Slurm Docker Cluster

This is a multi-container Slurm cluster using docker-compose. The compose file creates named volumes for persistent storage of MySQL data files as well as Slurm state and log directories.

Containers and Volumes

The compose file will run the following containers:

• mysql
• slurmdbd
• slurmctld
• c1 (slurmd)
• c2 (slurmd)

The compose file will create the following named volumes:

• etc_munge ( -> /etc/munge )
• etc_slurm ( -> /etc/slurm )
• slurm_jobdir ( -> /data )
• var_lib_mysql ( -> /var/lib/mysql )
• var_log_slurm ( -> /var/log/slurm )

Building the Docker Image

Build the image locally:

docker build -t slurm-docker-cluster:21.08.6 .

Build a different version of Slurm using Docker build args and the Slurm Git tag:

docker build --build-arg SLURM_TAG="slurm-19-05-2-1" -t slurm-docker-cluster:19.05.2 .

Or equivalently using docker-compose:

SLURM_TAG=slurm-19-05-2-1 IMAGE_TAG=19.05.2 docker-compose build

Starting the Cluster

Run docker-compose to instantiate the cluster:

IMAGE_TAG=19.05.2 docker-compose up -d

Register the Cluster with SlurmDBD

To register the cluster to the slurmdbd daemon, run the register_cluster.sh script:

./register_cluster.sh

Note: You may have to wait a few seconds for the cluster daemons to become ready before registering the cluster. Otherwise, you may get an error such as sacctmgr: error: Problem talking to the database: Connection refused.

You can check the status of the cluster by viewing the logs: docker-compose logs -f

Accessing the Cluster

Use docker exec to run a bash shell on the controller container:

docker exec -it slurmctld bash

From the shell, execute slurm commands, for example:

[root@slurmctld /]# sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
normal*      up 5-00:00:00      2   idle c[1-2]

Submitting Jobs

The slurm_jobdir named volume is mounted on each Slurm container as /data. Therefore, in order to see job output files while on the controller, change to the /data directory when on the slurmctld container and then submit a job:

[root@slurmctld /]# cd /data/
[root@slurmctld data]# sbatch --wrap="hostname"
Submitted batch job 2
[root@slurmctld data]# ls
slurm-2.out
[root@slurmctld data]# cat slurm-2.out
c1

Stopping and Restarting the Cluster

docker-compose stop
docker-compose start

Deleting the Cluster

To remove all containers and volumes, run:

docker-compose stop
docker-compose rm -f
docker volume rm slurm-docker-cluster_etc_munge slurm-docker-cluster_etc_slurm slurm-docker-cluster_slurm_jobdir slurm-docker-cluster_var_lib_mysql slurm-docker-cluster_var_log_slurm

Updating the Cluster

If you want to change the slurm.conf or slurmdbd.conf file without a rebuilding you can do so by calling

./update_slurmfiles.sh slurm.conf slurmdbd.conf

(or just one of the files). The Cluster will automatically be restarted afterwards with

docker-compose restart

This might come in handy if you add or remove a node to your cluster or want to test a new setting.

Additional Scitech Specific Modifications

This setup in addition

• Mounts nfs filesystem in the containers at /nfs.
• The home filesystem is mounted out of a volume named user_home.
• Sets up a bamboo user in the dockerized setup
• The public key for the bamboo user on scitech machines is picked up from bamboo_slurm_id_rsa.pub, and used for setup of the bamboo user in the slurm cluster setup.
• The SSH server set on the slurmctld container binds to 2222 on the host machine.
• The public key workflow_id_rsa.pub is used for transferring data into the slurm cluster

HTCondor Setup on Workflow Submit Node

By default, BOSCO submits job via port 22. There is no knob to change the port. To use a different port, on your bosco install, apply the patch file bosco_cluster-901.patch using the patch command as root

cd /usr/bin
patch -i /path/to/bosco_cluster-901.patch 

Also you need to edit /usr/sbin/remote_gahp and update the ssh port to 2222 from 22

Add cluster in Bosco on the Workflow Submit Node

Before running any jobs via BOSCO, we set up this docker slurm cluster on the workflow submit node from where jobs will be submitted to this SLURM cluster.

You need to run these commands as the user that submits the jobs. In SciTech case, that is user bamboo

[bamboo@bamboo ~]$condor_remote_cluster --add slurm-pegasus.isi.edu:2222 slurm
Enter the password to copy the ssh keys to slurm-pegasus.isi.edu:2222:
The authenticity of host '[slurm-pegasus.isi.edu]:2222 ([128.9.46.64]:2222)' can't be established.
ECDSA key fingerprint is SHA256:xp6i2HogEiwIZDO0QL0X7bUM2jAkReHyGo9bfljBqGk.
Are you sure you want to continue connecting (yes/no/[fingerprint])? yes
Warning: Permanently added '[slurm-pegasus.isi.edu]:2222,[128.9.46.64]:2222' (ECDSA) to the list of known hosts.
Enter passphrase for key '/scitech/shared/home/bamboo/.ssh/id_rsa': 
Downloading release build for slurm-pegasus.isi.edu:2222..
Unpacking..
Installing on cluster slurm-pegasus.isi.edu:2222.
Installation complete
The cluster slurm-pegasus.isi.edu:2222 has been added for remote submission
It is available to run jobs submitted with the following values:
> universe = grid
> grid_resource = batch slurm slurm-pegasus.isi.edu:2222
[bamboo@bamboo ~]$ 

To check cluster is added

[bamboo@bamboo ~]$ condor_remote_cluster --list
slurm-pegasus.isi.edu:2222/slurm

You can test the setup by

[bamboo@bamboo ~]$ condor_remote_cluster --test slurm-pegasus.isi.edu:2222
Testing ssh to slurm-pegasus.isi.edu:2222...Passed!
Testing remote submission...Passed!
Submission and log files for this job are in /scitech/shared/home/bamboo/bosco-test/boscotest.14Y7a
Waiting for jobmanager to accept job...Passed
Checking for submission to remote slurm cluster (could take ~30 seconds)...Passed!
Waiting for job to exit... this could take a while (waiting 60 seconds)...Failed
The job did not end in 60 seconds.  This is not always a bad thing...
Maybe condor is waiting longer to poll for job completion?
Here is the current status of the job:"


-- Schedd: bamboo.isi.edu : <128.9.46.30:9618?... @ 09/17/24 15:54:12
OWNER  BATCH_NAME     SUBMITTED   DONE   RUN    IDLE  TOTAL JOB_IDS
bamboo ID: 3904783   9/17 15:52      _      _      1      1 3904783.0

Total for query: 1 jobs; 0 completed, 0 removed, 1 idle, 0 running, 0 held, 0 suspended 
Total for all users: 1 jobs; 0 completed, 0 removed, 1 idle, 0 running, 0 held, 0 suspended

The corresponding test condor job can be found in the directory ~/bosco_test

bamboo@bamboo boscotest.zBVeb]$ pwd
/scitech/shared/home/bamboo/bosco-test/