Running Maestro on the cluster
Last updated on 2024-06-06 | Edit this page
Estimated time: 50 minutes
How do I run Maestro on the cluster?
What happens when we want to run on the cluster (“to run a batch job”) rather than the login node? The cluster we are using uses Slurm, and Maestro has built in support for Slurm. We just need to tell Maestro which resources we need Slurm to grab for our run.
First, we need to add a batch block to our YAML file,
where we’ll provide the names of the machine, bank, and queue in which
your jobs should run.
YML
batch:
type: slurm
host: ruby # enter the machine you'll run on
bank: guests # enter the bank to charge
queue: pbatch # partition in which your job should run
reservation: HPCC1B # reservation for this workshopSecond, we need to specify the number of nodes, number of processes,
and walltime for each step in our YAML file. This information
goes under each step’s run field. Here we specify 1 node, 1
process, and a time limit of 30 seconds:
Whereas run previously held only info about the command
we wanted to execute, steps run on the cluster include a specification
of the resources needed in order to execute. Note that
the format of the walltime includes quotation marks –
"{Hours}:{Minutes}:{Seconds}".
With these changes, our updated YAML file might look like
YML
---
description:
name: Hostnames
description: Report a node's hostname.
batch:
type: slurm
host: ruby # machine
bank: guests # bank
queue: pbatch # partition
reservation: HPCC1B # reservation for this workshop
study:
- name: hostname-login
description: Write the login node's hostname to a file
run:
cmd: |
hostname > hostname_login.txt
- name: hostname_batch
description: Write the node's hostname to a file
run:
cmd: |
hostname >> hostname.txt
nodes: 1
procs: 1
walltime: "00:00:30"Note that we left the rule hostname-login as is. Because
we do not specify any info for slurm under this original step’s
run field – like nodes, processes, or walltime – this step
will continue running on the login node and only
hostname_batch will be handed off to slurm.
Running on the cluster
Modify your YAML file, hostname.yaml to execute
hostname on the cluster. Run with 1 node and 1
process using the bank guests on the partition
pbatch on ruby.
If you run this multiple times, do you always run on the same node? (Is the hostname printed always the same?)
The contents of hostname.yaml should look something
like:
YML
description:
name: Hostnames
description: Report a node's hostname.
batch:
type: slurm
host: ruby # machine
bank: guests # bank
queue: pbatch # partition
reservation: HPCC1B # reservation for this workshop
study:
- name: hostname-login
description: Write the login node's hostname to a file
run:
cmd: |
hostname > hostname_login.txt
- name: hostname_batch
description: Write the node's hostname to a file
run:
cmd: |
hostname >> hostname.txt
nodes: 1
procs: 1
walltime: "00:00:30"Go ahead and run the job:
A directory called Hostname_... will be created. If you
look in the subdirectory hostname_batch, you’ll find a file
called hostname.txt with info about the compute node where
the hostname command ran. If you run the job multiple
times, you will probably land on different nodes; this means you’ll see
different node numbers in different hostname.txt files. If
you see the same number more than once, don’t worry! (If you want to
double check that the hostnames printed are not for login nodes, you can
run nodeattr -c login to check the IDs of all login nodes
on the system.)
Outputs from a batch job
When running in batch, maestro run ... will create a new
directory with the same naming scheme as seen in episode 1, and that
directory will contain subdirectories for all studies. The
hostname_batch subdirectory has four output files, but this
time the file ending with extension .sh is a slurm
submission script
OUTPUT
hostname.err hostname.out hostname.slurm.sh hostname.txtBASH
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=pvis
#SBATCH --account=lc
#SBATCH --time=00:00:30
#SBATCH --job-name="hostname"
#SBATCH --output="hostname.out"
#SBATCH --error="hostname.err"
#SBATCH --comment "Write the node's hostname to a file"
hostname > hostname.txtMaestro uses the info from your YAML file to write this script and
then submits it to the scheduler for you. Soon after you run on the
cluster via maestro run hostname.yaml, you should be able
to see the job running or finishing up in the queue with the command
squeue -u «your username».
OUTPUT
[2024-03-20 17:31:37: INFO] INFO Logging Level -- Enabled
[2024-03-20 17:31:37: WARNING] WARNING Logging Level -- Enabled
[2024-03-20 17:31:37: CRITICAL] CRITICAL Logging Level -- Enabled
[2024-03-20 17:31:37: INFO] Loading specification -- path = batch-hostname.yaml
[2024-03-20 17:31:37: INFO] Directory does not exist. Creating directories to ~/Hostnames_20240320-173137/logs
[2024-03-20 17:31:37: INFO] Adding step 'hostname-login' to study 'Hostnames'...
[2024-03-20 17:31:37: INFO] Adding step 'hostname_batch' to study 'Hostnames'...
[2024-03-20 17:31:37: INFO]
------------------------------------------
Submission attempts = 1
Submission restart limit = 1
Submission throttle limit = 0
Use temporary directory = False
Hash workspaces = False
Dry run enabled = False
Output path = ~/Hostnames_20240320-173137
------------------------------------------
Would you like to launch the study? [yn] y
Study launched successfully.OUTPUT
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
718308 pvis hostname janeh R 0:01 1 pascal13Key Points
- You can run on the cluster by including info for Slurm in your Maestro YAML file
- Maestro generates and submits its own batch scripts to your scheduler.
- Steps without Slurm parameters will run on the login node by default.