Katana Tweaks

This fork is tweaked to make the environment it generates amenable to katana. Tweaks include:

• bumping the CentOS version; katana requires at least gcc-7, gcc-8 is the default on CentOS 8
• changing scripts/custom-compute-install to install the necessary dependencies

dev-cluster-deployment.yaml is a good starting point for a katana cluster.

A note: building katana in CentOS requires module load mpi because of how CentOS installs mpi. Other than that the build steps are pretty much the same.

from here down is the original readme

Slurm on Google Cloud Platform

NOTE: This will be the last release supporting Deployment Manager. Please migrate your workflows to Terraform (found in the tf folder). All future features / functionality will be integrated with Terraform.

The following describes setting up a Slurm cluster using Google Cloud Platform, bursting out from an on-premise cluster to nodes in Google Cloud Platform and setting a multi-cluster/federated setup with a cluster that resides in Google Cloud Platform.

Also, checkout the Slurm on GCP code lab.

The supplied scripts can be modified to work with your environment.

SchedMD provides professional services to help you get up and running in the cloud environment. SchedMD Commercial Support

Issues and/or enhancement requests can be submitted to SchedMD's Bugzilla.

Also, join comunity discussions on either the Slurm User mailing list or the Google Cloud & Slurm Community Discussion Group.

Contents

• Stand-alone Cluster in Google Cloud Platform
  • Install using Deployment Manager
  • Install using Terraform (Beta)
  • Image-based Scaling
  • Installing Custom Packages
  • Accessing Compute Nodes Directly
  • OS Login
  • Preemptible VMs
• Hybrid Cluster for Bursting from On-Premise
  • Node Addressing
  • Configuration Steps
  • Users and Groups in a Hybrid Cluster
• Multi-Cluster / Federation
• Troubleshooting

Stand-alone Cluster in Google Cloud Platform

The supplied scripts can be used to create a stand-alone cluster in Google Cloud Platform. The scripts setup the following scenario:

• 1 - controller node
• N - login nodes
• Multiple partitions with their own machine type, gpu type/count, disk size, disk type, cpu platform, and maximum node count.

The default image for the instances is CentOS 7.

On the controller node, slurm is installed in: /apps/slurm/<slurm_version> with the symlink /apps/slurm/current pointing to /apps/slurm/<slurm_version>.

The login nodes mount /apps and /home from the controller node.

Install using Deployment Manager

To deploy, you must have a GCP account and either have the GCP Cloud SDK installed on your computer or use the GCP Cloud Shell.

Steps:

1. Edit the slurm-cluster.yaml file and specify the required values

   NOTE: For a complete list of available options and their definitions, check out the schema file.

2. Spin up the cluster.

   Assuming that you have gcloud configured for your account, you can just run:

   $ gcloud deployment-manager deployments [--project=<project id>] create slurm --config slurm-cluster.yaml
   

3. Check the cluster status.

   You can see that status of the deployment by viewing: https://console.cloud.google.com/deployments

   and viewing the new instances: https://console.cloud.google.com/compute/instances

   To verify the deployment, ssh to the login node and run sinfo to see how many nodes have registered and are in an idle state.

   A message will be broadcast to the terminal when the installation is complete. If you log in before the installation is complete, you will either need to re-log in after the installation is complete or start a new shell (e.g. /bin/bash) to get the correct bash profile.

   $ gcloud compute [--project=<project id>] ssh [--zone=<zone>] g1-login0
   ...
   [bob@g1-login0 ~]$ sinfo
   PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
   debug*       up   infinite      8  idle~ g1-compute-0-[1-9]
   debug*       up   infinite      2   idle g1-compute-0-[0-1]
   

   NOTE: By default, Slurm will hide nodes that are in a power_save state -- "cloud" nodes. The GCP Slurm scripts configure PrivateData=cloud in the slurm.conf so that the "cloud" nodes are always shown. This is done so that nodes that get marked down can be easily seen.

4. Submit jobs on the cluster.

   [bob@g1-login0 ~]$ sbatch -N2 --wrap="srun hostname"
   Submitted batch job 2
   [bob@g1-login0 ~]$ cat slurm-2.out
   g1-compute-0-0
   g1-compute-0-1
   

5. Tearing down the deployment.

   $ gcloud deployment-manager [--project=<project id>] deployments delete slurm
   

   NOTE: If additional resources (instances, networks) are created other than the ones created from the default deployment then they will need to be destroyed before deployment can be removed.

Install using Terraform (Beta)

To deploy, you must have a GCP account and either have the GCP Cloud SDK and Terraform installed on your computer or use the GCP Cloud Shell.

Steps:

1. cd to tf/examples/basic

2. Edit the basic.tfvars file and specify the required values

3. Deploy the cluster

   $ terraform init
   $ terraform apply -var-file=basic.tfvars
   

4. Tearing down the cluster

   $ terraform destroy -var-file=basic.tfvars
   

   NOTE: If additional resources (instances, networks) are created other than the ones created from the default deployment then they will need to be destroyed before deployment can be removed.

