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https://github.com/Duke-GCB/calrissian
CWL on Kubernetes
https://github.com/Duke-GCB/calrissian
cwl cwl-workflow cwl-workflows kubernetes
Last synced: 3 months ago
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CWL on Kubernetes
- Host: GitHub
- URL: https://github.com/Duke-GCB/calrissian
- Owner: Duke-GCB
- License: mit
- Created: 2018-12-18T20:03:14.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2024-05-02T21:58:26.000Z (9 months ago)
- Last Synced: 2024-10-05T08:09:33.361Z (4 months ago)
- Topics: cwl, cwl-workflow, cwl-workflows, kubernetes
- Language: Python
- Homepage: https://duke-gcb.github.io/calrissian/
- Size: 1.19 MB
- Stars: 42
- Watchers: 7
- Forks: 16
- Open Issues: 22
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Codemeta: codemeta.json
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README
# Calrissian
CWL on Kubernetes
[](https://badge.fury.io/py/calrissian)
## Overview
Calrissian is a [CWL](https://www.commonwl.org) implementation designed to run inside a Kubernetes cluster. Its goal is to be highly efficient and scalable, taking advantage of high capacity clusters to run many steps in parallel.
## Cluster Requirements
Calrissian requires a [Kubernetes](https://kubernetes.io) or [Openshift](https://www.openshift.com)/[OKD](https://www.okd.io) cluster, configured to provision [PersistentVolumes](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with the `ReadWriteMany` access mode. Kubernetes installers and cloud providers don't usually include this type of storage, so it may require additional configuration.
Calrissian has been tested with NFS using the [nfs-client-provisioner](https://github.com/kubernetes-incubator/external-storage/tree/master/nfs-client) and with GlusterFS using [OKD Containerized GlusterFS](https://docs.okd.io/3.11/install_config/persistent_storage/persistent_storage_glusterfs.html). Many cloud providers have an NFS offering, which integrates easily using the nfs-client-provisioner.
## Scalability / Resource Requirements
Calrissian is designed to issue tasks in parallel if they are independent, and thanks to Kubernetes, should be able to run very large parallel workloads.
When running `calrissian`, you must provide a limit the the number of CPU cores (`--max-cores`) and RAM megabytes (`--max-ram`) to use concurrently. Calrissian will use CWL [ResourceRequirements](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement) to track usage and stay within the limits provided. We highly recommend using accurate ResourceRequirements in your workloads, so that they can be scheduled efficiently and are less likely to be terminated or refused by the cluster.
`calrissian` parameters can be provided via a JSON configuration file either stored under `~/.calrissian/default.json` or provided via the `--conf` option.
Below an example of such a file:
```json
{
"max_ram": "16G",
"max_cores": "10",
"outdir": "/calrissian",
"tmpdir_prefix": "/calrissian/tmp"
}
```
## CWL Conformance
Calrissian leverages [cwltool](https://github.com/common-workflow-language/cwltool) heavily and most conformance tests for CWL v1.0. Please see [conformance](conformance) for further details and processes.
To view open issues related to conformance, see the [conformance](https://github.com/Duke-GCB/calrissian/issues?q=is%3Aopen+is%3Aissue+label%3Aconformance) label on the issue tracker.
## Setup
Please see [examples](examples) for installation and setup instructions.
## Environment Variables
Calrissian's behaviors can be customized by setting the following environment variables in the container specification.
### Pod lifecycle
By default, pods for a job step will be deleted after termination
- `CALRISSIAN_DELETE_PODS`: Default `true`. If `false`, job step pods will not be deleted.
### Kubernetes API retries
When encountering a Kubernetes API exception, Calrissian uses a library to retry API calls with an exponential backoff. See the [tenacity documentation](https://tenacity.readthedocs.io/en/latest/index.html#waiting-before-retrying) for details.
- `RETRY_MULTIPLIER`: Default `5`. Unit for multiplying the exponent interval.
- `RETRY_MIN`: Default `5`. Minimum interval between retries.
- `RETRY_MAX`: Default `1200`. Maximum interval between retries.
- `RETRY_ATTEMPTS`: Default `10`. Max number of retries before giving up.