qsub is a command line tool used for submitting batch jobs. It has basic functionality defined in the POSIX standard. Various high-performance computing (HPC) job schedulers, such as Grid Engine, SLURM, LSF, and Torque, offer an extended version of qsub with additional features.
This repository offers a simplified implementation of qsub for running jobs locally, in Docker containers, on Kubernetes, Google Batch, PubSub, and more. It enables users to easily submit and manage batch jobs in different environments.
qsub can be build directly from the sources or alternatively pre-build binaries for darwin and linux can be downloaded from the builds dir.
By using a DRMAA2 compatible JSON file jobs can be submitted to several backends:
- Google Batch (-b googlebatch)
- Local Process (-b process)
- Docker (-b docker)
- Sending a DRMAA2 JobTemplate wrapped as CloudEvent into Google PubSub (-b pubsub)
- Sending a job to a remote "qsub --server" (-b server)
See some examples here.
qsub -b process -j ./jobtemplate.json
In order to let the sleep command run in the Kubernetes cluster which is selected in the current context (./kube/config) you need to specify the container image as well as the command to be executed in the container (potentially with its arguments).
qsub --image busybox:latest sleep 123
It returns the ID of the job.
The container image can also be set beforehand as environment variable.
export QSUB_IMAGE=busybox:latest
qsub sleep 123
The corresponding pods can be showed with the ID returned back on command line:
kubectl describe pod -l job-name=ID
The image name (--img) as well as the command which should be executed in the container derived from the image are mandatory.
Following optional arguments are currently available.
The job name must be unique otherwise job submission will fail.
qsub --image busybox:latest -N unique sleep 123
Submitted job with ID unique
kubectl get jobs unique
NAME DESIRED SUCCESSFUL AGE
unique 1 0 14s
Jobs can be submitted to a specific kubernetes namespace.
qsub --namespace default --image busybox:latest sleep 123
Kubernetes allows to attach labels to pods. Labels are key-value pairs which can be defined with the -l argument.
Environment variables for the jobs can be set by passing them into -v. There are two ways of doing so: as key-value pairs, or just by name.
Following example sets ENV1 to VALUE1 and ENV2 to VALUE2 (using the value from the current context).
export ENV2=VALUE2
qsub --image busybox:latest -v ENV1=VALUE1,ENV2 sleep 123
In order to let the job be scheduled by a non-default scheduler (like poseidon or kube-batch) the --scheduler argument can be used.
qsub --scheduler poseidon --img busybox:latest sleep 123