Image-based Scaling

The deployment will create a <cluster_name>-compute-#-image instance, where # is the index in the array of partitions, for each partition that is a base compute instance image. After installing necessary packages, the instance will be stopped and an image of the instance will be created. Subsequent bursted compute instances will use this image -- shortening the creation and boot time of new compute instances. While the compute image is running, the respective partitions will be marked as "down" to prevent jobs from launching until the image is created. After the image is created, the partition will be put into an "up" state and jobs can then run.

NOTE: When creating a compute image that has gpus attached, the process can take about 10 minutes.

If the compute image needs to be updated, it can be done with the following command:

$ gcloud compute images create <cluster_name>-compute-#-image-$(date '+%Y-%m-%d-%H-%M-%S') \
                               --source-disk <instance name> \
                               --source-disk-zone <zone> --force \
                               --family <cluster_name>-compute-#-image-family

Existing images can be viewed on the console's Images page.

Installing Custom Packages

There are two files, custom-controller-install and custom-compute-install, in the scripts directory that can be used to add custom installations for the given instance type. The files will be executed during startup of the instance types.

Accessing Compute Nodes Directly

There are multiple ways to connect to the compute nodes:

1. If the compute nodes have external IPs you can connect directly to the compute nodes. From the VM Instances page, the SSH drop down next to the compute instances gives several options for connecting to the compute nodes.
2. With IAP configured, you can SSH to the nodes regardless of external IPs or not. See https://cloud.google.com/iap/docs/enabling-compute-howto.
3. Use Slurm to get an allocation on the nodes.

   $ srun --pty $SHELL
   [g1-login0 ~]$ srun --pty $SHELL
   [g1-compute-0-0 ~]$
   

OS Login

By default, all instances are configured with OS Login.

OS Login lets you use Compute Engine IAM roles to manage SSH access to Linux instances and is an alternative to manually managing instance access by adding and removing SSH keys in metadata. https://cloud.google.com/compute/docs/instances/managing-instance-access

This allows user uid and gids to be consistent across all instances.

When sharing a cluster with non-admin users, the following IAM rules are recommended:

1. Create a group for all users in admin.google.com.
2. At the project level in IAM, grant the Compute Viewer and Service Account User roles to the group.
3. At the instance level for each login node, grant the Compute OS Login role to the group.
   1. Make sure the Info Panel is shown on the right.
   2. On the compute instances page, select the boxes to the left of the login nodes.
   3. Click Add Members and add the Compute OS Login role to the group.
4. At the organization level, grant the Compute OS Login External User role to the group if the users are not part of the organization.
5. To allow ssh to login nodes without external IPs, configure IAP for the group.
   1. Go to the Identity-Aware Proxy page
   2. Select project
   3. Click SSH AND TCP RESOURCES tab
   4. Select boxes for login nodes
   5. Add group as a member with the IAP-secured Tunnel User role
   6. Reference: https://cloud.google.com/iap/docs/enabling-compute-howto

This allows users to access the cluster only through the login nodes.

Preemptible VMs

With preemptible_bursting on, when a node is found preempted, or stopped, the slurmsync script will mark the node as "down" and will attempt to restart the node. If there were any batch jobs on the preempted node, they will be requeued -- interactive (e.g. srun, salloc) jobs can't be requeued.

Hybrid Cluster for Bursting from On-Premise

Bursting out from an on-premise cluster is done by configuring the ResumeProgram and the SuspendProgram in the slurm.conf to resume.py, suspend.py in the scripts directory. config.yaml should be configured so that the scripts can create and destroy compute instances in a GCP project. See Cloud Scheduling Guide for more information.

Pre-reqs:

1. VPN between on-premise and GCP
2. bidirectional DNS between on-premise and GCP
3. Open ports to on-premise
   1. slurmctld
   2. slurmdbd
   3. SrunPortRange
4. Open ports in GCP for NFS from on-premise

Node Addressing

There are two options: 1) setup DNS between the on-premise network and the GCP network or 2) configure Slurm to use NodeAddr to communicate with cloud compute nodes. In the end, the slurmctld and any login nodes should be able to communicate with cloud compute nodes, and the cloud compute nodes should be able to communicate with the controller.

• Configure DNS peering

  1. GCP instances need to be resolvable by name from the controller and any login nodes.
  2. The controller needs to be resolvable by name from GCP instances, or the controller ip address needs to be added to /etc/hosts. https://cloud.google.com/dns/zones/#peering-zones

• Use IP addresses with NodeAddr

  1. disable cloud_dns in slurm.conf
  2. disable hierarchical communication in slurm.conf: TreeWidth=65533
  3. set update_node_addrs to true in config.yaml
  4. add controller's ip address to /etc/hosts on compute image

Configuration Steps

1. Create a base instance

   Create a bare image and install and configure the packages (including Slurm) that you are used to for a Slurm compute node. Then create an image from it creating a family either in the form "<cluster_name>-compute-#-image-family" or in a name of your choosing.

