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.

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 )

Build the image locally:

docker build -t slurm-docker-cluster:19.05.1 .

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 .

Note: You will need to update the container image version in docker-compose.yml.

Run docker-compose to instantiate the cluster:

docker-compose up -d

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

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]

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="uptime"
Submitted batch job 2
[root@slurmctld data]# ls
slurm-2.out

docker-compose stop
docker-compose start

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

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

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

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 ~]$ bosco_cluster --add slurm-pegasus.isi.edu slurm
Cluster slurm-pegasus.isi.edu already installed
Reinstalling on slurm-pegasus.isi.edu
Enter the password to copy the ssh keys to slurm-pegasus.isi.edu:
Enter passphrase for key '/scitech/shared/home/bamboo/.ssh/id_rsa': 
Downloading release build for slurm-pegasus.isi.edu.
Unpacking.
You are not running as the factory user. Glideins disabled.
Installing on cluster slurm-pegasus.isi.edu.
Installation complete
The cluster slurm-pegasus.isi.edu 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
[bamboo@bamboo ~]$ 

To check cluster is added

[bamboo@bamboo ~]$ bosco_cluster --list
corbusier.isi.edu/slurm
slurm-pegasus.isi.edu/slurm

You can test the setup by

[bamboo@bamboo ~]$ bosco_cluster --test slurm-pegasus.isi.edu
Testing ssh to slurm-pegasus.isi.edu...Passed!
Testing remote submission...Passed!
Submission and log files for this job are in /scitech/shared/home/bamboo/bosco-test/boscotest.zBVeb
Waiting for jobmanager to accept job...Passed

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

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