Azure HDInsight (#24)

* Cleanup region azure

* mend

README.md

@@ -24,6 +24,7 @@ Table of Contents
     * [EMR Serverless](#emr-serverless)
 * [Azure](#azure-1)
     * [Login](#login)
+    * [HDInsight](#hdinsight)
     * [AKS](#aks)
 * [GCP](#gcp-1)
     * [Login](#login-2)
@@ -67,6 +68,7 @@ as well. Check code comments for details.
 | GCP   | Dataproc  |2.0.27-ubuntu18| 3.1.3  | 1.0.0   | 0.3.3   |   -|
 | GCP   | Dataproc Serverless|1.0.21| 3.2.2  | 1.1.0   | 0.4.1   | gcr.io/${TF_VAR_project_name}/spark-py:pysequila-0.4.1-dataproc-latest  |
 | Azure | AKS       |1.23.12|3.2.2|1.1.0|0.4.1| docker.io/biodatageeks/spark-py:pysequila-0.4.1-aks-latest|
+| Azure | HDInsight| 5.0.300.1 | 3.2.2 | 1.1.0 | 0.4.1 |- |
 | AWS   | EKS|1.23.9 | 3.2.2 | 1.1.0 | 0.4.1 | docker.io/biodatageeks/spark-py:pysequila-0.4.1-eks-latest|
 | AWS   | EMR Serverless|emr-6.7.0 | 3.2.1 | 1.1.0 | 0.4.1 |- |
 
@@ -118,8 +120,10 @@ terraform init
 
 ## Using SeQuiLa cli Docker image for Azure
 ```bash
+export TF_VAR_region=westeurope
 docker pull biodatageeks/sequila-cloud-cli:latest
 docker run --rm -it \
+    -e TF_VAR_region=${TF_VAR_region} \
     -e TF_VAR_pysequila_version=${TF_VAR_pysequila_version} \
     -e TF_VAR_sequila_version=${TF_VAR_sequila_version} \
     -e TF_VAR_pysequila_image_aks=${TF_VAR_pysequila_image_aks} \
@@ -162,7 +166,7 @@ terraform init
 
 ## Azure
 * [AKS (Azure Kubernetes Service)](#AKS): :white_check_mark:
-
+* [HDInsight](#hdinsight): :white_check_mark:
 ## AWS
 * [EMR Serverless](#emr-serverless): :white_check_mark:
 * [EKS(Elastic Kubernetes Service)](#EKS): :white_check_mark:
@@ -277,6 +281,60 @@ az login
 az account set --subscription "Azure subscription 1"
 ```
 
+## HDInsight
+:bulb: According to the [release notes](https://learn.microsoft.com/en-us/azure/hdinsight/hdinsight-50-component-versioning?source=recommendations) 
+HDInisght 5.0 comes with Apache Spark 3.1.2. Unfortunately it is 3.0.2:
+
+![img.png](doc/images/hdinsight-spark-version.png)
+
+Since HDInsight is in fact a full-fledged Hadoop cluster we were able to add to the Terraform module support for Apache Spark 3.2.2 using
+[a script action](https://learn.microsoft.com/en-us/azure/hdinsight/hdinsight-hadoop-customize-cluster-linux) mechanism.
+
+
+### Deploy
+```bash
+export TF_VAR_hdinsight_gateway_password=$(tr -dc A-Za-z0-9 </dev/urandom | head -c 16 ; echo '')
+export TF_VAR_hdinsight_ssh_password=$(tr -dc A-Za-z0-9 </dev/urandom | head -c 16 ; echo '')
+terraform apply -var-file=../../env/azure.tfvars -var-file=../../env/azure-hdinsight.tfvars -var-file=../../env/_all.tfvars
+```
+Check Terraform output variables for ssh connection string, credentials and Spark Submit command, e.g.
+```bash
+Apply complete! Resources: 0 added, 0 changed, 0 destroyed.
+
+Outputs:
+
+hdinsight_gateway_password = "w8aN6oVSJobq7eu4"
+hdinsight_ssh_password = "wun6RzBBPWD9z9ke"
+pysequila_submit_command = <<EOT
+export SPARK_HOME=/opt/spark
+spark-submit \
+--master yarn \
+--packages org.biodatageeks:sequila_2.12:1.1.0 \
+--conf spark.pyspark.python=/usr/bin/miniforge/envs/py38/bin/python3 \
+--conf spark.driver.cores=1 \
+--conf spark.driver.memory=1g \
+--conf spark.executor.cores=1 \
+--conf spark.executor.memory=3g \
+--conf spark.executor.instances=1 \
+--conf spark.files=wasb://sequila@sequilai1aayxsd.blob.core.windows.net/data/Homo_sapiens_assembly18_chr1_chrM.small.fasta,wasb://sequila@sequilai1aayxsd.blob.core.windows.net/data/Homo_sapiens_assembly18_chr1_chrM.small.fasta.fai \
+wasb://sequila@sequilai1aayxsd.blob.core.windows.net/jobs/pysequila/sequila-pileup.py
+
+EOT
+ssh_command = "ssh sequila@sequila-6lsnhqtc-ssh.azurehdinsight.net"
+```
+
+### Run
+1. Use `ssh_command` and `hdinsight_ssh_password` to connect to the head node.
+2. Run `pysequila_submit_command` command.
+
+![img.png](doc/images/hdinsight-job.png)
+![img.png](doc/images/hdinsight-job-2.png)
+
+### Cleanup
+```bash
+terraform destroy -var-file=../../env/azure.tfvars -var-file=../../env/azure-hdinsight.tfvars -var-file=../../env/_all.tfvars
+```
+
 ## AKS
 ### Deploy
 