2. Create a service account and service account key that will have access to create and delete instances in the remote project.

3. Install scripts

   Install the resume.py, suspend.py, slurmsync.py and config.yaml.example from the slurm-gcp repository's scripts directory to a location on the slurmctld. Rename config.yaml.example to config.yaml and modify the approriate values.

   Add the path of the service account key to google_app_cred_path in config.yaml.

   Add the compute_image_family to each partition if different than the naming schema, "<cluster_name>-compute-#-image-family".

4. Modify slurm.conf:

   PrivateData=cloud
   
   SuspendProgram=/path/to/suspend.py
   ResumeProgram=/path/to/resume.py
   ResumeFailProgram=/path/to/suspend.py
   SuspendTimeout=600
   ResumeTimeout=600
   ResumeRate=0
   SuspendRate=0
   SuspendTime=300
   
   # Tell Slurm to not power off nodes. By default, it will want to power
   # everything off. SuspendExcParts will probably be the easiest one to use.
   #SuspendExcNodes=
   #SuspendExcParts=
   
   SchedulerParameters=salloc_wait_nodes
   SlurmctldParameters=cloud_dns,idle_on_node_suspend
   CommunicationParameters=NoAddrCache
   LaunchParameters=enable_nss_slurm
   
   SrunPortRange=60001-63000
   

5. Add a cronjob/crontab to call slurmsync.py to be called by SlurmUser.

   e.g.

   */1 * * * * /path/to/slurmsync.py
   

6. Test

   Try creating and deleting instances in GCP by calling the commands directly as SlurmUser.

   ./resume.py g1-compute-0-0
   ./suspend.py g1-compute-0-0
   

Users and Groups in a Hybrid Cluster

The simplest way to handle user synchronization in a hybrid cluster is to use nss_slurm. This permits passwd and group resolution for a job on the compute node to be serviced by the local slurmstepd process rather than some other network-based service. User information is sent from the controller for each job and served by the slurm step daemon. nss_slurm needs to be installed on the compute node image, which it is when the image is created with deployment manager or Terraform. For details on how to configure nss_slurm, see https://slurm.schedmd.com/nss_slurm.html.

Multi-Cluster / Federation

Slurm allows the use of a central SlurmDBD for multiple clusters. By doing this, it also allows the clusters to be able to communicate with each other. This is done by the client commands first checking with the SlurmDBD for the requested cluster's IP address and port which the client then uses to communicate directly with the cluster.

Some possible scenarios:

• An on-premise cluster and a cluster in GCP sharing a single SlurmDBD.
• An on-premise cluster and a cluster in GCP each with their own SlurmDBD but having each SlurmDBD know about each other using AccountingStorageExternalHost in each slurm.conf.

The following considerations are needed for these scenarios:

• Regardless of location for the SlurmDBD, both clusters need to be able to talk to the each SlurmDBD and controller.
  • A VPN is recommended for traffic between on-premise and the cloud.
• In order for interactive jobs (srun, salloc) to work from the login nodes to each cluster, the compute nodes must be accessible from the login nodes on each cluster.
  • It may be easier to only support batch jobs between clusters.
    • Once a batch job is on a cluster, srun functions normally.
• If a firewall exists, srun communications most likely need to be allowed through it. Configure SrunPortRange to define a range for ports for srun communications.
• Consider how to present file systems and data movement between clusters.
• NOTE: All clusters attached to a single SlurmDBD must share the same user space (e.g. same uids across all the clusters).
• NOTE: Either all clusters and the SlurmDBD must share the same MUNGE key or use a separate MUNGE key for each cluster and another key for use between each cluster and the SlurmDBD. In order for cross-cluster interactive jobs to work, the clusters must share the same MUNGE key. See the following for more information:
  Multi-Cluster Operation
  Accounting and Resource Limits

For more information see:
Multi-Cluster Operation
Federated Scheduling Guide

Troubleshooting

1. Nodes aren't bursting?

   1. Check /var/log/slurm/resume.log for any errors
   2. Try creating nodes manually by calling resume.py manually as the "slurm" user.
      • NOTE: If you run resume.py manually with root, subsequent calls to resume.py by the "slurm" user may fail because resume.py's log file will be owned by root.
   3. Check the slurmctld logs
      • /var/log/slurm/slurmctld.log
      • Turn on the PowerSave debug flag to get more information. e.g.

        $ scontrol setdebugflags +powersave
        ...
        $ scontrol setdebugflags -powersave
        

2. Cluster environment not fully coming up
   For example:

   • Slurm not being installed
   • Compute images never being stopped
   • etc.
   1. Check syslog (/var/log/messages) on instances for any errors. HINT: search for last mention of "startup-script."

3. General debugging

   • check logs
     • /var/log/messages
     • /var/log/slurm/*.log
     • NOTE: syslog and all Slurm logs can be viewed in GCP Console's Logs Viewer.
   • check GCP quotas