Auto-scaling Azure Kubernetes cluster without shared filesystem

In this tutorial we will show how to execute a Snakemake workflow on an auto-scaling Azure Kubernetes cluster without a shared file-system. While Kubernetes is mainly known as microservice orchestration system with self-healing properties, we will use it here simply as auto-scaling compute orchestrator. One could use persistent volumes in Kubernetes as shared file system, but this adds an unnecessary level of complexity and most importantly costs. Instead we use cheap Azure Blob storage, which is used by Snakemake to automatically stage data in and out for every job.

Following the steps below you will

  1. set up Azure Blob storage, download the Snakemake tutorial data and upload to Azure

  2. then create an Azure Kubernetes (AKS) cluster

  3. and finally run the analysis with Snakemake on the cluster


To go through this tutorial, you need the following software installed:

You should install conda as outlined in the tutorial, and then install full snakemake with:

conda create -c bioconda -c conda-forge -n snakemake snakemake

Make sure that the kubernetes and azure-storage-blob modules are installed in this environment. Should they be missing install with:

pip install kubernetes
pip install azure-storage-blob

In addition you will need the Azure CLI command installed.

Create an Azure storage account and upload data

We will be starting from scratch, i.e. we will create a new resource group and storage account. You can obviously reuse existing resources instead.

# change the following names as required
# azure region where to run:
# name of the resource group to create:
# name of storage account to create (all lowercase, no hyphens etc.):

# create a resource group with name and in region as defined above
az group create --name $resgroup --location $region
# create a general purpose storage account with cheapest SKU
az storage account create -n $stgacct -g $resgroup --sku Standard_LRS -l $region

Get a key for that account and save it as stgkey for later use:

stgkey=$(az storage account keys list -g $resgroup -n $storageacct | head -n1 | cut -f 3)

Next, you will create a storage container (think: bucket) to upload the Snakemake tutorial data to:

az storage container create --resource-group $resgroup --account-name $stgacct \
    --account-key $stgkey --name snakemake-tutorial
cd /tmp
git clone
cd snakemake-tutorial-data
az storage blob upload-batch -d snakemake-tutorial --account-name $stgacct \
    --account-key $stgkey -s data/ --destination-path data

We are using az storage blob for uploading, because that az is already installed. A more efficient way of uploading would be to use azcopy.

Create an auto-scaling Kubernetes cluster

# change the cluster name as you like
az aks create --resource-group $resgroup --name $clustername \
    --vm-set-type VirtualMachineScaleSets --load-balancer-sku standard --enable-cluster-autoscaler \
    --node-count 1 --min-count 1 --max-count 3 --node-vm-size Standard_D3_v2

There is a lot going on here, so let’s unpack it: this creates an auto-scaling Kubernetes cluster (--enable-cluster-autoscaler) called $clustername (i.e. snakemaks-aks), which starts out with one node (--node-count 1) and has a maximum of three nodes (--min-count 1 --max-count 3). For real world applications you will want to increase the maximum count and also increase the VM size. You could for example choose a large instance from the DSv2 series and add a larger disk with (--node-osdisk-size) if needed. See here for more info on Linux VM sizes.

Note, if you are creating the cluster in the Azure portal, click on the ellipsis under node-pools to find the auto-scaling option.

Next, let’s fetch the credentials for this cluster, so that we can actually interact with it.

az aks get-credentials --resource-group $resgroup --name $clustername
# print basic cluster info
kubectl cluster-info

Running the workflow

Below we will task Snakemake to install software on the fly with conda. For this we need a Snakefile with corresponding conda environment yaml files. You can download the package containing all those files here. After downloading, unzip it and cd into the newly created directory.

$ cd /tmp
$ unzip ~/Downloads/
$ cd snakedir
$ find .

Now, we will need to setup the credentials that allow the Kubernetes nodes to read and write from blob storage. For the AzBlob storage provider in Snakemake this is done through the environment variables AZ_BLOB_ACCOUNT_URL and optionally AZ_BLOB_CREDENTIAL. See the documentation for more info. AZ_BLOB_ACCOUNT_URL takes the form https://<accountname> and may also contain a shared access signature (SAS), which is a powerful way to define fine grained and even time controlled access to storage on Azure. The SAS can be part of the URL, but if it’s missing, then you can set it with AZ_BLOB_CREDENTIAL or alternatively use the storage account key. To keep things simple we’ll use the storage key here, since we already have it available, but a SAS is generally more powerful. We’ll pass those variables on to the Kubernetes with --envvars (see below).

