gridtk 3.0.1

GridTK: Slurm Job Management for Humans

GridTK: Slurm Job Management for Humans

Introduction

GridTK is a powerful command-line tool designed to simplify the management of Slurm jobs. At its core, GridTK provides a drop-in replacement for sbatch, gridtk submit, which allows you to get started quickly. This tutorial will guide you through the process of using the gridtk script to efficiently manage your Slurm workloads. We will cover the basics of installation, submission, monitoring, and various commands provided by GridTK.

Prerequisites

Before diving into GridTK, ensure you have the following prerequisites:

1. A working Slurm setup.
2. pipx installed.
3. GridTK installed (instructions provided below).

Installation

To install GridTK, open your terminal and run the following command:

$ pipx install gridtk

It is not recommended to install GridTK using pip install gridtk in the same environment as your experiments. GridTK does not need to be installed in the same environment as your experiments and its dependencies may conflict with your experiments' dependencies.

Basic Usage

In this section, we will cover the basic commands and usage of the GridTK script. The primary goal is to help you get familiar with submitting, monitoring, and managing your Slurm jobs using GridTK.

Submitting a Job

To submit a job script, use gridtk submit. For example, given the script (job.sh) below:

#!/bin/bash

echo "Hello, GridTK!"

Submit the job using gridtk submit:

$ gridtk submit job.sh
1

where 1 is the local job id (not the slurm job id) for your job. The job numbers always start with 1 which is easier to remember than the slurm job id.

gridtk submit is a drop-in replacement for sbatch and accepts the same options while adding its own. Run gridtk submit --help to see the list of gridtk submit specific options and run sbatch --help to see the full list of options for sbatch.

Note that your slurm cluster may require you to specify a partition, an account, or another option. You can do so by adding them to gridtk submit --account=myaccount --partition=mypartition job.sh or setting default values using environment variables such as SBATCH_ACCOUNT and SBATCH_PARTITION.

Monitoring Jobs

Use the gridtk list command to view the status of your jobs:

$ gridtk list
  job-id    grid-id  nodes    state        job-name    output                  dependencies    command
--------  ---------  -------  -----------  ----------  ----------------------  --------------  --------------------
       1     136132  None     PENDING (0)  gridtk      logs/gridtk.136132.out                  gridtk submit job.sh

gridtk list will only show jobs that are submitted using gridtk submit in the current folder. You can see the submitted job got a local job id of 1 and a slurm job id of 136132. It is in the PENDING state and its name is gridtk by default (it is recommended to give a meaningful name using the gridtk submit --job-name option). The output files are written to the logs/ directory by default (you may change the directory with the gridtk --logs-dir option). GridTK manages the log files for you, so you don't have to worry about knowing where they are stored or cleaning them up.

For detailed information about a specific job, use the report command:

$ gridtk report -j 1
Job ID: 1
Name: gridtk
State: COMPLETED (0)
Nodes: None
Submitted command: ['sbatch', '--job-name', 'gridtk', '--output', 'logs/gridtk.%j.out', '--error', 'logs/gridtk.%j.out', 'job.sh']
Output file: logs/gridtk.136132.out
Hello, GridTK!

where you can see the exact sbatch command that was used to submit the job and the output of the job.

Stopping and Deleting a Job

To stop a running or pending job, use the gridtk stop command:

$ gridtk stop -j 1
Stopped job 1 with slurm id 136132

Stopped jobs will be still available in the job list:

$ gridtk list
  job-id    slurm-id  nodes    state          job-name    output                  dependencies    command
--------  ----------  -------  -------------  ----------  ----------------------  --------------  --------------------
       1      136137  None     CANCELLED (0)  gridtk      logs/gridtk.136137.out                  gridtk submit job.sh

and can be resubmitted using the gridtk resubmit command (more details on resubmit further down) and you can still view their output using the gridtk report command.

