arvados / arvados-k8s

Arvados is a free software distributed computing platform for bioinformatics, data science, and high throughput analysis of massive data sets. Arvados supports a variety of cloud, cluster and HPC environments.

Arvados on Kubernetes

This repository contains a Helm chart for Arvados.

Documentation can be found at http://doc.arvados.org/install/arvados-on-kubernetes.html

Community

The arvados/community channel channel at gitter.im is available for live discussion and support.

The Arvados user mailing list is a forum for general discussion, questions, and news about Arvados development. The Arvados developer mailing list is a forum for more technical discussion, intended for developers and contributors to Arvados.

Development

Arvados public bug tracker

Continuous integration

Instructions for setting up a development environment and working on specific components can be found on the "Hacking Arvados" page of the Arvados wiki.

Contributing

When making a pull request, please ensure every git commit message includes a one-line Developer Certificate of Origin. If you have already made commits without it, fix them with git commit --amend or git rebase.

When adding a file, please make sure to add the appropriate copyright header, as described in the Coding Standards.

Licensing

Arvados is Free Software. See COPYING for information about Arvados Free Software licenses.

arvados-k8s's Issues

Keep server configuration

I am follow the instuctions here: https://doc.arvados.org/v2.0/install/arvados-on-kubernetes-minikube.html.

When looking at the pods kubectl get pods I found that the keep servers didn't start, the pod logs said it couldn't create keepdata/because it already existed. When I make a change to file charts/arvados/templates/keep-store-deployment.yaml to remove the command mkdir /keepdata && from the arvados-keep-store container command, it starts.

However, I can't run the tests/minikube.sh command:

./minikube.sh 
Sat 27 Feb 09:29:31 GMT 2021
Sat 27 Feb 09:29:31 GMT 2021
cluster health OK
uploading requirements for CWL hasher
2021-02-27 09:29:32 arvados.arv_put[471216] INFO: Creating new cache file at [..]/.cache/arvados/arv-put/4e225fee0fa635477f56d1e722560dfa
0M / 0M 100.0% 2021-02-27 09:29:32 arvados.arv_put[471216] INFO: 

2021-02-27 09:29:32 arvados.arv_put[471216] INFO: Collection saved as 'Saved at 2021-02-27 09:29:32 UTC by [..]'
vwxyz-4zz18-cfwmwwouqwsvjpw
uploading Arvados jobs image for CWL hasher
running CWL hasher
INFO /home/[..]/bin/cwl-runner 2.1.2, arvados-python-client 2.1.2, cwltool 3.0.20200807132242
INFO Resolved 'hasher-workflow.cwl' to '[..]/arvados-k8s/tests/cwl-diagnostics-hasher/hasher-workflow.cwl'
INFO hasher-workflow.cwl:1:1: Unknown hint WorkReuse
INFO Using cluster vwxyz (https://192.168.49.2:444/)
INFO Using collection cache size 256 MiB
INFO hasher-workflow.cwl:1:1: Unknown hint WorkReuse
INFO [container hasher-workflow.cwl] submitted container_request vwxyz-xvhdp-40c7qtbemiuv2z6
INFO [container hasher-workflow.cwl] vwxyz-xvhdp-40c7qtbemiuv2z6 is Final
ERROR [container hasher-workflow.cwl] (vwxyz-dz642-4fn7xqmlmk5xcme) error log:
  ** log is empty **
ERROR Overall process status is permanentFail
INFO Final output collection None
{}
WARNING Final process status is permanentFail