:

Name Description Required Default
script The name of the script to run yes
tag The tag to select which resources will run this step yes
sudo Boolean flag for whether to run the script with sudo no False
deps A list of dependent files to be copied on the install_from VM as well no
args A list containing the arguments for the script no
copy This is a list of files to copy to each resource from the install_from VM and assumes the file will have been downloaded as a previous step no

Note: the script to run be the path relative to either the $azhpc_dir/scripts or a local scripts directory for the project. The local directory will take precedence over the $azhpc_dir/scripts.

Cycle Cloud dictionary

This describes the CycleCloud clusters configuration and projects to be uploaded to the current CycleCloud installation.

Name Description Required Default
clusters Dictionary of CycleCloud Clusters parameters yes
projects Dictionary of CycleCloud projects init scripts yes

CycleCloud cluster dictionary

This describes the template and parameters to be applied on a CycleCloud cluster.

Name Description Required Default
template The name of the template used to create the cluster. yes
parameters Dictionary of parameters defined in the template. The parameter list can be retrieved with the cyclecloud export_parameters command yes

For ClusterInitSpecdefinition use thie following format, and make sure to use the same spec name in the projects dictionary

      "xxxClusterInitSpecs": {
          "projectname:specname:i.j.k": {
              "Order": 10000,
              "Name": "projectname:specname:i.j.k",
              "Spec": "specname",
              "Project": "projectname",
              "Version": "i.j.k",
              "Locker": "azure-storage"
          }
      }

CycleCloud projects dictionary

This describes the CycleCloud project containing cluster-init wrapper scripts to be uploaded in the CycleCloud locker. Each project name has to follow the CycleCloud naming convention projectname:specname:i.j.k and contains an array of scripts described below :

Name Description Required Default
script The name of the script to run yes
deps A list of dependent files no
args A list containing the arguments for the script no

Macros in the config file

For the most part the configuration is just a standard JSON file although there are a few translations that can take place:

Syntax Description
variables.<name> Read a variable the variables dictionary
secret.<KEY-VAULT>.<SECRET-NAME> Read a secret stored in an existing vault
sasurl.<STORAGE-ACCOUNT>.<STORAGE-PATH>[,<PERMISSION>[,<DURATION>]] Create a SAS URL with permissions
fqdn.<RESOURCE-NAME> Retrieve a resource FQDN
sakey.<STORAGE-ACCOUNT> Retrieve a storage key
saskey.<STORAGE-ACCOUNT>.<STORAGE-PATH>[,<PERMISSION>[,<DURATION>]] Create a SAS KEY with permissions
laworkspace.<RESOURCE-GROUP>.<NAME> Retrieve a Log Analytics workspace id
lakey.<RESOURCE-GROUP>.<NAME> Retrieve a Log Analytics key
acrkey.<ACR-REPONAME> Retrieve an Azure Container Registry key
image.<RESOURCE-GROUP>.<NAME> Retrieve a Custom Image id

Variables

If a value is prefixed with variables. then it will take the value from the proceeding JSON path under the variables section. For example:

{
    "location": "variables.location",
    "variables": {
        "location": "westus2"
    }
}

In the example above, the location will be taken from variables.location.

Secrets

The scripts allow secrets to be stored in keyvault. To read from keyvault use the following format: secret.<KEY-VAULT>.<KEY-NAME>.

Note: this assumes the key vault is set up and the key is already stored there.

SAS URL

The config file can create a URL with a SAS key for a file in storage. This is the format: sasurl.<STORAGE-ACCOUNT>.<STORAGE-PATH>[,<PERMISSION>[,<DURATION>]]. PERMISSIONS are not required and is a list of letter for access permission : r, w, d, l. DURATION is optional and is an integer value and a unit which can be either h, d, or y (for hours, days, or years). The default for PERMISSIONS is r and the default for DURATION is 2h.

Note: the <STORAGE-PATH> should start at the container (and do not have a preceeding /)

Fqdn

The scripts allow FQDN of resources to be retrieved. This is the format: fqdn.<RESOURCE-NAME>.