cloud/aws/main.tf

@@ -39,6 +39,7 @@ module "emr-job" {
   source             = "../../modules/aws/emr-serverless"
   aws-emr-release    = var.aws-emr-release
   bucket             = module.storage.bucket
+  spark_version      = var.spark_version
   pysequila_version  = var.pysequila_version
   sequila_version    = var.sequila_version
   data_files         = [for f in var.data_files : "s3://${module.storage.bucket}/data/${f}" if length(regexall("fasta", f)) > 0]

cloud/aws/variables.tf

@@ -55,4 +55,4 @@ variable "eks_preemptible" {
   type        = bool
   default     = true
   description = "Enable preemtible(spot) instance in a Kubernetes pool"
-}
+}

cloud/azure/README.md

@@ -19,6 +19,7 @@ No providers.
 | <a name="module_aks"></a> [aks](#module\_aks) | ../../modules/azure/aks | n/a |
 | <a name="module_azure-resources"></a> [azure-resources](#module\_azure-resources) | ../../modules/azure/resource-mgmt | n/a |
 | <a name="module_azure-staging-blob"></a> [azure-staging-blob](#module\_azure-staging-blob) | ../../modules/azure/jobs-code | n/a |
+| <a name="module_hdinsight"></a> [hdinsight](#module\_hdinsight) | ../../modules/azure/hdinsight | n/a |
 | <a name="module_spark-on-k8s-operator-aks"></a> [spark-on-k8s-operator-aks](#module\_spark-on-k8s-operator-aks) | ../../modules/kubernetes/spark-on-k8s-operator | n/a |
 
 ## Resources
@@ -30,15 +31,22 @@ No resources.
 | Name | Description | Type | Default | Required |
 |------|-------------|------|---------|:--------:|
 | <a name="input_azure-aks-deploy"></a> [azure-aks-deploy](#input\_azure-aks-deploy) | Deploy AKS cluster | `bool` | `false` | no |
+| <a name="input_azure-hdinsight-deploy"></a> [azure-hdinsight-deploy](#input\_azure-hdinsight-deploy) | Deploy HDInsight cluster | `bool` | `false` | no |
 | <a name="input_data_files"></a> [data\_files](#input\_data\_files) | Data files to copy to staging bucket | `list(string)` | n/a | yes |
+| <a name="input_hdinsight_gateway_password"></a> [hdinsight\_gateway\_password](#input\_hdinsight\_gateway\_password) | Hadoop gateway password (i.e. Ambari, YARN UI console, etc) | `string` | `null` | no |
+| <a name="input_hdinsight_ssh_password"></a> [hdinsight\_ssh\_password](#input\_hdinsight\_ssh\_password) | SSH password to all nodes in the cluster | `string` | `null` | no |
 | <a name="input_pysequila_image_aks"></a> [pysequila\_image\_aks](#input\_pysequila\_image\_aks) | AKS PySeQuiLa image | `string` | n/a | yes |
 | <a name="input_pysequila_version"></a> [pysequila\_version](#input\_pysequila\_version) | PySeQuiLa version | `string` | n/a | yes |
 | <a name="input_region"></a> [region](#input\_region) | Location of the cluster | `string` | n/a | yes |
 | <a name="input_sequila_version"></a> [sequila\_version](#input\_sequila\_version) | SeQuiLa version | `string` | n/a | yes |
 | <a name="input_spark_version"></a> [spark\_version](#input\_spark\_version) | Apache Spark version | `string` | `"3.2.2"` | no |
-| <a name="input_zone"></a> [zone](#input\_zone) | Zone of the cluster | `string` | n/a | yes |
 