To delete a job (and its log file), use the gridtk delete command:

$ gridtk delete -j 1
Deleted job 1 with slurm id 136137

Resubmitting a Job

If a job fails or is stopped, you can resubmit it using the gridtk resubmit command:

$ gridtk submit job.sh
1

$ gridtk stop -j 1
Stopped job 1 with slurm id 136139

$ gridtk resubmit -j 1
Resubmitted job 1

$ gridtk list
  job-id    slurm-id  nodes    state        job-name    output                  dependencies    command
--------  ----------  -------  -----------  ----------  ----------------------  --------------  --------------------
       1      136140  None     PENDING (0)  gridtk      logs/gridtk.136140.out                  gridtk submit job.sh

Notice how the resubmitted job got a new slurm job id of 136140.

Advanced Usage

GridTK provides several advanced commands to help with more complex job management tasks. These include job dependencies, array jobs, and resource management.

Job Submission without a Script

Since GridTK keeps track of both the sbatch options and the command to run, you can skip creating a script and submit a job directly from the command line. This is done by using --- (3 dashes) to separate the sbatch options from the command to run:

$ gridtk submit --job-name=gridtk-no-script --- echo 'Hello, GridTK!'
2

This syntax is unique to gridtk submit and is not supported by sbatch.

$ gridtk list
  job-id    slurm-id  nodes    state        job-name          output                            dependencies    command
--------  ----------  -------  -----------  ----------------  --------------------------------  --------------  ------------------------------------
       1      136140  None     PENDING (0)  gridtk            logs/gridtk.136140.out                            gridtk submit job.sh
       2      136142  None     PENDING (0)  gridtk-no-script  logs/gridtk-no-script.136142.out                  gridtk submit --- echo Hello, GridTK!

What happens is that gridtk submit creates a temporary script with the command to run and submits it to slurm. The temporary script is deleted after the job is submitted. The content of this temporary script can be viewed using the gridtk report command:

$ gridtk report -j 2
Job ID: 2
Name: gridtk-no-script
State: PENDING (0)
Nodes: None
Submitted command: ['sbatch', '--job-name', 'gridtk-no-script', '--output', 'logs/gridtk-no-script.%j.out', '--error', 'logs/gridtk-no-script.%j.out', '/tmp/tmpegoy2ma1.sh']
Content of the temporary script:
#!/bin/bash
echo 'Hello, GridTK!'

Output file: logs/gridtk-no-script.136142.out

This is a fast, convenient, and recommended way to submit a job without having to create a script and since everything is tracked by GridTK, you still benefit from the same reproducibility guarantees.

Job Dependencies

To submit a job that depends on another job, use the --dependency flag:

$ gridtk submit --dependency=<job_id> job.sh

The --dependency flag takes the same values as in sbatch except that you need to specify local job ids instead of slurm job ids.

Repeat Jobs

You can submit the same script N times using the --repeat flag:

$ gridtk submit --repeat=3 job.sh

This will submit 3 jobs with the same script and the same options where each job will depend on the previous one. This is useful if your script can resume from a checkpoint and you want to run it effectively for a longer time than allowed by policy.

Monitoring Jobs

While gridtk list and gridtk report are useful for checking the status of jobs, you might get more information about your jobs using squeue, scontrol, and sacct. Here are some useful commands:

• Get information about a specific job: scontrol show job <slurm_job_id>
• Get information about a completed or failed job: sacct -j <slurm_job_id>.
• See ALL your jobs: squeue --me
• Cancel ALL your jobs: scancel --me
• View current QOS policies:

  sacctmgr show qos format=Name%20,Priority,Flags%30,MaxWall,MaxTRESPU%20,MaxJobsPU,MaxSubmitPU,MaxTRESPA%25
  

• Find out which accounts your username has access to:

  sacctmgr list associations
  # or
  sacctmgr -n -p list assoc where user=$USER | awk '-F|' '{print "   "$2}'
  

Tab Completion

GridTK supports tab completion for the gridtk command. To enable it, add the following line to your ~/.bashrc file:

eval "$(_GRIDTK_COMPLETE=bash_source gridtk)"

or for zsh add the following line to your ~/.zshrc file:

eval "$(_GRIDTK_COMPLETE=zsh_source gridtk)"