Note: this assumes the resource name to be in the same resource group than the one defined in the configuration file.

Storage Account Key

The scripts allow storage account key be retrieved. This is the format: sakey.<STORAGE-ACCOUNT>.

Note: this assumes the storage account to be in the same resource group than the one defined in the configuration file.

Storage SAS Key

The config file can create a SAS key for a file in storage. This is the format: saskey.<STORAGE-ACCOUNT>.<STORAGE-PATH>[,<PERMISSION>[,<DURATION>]]. PERMISSIONS are not required and is a list of letter for access permission : r, w, d, l. DURATION is optional and is an integer value and a unit which can be either h, d, or y (for hours, days, or years). The default for PERMISSIONS is r and the default for DURATION is 2h.

Note: the <STORAGE-PATH> should start at the container (and do not have a preceeding /)

Log Analytics workspace id

The config file allow to retrieve a Log Analytics workspace id. This is the format : laworkspace.<RESOURCE-GROUP>.<NAME>.

Note : The Log Analytics Workspace <NAME> need to exists in the resource group <RESOURCE-GROUP>

Log Analytics key

The config file allow to retrieve a Log Analytics key. This is the format : lakey.<RESOURCE-GROUP>.<NAME>.

Note : The Log Analytics Workspace <NAME> need to exists in the resource group <RESOURCE-GROUP>

ACR Key

The config file allow to retrieve an Azure Container Registry key. This is the format : acrkey.<ACR-REPONAME>.

Note : The Azure Container Registry repositery <ACR-REPONAME> need to exists

Custom Image Id

The config file allow to retrieve a custom image id. This is the format : image.<RESOURCE-GROUP>.<NAME>.

Referencing variables in variables names

There are some situation where you want to use variable values inside other variables like a keyvault name or a storage account name. To do this just enclose it with double curly braces {{}} like this :

    "variables": {
        "storage_account": "foo",
        "storage_key": "sakey.{{variables.storage_account}}",
        "la_resourcegroup": "myrg",
        "la_name": "myla",
        "log_analytics_workspace": "laworkspace.{{variables.la_resourcegroup}}.{{variables.la_name}}",
        "log_analytics_key": "lakey.{{variables.la_resourcegroup}}.{{variables.la_name}}",
    }

Commands

To set up the environment you first need to source $azhpc_dir/install.sh. This is only required once and will create a bin directory with all the commands aliases. It will also set the PATH for the current session (and so there is no issue in running multiple times but you may prefer to just add the bin directory to your bashrc).

The new version is now implemneted in Python and it will by default reuse the Python version provided as part of the Azure CLI.

Aliases have been created to allow an easier usage as well as a backward compatibility with the bash only version :

Aliases Description
azhpc-build Build the resources defined in the config file
azhpc-connect This will connect to a node in a running cluster
azhpc-destroy This will delete the resource group defined in the config file
azhpc-run_install Just run the install and assume the resource are already there
azhpc-get This will return the value of a variable from the config file
azhpc-init Update or create variables in the config file
azhpc-preprocess Preprocess the configuration file
azhpc-run Run a command on one of multiple resources
azhpc-scp Uses the scp to copy a file to/from the remote resource
azhpc-status Show the uptime for all the resources in the project
azhpc-watch This shows the provisioning state of all the resources in the project

azhpc-build

This will build you complete setup from the configuration file.

usage: azhpc build [-h] [--config-file CONFIG_FILE] [--debug] [--no-color]

deploy the config

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output
  --no-vnet             do not create vnet resources in the arm template

azhpc-connect

This will connect to a node in a running cluster.

usage: azhpc connect [-h] [--config-file CONFIG_FILE] [--debug] [--no-color]
                     [--user USER]
                     resource ...

connect to a resource

positional arguments:
  resource              the resource to connect to
  args                  additional arguments will be passed to the ssh command

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output
  --user USER, -u USER  the user to connect as

azhpc-destroy

Delete the resource group specified in the configuration file.

usage: azhpc destroy [-h] [--config-file CONFIG_FILE] [--debug] [--no-color]
                     [--force] [--no-wait]

delete the resource group

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output
  --force               delete resource group immediately
  --no-wait             do not wait for resources to be deleted

azhpc-run_install

Just run the install and assume the resources are already there.