 ## Outputs
 
-No outputs.
+| Name | Description |
+|------|-------------|
+| <a name="output_hdinsight_gateway_password"></a> [hdinsight\_gateway\_password](#output\_hdinsight\_gateway\_password) | n/a |
+| <a name="output_hdinsight_ssh_password"></a> [hdinsight\_ssh\_password](#output\_hdinsight\_ssh\_password) | n/a |
+| <a name="output_pysequila_submit_command"></a> [pysequila\_submit\_command](#output\_pysequila\_submit\_command) | n/a |
+| <a name="output_ssh_command"></a> [ssh\_command](#output\_ssh\_command) | n/a |
 <!-- END OF PRE-COMMIT-TERRAFORM DOCS HOOK -->

cloud/azure/main.tf

@@ -3,7 +3,7 @@
 module "azure-resources" {
   source = "../../modules/azure/resource-mgmt"
   region = var.region
-  count  = var.azure-aks-deploy ? 1 : 0
+  count  = (var.azure-aks-deploy || var.azure-hdinsight-deploy) ? 1 : 0
 }
 
 module "azure-staging-blob" {
@@ -16,7 +16,26 @@ module "azure-staging-blob" {
   pysequila_version   = var.pysequila_version
   sequila_version     = var.sequila_version
   pysequila_image_aks = var.pysequila_image_aks
-  count               = var.azure-aks-deploy ? 1 : 0
+  count               = (var.azure-aks-deploy || var.azure-hdinsight-deploy) ? 1 : 0
+}
+
+#### Azure HDInsight
+module "hdinsight" {
+  depends_on                 = [module.azure-staging-blob]
+  source                     = "../../modules/azure/hdinsight"
+  region                     = var.region
+  resource_group             = module.azure-resources[0].resource_group
+  storage_container_id       = module.azure-resources[0].storage_container_id
+  storage_account_access_key = module.azure-resources[0].storage_account_access_key
+  storage_container_name     = module.azure-resources[0].azurerm_storage_container
+  storage_account_name       = module.azure-resources[0].storage_account
+  pysequila_version          = var.pysequila_version
+  sequila_version            = var.sequila_version
+  node_ssh_password          = var.hdinsight_ssh_password
+  gateway_password           = var.hdinsight_gateway_password
+  data_files                 = [for f in var.data_files : "wasb://sequila@${module.azure-resources[0].storage_account}.blob.core.windows.net/data/${f}" if length(regexall("fasta", f)) > 0]
+  count                      = var.azure-hdinsight-deploy ? 1 : 0
+
 }
 
 

cloud/azure/output.tf

@@ -0,0 +1,15 @@
+output "hdinsight_gateway_password" {
+  value = try(module.hdinsight[0].hdinsight_gateway_password, "No HDInsight setup.")
+}
+
+output "hdinsight_ssh_password" {
+  value = try(module.hdinsight[0].hdinsight_ssh_password, "No HDInsight setup.")
+}
+
+output "ssh_command" {
+  value = try(module.hdinsight[0].ssh_command, "No HDInsight setup.")
+}
+
+output "pysequila_submit_command" {
+  value = try(module.hdinsight[0].pysequila_submit_command, "No HDInsight setup.")
+}

cloud/azure/variables.tf

@@ -23,11 +23,6 @@ variable "region" {
   description = "Location of the cluster"
 }
 
-variable "zone" {
-  type        = string
-  description = "Zone of the cluster"
-}
-
 variable "data_files" {
   type        = list(string)
   description = "Data files to copy to staging bucket"
@@ -37,4 +32,22 @@ variable "azure-aks-deploy" {
   type        = bool
   default     = false
   description = "Deploy AKS cluster"
+}
+
+variable "azure-hdinsight-deploy" {
+  type        = bool
+  default     = false
+  description = "Deploy HDInsight cluster"
+}
+
+variable "hdinsight_gateway_password" {
+  type        = string
+  default     = null
+  description = "Hadoop gateway password (i.e. Ambari, YARN UI console, etc)"
+}
+
+variable "hdinsight_ssh_password" {
+  type        = string
+  default     = null
+  description = "SSH password to all nodes in the cluster"
 }

env/azure-hdinsight.tfvars

@@ -0,0 +1 @@
+azure-hdinsight-deploy = true

env/azure.tfvars

@@ -1 +0,0 @@
-region = "westeurope"

modules/azure/aks/README.md

@@ -28,7 +28,7 @@ No modules.
 | <a name="input_machine_type"></a> [machine\_type](#input\_machine\_type) | Azure machine type | `string` | `"Standard_D2_v2"` | no |
 | <a name="input_max_node_count"></a> [max\_node\_count](#input\_max\_node\_count) | Maximum number of AKS nodes | `number` | `2` | no |
 | <a name="input_region"></a> [region](#input\_region) | Location of the cluster | `string` | n/a | yes |
-| <a name="input_resource_group"></a> [resource\_group](#input\_resource\_group) | n/a | `string` | n/a | yes |
+| <a name="input_resource_group"></a> [resource\_group](#input\_resource\_group) | Azure resource group | `string` | n/a | yes |
 