Now you are ready to run the analysis:

export AZ_BLOB_ACCOUNT_URL="https://${stgacct}"
export AZ_BLOB_CREDENTIAL="$stgkey"
snakemake --kubernetes \
    --default-remote-prefix snakemake-tutorial --default-remote-provider AzBlob \
    --envvars AZ_BLOB_ACCOUNT_URL AZ_BLOB_CREDENTIAL --use-conda --jobs 3

This will use the default Snakemake image from Dockerhub. If you would like to use your own, make sure that the image contains the same Snakemake version as installed locally and also supports Azure Blob storage. If you plan to use your own image hosted on

Azure Container Registries (ACR), make sure to attach the ACR to your Kubernetes cluster. See here for more info.

While Snakemake is running the workflow, it prints handy debug statements per job, e.g.:

kubectl describe pod snakejob-c4d9bf9e-9076-576b-a1f9-736ec82afc64
kubectl logs snakejob-c4d9bf9e-9076-576b-a1f9-736ec82afc64

With these you can also follow the scale-up of the cluster:

Type     Reason             Age                From                Message
----     ------             ----               ----                -------
Warning  FailedScheduling   60s (x3 over 62s)  default-scheduler   0/1 nodes are available: 1 Insufficient cpu.
Normal   TriggeredScaleUp   50s                cluster-autoscaler  pod triggered scale-up: [{aks-nodepool1-17839284-vmss 1->3 (max: 3)}]

After a while you will see three nodes (each running one BWA job), which was defined as the maximum above while creating your Kubernetes cluster:

$ kubectl get nodes
NAME                                STATUS   ROLES   AGE   VERSION
aks-nodepool1-17839284-vmss000000   Ready    agent   74m   v1.15.11
aks-nodepool1-17839284-vmss000001   Ready    agent   11s   v1.15.11
aks-nodepool1-17839284-vmss000002   Ready    agent   62s   v1.15.11

To get detailed information including historical data about used resources, check Insights in the Azure portal under your AKS cluster Monitoring/Insights. The alternative is an instant snapshot on the command line:

$ kubectl top node
NAME                                CPU(cores)   CPU%   MEMORY(bytes)   MEMORY%
aks-nodepool1-17839284-vmss000000   217m         5%     1796Mi          16%
aks-nodepool1-17839284-vmss000001   1973m        51%    529Mi           4%
aks-nodepool1-17839284-vmss000002   698m         18%    1485Mi          13%

After completion all results including logs can be found in the blob container. You will also find results listed in the first Snakefile target downloaded to the working directoy.

$ find snakemake-tutorial/

$ az storage blob list  --container-name snakemake-tutorial --account-name $stgacct --account-key $stgkey -o table
Name                     Blob Type    Blob Tier    Length    Content Type                       Last Modified              Snapshot
-----------------------  -----------  -----------  --------  ---------------------------------  -------------------------  ----------
calls/all.vcf            BlockBlob    Hot          90986     application/octet-stream           2020-06-08T05:11:31+00:00
data/genome.fa           BlockBlob    Hot          234112    application/octet-stream           2020-06-08T03:26:54+00:00
# etc.
logs/mapped_reads/A.log  BlockBlob    Hot          346       application/octet-stream           2020-06-08T04:59:50+00:00
mapped_reads/A.bam       BlockBlob    Hot          2258058   application/octet-stream           2020-06-08T04:59:50+00:00
sorted_reads/A.bam       BlockBlob    Hot          2244660   application/octet-stream           2020-06-08T05:03:41+00:00
sorted_reads/A.bam.bai   BlockBlob    Hot          344       application/octet-stream           2020-06-08T05:06:25+00:00
# same for samples B and C

Now that the execution is complete, the AKS cluster will scale down automatically. If you are not planning to run anything else, it makes sense to shut down it down entirely:

az aks delete --name akscluster --resource-group $resgroup