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output
  --step STEP           the install step to start running

azhpc-get

Retrieve a value from the variables in the config file

usage: azhpc get [-h] [--config-file CONFIG_FILE] [--debug] [--no-color] path

get a config value

positional arguments:
  path                  the json path to evaluate

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output

azhpc-init

This utility initialises a new project and can set variables in the config file. The config argument can be a file or a directory where the contents are copied to the new project directory. If a directory is chosen then all files will be copied and any json files will have the variables replaced.

The -s option can be used to search for any variables with are <NOT-SET> in a config file. The output will be a string with the -v option containing all the variables to set.

usage: azhpc init [-h] [--config-file CONFIG_FILE] [--debug] [--no-color]
                  [--show] [--dir DIR] [--vars VARS]

initialise a project

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output
  --show, -s            display all vars that are <NOT-SET>
  --dir DIR, -d DIR     output directory
  --vars VARS, -v VARS  variables to replace in format VAR=VAL(,VAR=VAL)*

azhpc-preprocess

Preprocess the config file for any errors.

usage: azhpc preprocess [-h] [--config-file CONFIG_FILE] [--debug]
                        [--no-color]

preprocess the config file

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output

azhpc-run

This is a utility to run a command on one or more resource. Behind the scenes it uses the pssh command.

usage: azhpc run [-h] [--config-file CONFIG_FILE] [--debug] [--no-color]
                 [--user USER] [--nodes NODES]
                 ...

run a command on the specified resources

positional arguments:
  args                  the command to run

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output
  --user USER, -u USER  the user to run as
  --nodes NODES, -n NODES
                        the resources to run on (comma separated for multiple)

azhpc-scp

This uses the scp to copy a file (or directory if -r is added) to/from the remote resource. The resource hostname should be used.

usage: azhpc scp [-h] [--config-file CONFIG_FILE] [--debug] [--no-color] ...

secure copy

positional arguments:
  args                  the arguments passed to scp (use '--' to separate scp
                        arguments)

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output

azhpc-status

This is a utility to show the uptime for all the resources in the project

usage: azhpc status [-h] [--config-file CONFIG_FILE] [--debug] [--no-color]

show status of all the resources

optional arguments:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -c CONFIG_FILE
                        config file
  --debug               increase output verbosity
  --no-color            turn off color in output

azhpc-watch

This shows the provisioning state of all the resources in the project. If the -u option is used this will update for the specified interval time.

Command:
    azhpc-watch [options]

Arguments
    -h --help  : diplay this help
    -c --config: config file to use
                 default: config.json
    -u --update: update time in seconds
                 Use 0 for no updates
                 default: 0

HOWTO

Setting up Azure Key Vault

This is the command to create a Key Vault:

az keyvault create --name <keyvault-name> --resource-group <my-resource-group>

This is how you can add a secret:

az keyvault secret set --vault-name <keyvault-name> --name "<secret-name>" --value "<secret-vault>"

This can be accessed in the config file using the following value:

secret.<keyvault-name>.<secret-name>

Windows Subsystem for Linux

The private key needs to have access rights of 0600; when using WSL on the NTFS drive (c: drive); that is by default not allowed. To get this working: add the metadata option to the mount:

sudo umount /mnt/c
sudo mount -t drvfs C: /mnt/c -o metadata

or better, have an wsl.conf which adds the metadata when starting:

[automount]
enabled=true
options=metadata,uid=1000,gid=1000,umask=022

Contributing

This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.

When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.

This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact opencode@microsoft.com with any additional questions or comments.

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This repository provides easy automation scripts for building a HPC environment in Azure. It also includes examples to build e2e environment and run some of the key HPC benchmarks and applications.

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