 ## Outputs
 

modules/azure/aks/variables.tf

@@ -4,7 +4,8 @@ variable "region" {
 }
 
 variable "resource_group" {
-  type = string
+  type        = string
+  description = "Azure resource group"
 }
 
 variable "machine_type" {

modules/azure/hdinsight/README.md

@@ -0,0 +1,54 @@
+# hdinsight
+
+<!-- BEGINNING OF PRE-COMMIT-TERRAFORM DOCS HOOK -->
+## Requirements
+
+No requirements.
+
+## Providers
+
+| Name | Version |
+|------|---------|
+| <a name="provider_azurerm"></a> [azurerm](#provider\_azurerm) | n/a |
+| <a name="provider_random"></a> [random](#provider\_random) | n/a |
+
+## Modules
+
+No modules.
+
+## Resources
+
+| Name | Type |
+|------|------|
+| [azurerm_hdinsight_spark_cluster.sequila](https://registry.terraform.io/providers/hashicorp/azurerm/latest/docs/resources/hdinsight_spark_cluster) | resource |
+| [azurerm_storage_blob.sequila](https://registry.terraform.io/providers/hashicorp/azurerm/latest/docs/resources/storage_blob) | resource |
+| [azurerm_storage_blob.spark](https://registry.terraform.io/providers/hashicorp/azurerm/latest/docs/resources/storage_blob) | resource |
+| [random_string.random-suffix](https://registry.terraform.io/providers/hashicorp/random/latest/docs/resources/string) | resource |
+
+## Inputs
+
+| Name | Description | Type | Default | Required |
+|------|-------------|------|---------|:--------:|
+| <a name="input_data_files"></a> [data\_files](#input\_data\_files) | Data files to copy to staging bucket | `list(string)` | n/a | yes |
+| <a name="input_gateway_password"></a> [gateway\_password](#input\_gateway\_password) | Hadoop gateway password (i.e. Ambari, YARN UI console, etc) | `string` | n/a | yes |
+| <a name="input_hdinsight_version"></a> [hdinsight\_version](#input\_hdinsight\_version) | HDInsight version | `string` | `"5.0"` | no |
+| <a name="input_node_ssh_password"></a> [node\_ssh\_password](#input\_node\_ssh\_password) | SSH password to all nodes in the cluster | `string` | n/a | yes |
+| <a name="input_pysequila_version"></a> [pysequila\_version](#input\_pysequila\_version) | PySeQuiLa version | `string` | n/a | yes |
+| <a name="input_region"></a> [region](#input\_region) | Location of the cluster | `string` | n/a | yes |
+| <a name="input_resource_group"></a> [resource\_group](#input\_resource\_group) | Azure resource group | `string` | n/a | yes |
+| <a name="input_sequila_version"></a> [sequila\_version](#input\_sequila\_version) | SeQuiLa version | `string` | n/a | yes |
+| <a name="input_spark_version"></a> [spark\_version](#input\_spark\_version) | Apache Spark version | `string` | `"3.2.2"` | no |
+| <a name="input_storage_account_access_key"></a> [storage\_account\_access\_key](#input\_storage\_account\_access\_key) | Storage account access key | `string` | n/a | yes |
+| <a name="input_storage_account_name"></a> [storage\_account\_name](#input\_storage\_account\_name) | n/a | `string` | n/a | yes |
+| <a name="input_storage_container_id"></a> [storage\_container\_id](#input\_storage\_container\_id) | Azure storage container | `string` | n/a | yes |
+| <a name="input_storage_container_name"></a> [storage\_container\_name](#input\_storage\_container\_name) | n/a | `string` | n/a | yes |
+
+## Outputs
+
+| Name | Description |
+|------|-------------|
+| <a name="output_hdinsight_gateway_password"></a> [hdinsight\_gateway\_password](#output\_hdinsight\_gateway\_password) | n/a |
+| <a name="output_hdinsight_ssh_password"></a> [hdinsight\_ssh\_password](#output\_hdinsight\_ssh\_password) | n/a |
+| <a name="output_pysequila_submit_command"></a> [pysequila\_submit\_command](#output\_pysequila\_submit\_command) | n/a |
+| <a name="output_ssh_command"></a> [ssh\_command](#output\_ssh\_command) | n/a |
+<!-- END OF PRE-COMMIT-TERRAFORM DOCS HOOK -->