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Jarett DeAngelis
@jdkruzr
when I try to do that first line after I become_user git with Ansible, I get this: FATAL: unknown git/gitolite command: 'cat .ssh/id_rsa.pub'
in fact it also happens on the command line without Ansible:
git@arvados-api:/home/jtd$ ssh -o stricthostkeychecking=no localhost cat .ssh/id_rsa.pub
FATAL: unknown git/gitolite command: 'cat .ssh/id_rsa.pub'
why is it trying to execute gitolite? did gitolite become its shell at some point?
(I just checked, the answer is no)
and why do we want to delete .ssh/authorized_keys after all that work?
Peter Amstutz
@tetron
@/all the Arvados biweekly user group meeting will be starting shortly https://forum.arvados.org/t/arvados-user-group-video-chat/47
Maxat Kulmanov
@coolmaksat
Hi,
I'm getting this error after upgrading to the latest version:
2021-07-13T07:58:13.785717454Z ERROR Unhandled error:
2021-07-13T07:58:13.785717454Z 'NoneType' object has no attribute 'target'
2021-07-13T07:58:13.785717454Z Traceback (most recent call last):
2021-07-13T07:58:13.785717454Z File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/main.py", line 1205, in main
2021-07-13T07:58:13.785717454Z tool, initialized_job_order_object, runtimeContext, logger=_logger
2021-07-13T07:58:13.785717454Z File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 775, in arv_executor
2021-07-13T07:58:13.785717454Z self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output)
2021-07-13T07:58:13.785717454Z File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 467, in make_output_collection
2021-07-13T07:58:13.785717454Z adjustFileObjs(outputObj, rewrite)
2021-07-13T07:58:13.785717454Z File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/utils.py", line 353, in adjustFileObjs
2021-07-13T07:58:13.785717454Z visit_class(rec, ("File",), op)
2021-07-13T07:58:13.785717454Z File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/utils.py", line 295, in visit_class
2021-07-13T07:58:13.785717454Z visit_class(rec[d], cls, op)
2021-07-13T07:58:13.785717454Z File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/utils.py", line 293, in visit_class
2021-07-13T07:58:13.785717454Z op(rec)
2021-07-13T07:58:13.785717454Z File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 461, in rewrite
2021-07-13T07:58:13.785717454Z fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
2021-07-13T07:58:13.785717454Z AttributeError: 'NoneType' object has no attribute 'target'
All steps in the workflow are finished successfully
and it was running with version 2.1
Maxat Kulmanov
@coolmaksat
I found that it happens when workflow has an output of type Directory
Peter Amstutz
@tetron
@coolmaksat do you want to post some of your CWL on here https://forum.arvados.org/
Maxat Kulmanov
@coolmaksat
Okay, thank you
Peter Amstutz
@tetron
@/all Arvados 2.2.1 is released: https://arvados.org/release-notes/2.2.1/
Jarett DeAngelis
@jdkruzr
@tetron is 2.2 compatible with Ubuntu 20.04 now?
I feel like that was in a changelog at some point
or a plan somewhere
Ward Vandewege
@cure
@jdkruzr yes - cf. the 2.2.0 release notes: https://arvados.org/release-notes/2.2.0/
Jarett DeAngelis
@jdkruzr
thanks @cure. also is it normal that previews of items in a collection work in wb1 but are not present in wb2?
images for example
Cibin S B
@cibinsb
Hi All,
Following from the instuctions here: https://doc.arvados.org/v2.0/install/arvados-on-kubernetes-minikube.html. I installed arvados on minikube successfully, however when ran tests/minikube.sh command:
(py36) cibin@cibins-beast-13-9380:~/EBI/arvados-k8s/tests$ ./minikube.sh 
Monday 26 July 2021 10:26:47 PM IST
Monday 26 July 2021 10:26:48 PM IST
cluster health OK
uploading requirements for CWL hasher
2021-07-26 22:26:48 arvados.arv_put[202690] INFO: Creating new cache file at /home/cibin/.cache/arvados/arv-put/349acdb1f48e6a0369aa03e95afda6c7
0M / 0M 100.0% 2021-07-26 22:26:49 arvados.arv_put[202690] INFO: 

2021-07-26 22:26:49 arvados.arv_put[202690] INFO: Collection saved as 'Saved at 2021-07-26 16:56:48 UTC by cibin@cibins-beast-13-9380'
vwxyz-4zz18-zkx2s1uzrhznn4d
uploading Arvados jobs image for CWL hasher
running CWL hasher
INFO /home/cibin/anaconda3/envs/py36/bin/cwl-runner 2.2.1, arvados-python-client 2.2.1, cwltool 3.0.20210319143721
INFO Resolved 'hasher-workflow.cwl' to 'file:///home/cibin/EBI/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/)
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-z35egb6cw09u3a3
INFO Monitor workflow progress at https://192.168.49.2/processes/vwxyz-xvhdp-z35egb6cw09u3a3
INFO [container hasher-workflow.cwl] vwxyz-xvhdp-z35egb6cw09u3a3 is Final
ERROR [container hasher-workflow.cwl] (vwxyz-dz642-ua97ck3433k2qvx) error log:
  ** log is empty **
ERROR Overall process status is permanentFail
INFO Final output collection None
INFO Output at https://192.168.49.2/collections/None
{}
WARNING Final process status is permanentFail
2 replies
Ward Vandewege
@cure
@cibinsb I can reproduce this failure, I will have a look
5 replies
Ward Vandewege
@cure

thanks @cure. also is it normal that previews of items in a collection work in wb1 but are not present in wb2?

@jdkruzr cf. https://doc.arvados.org/v2.2/install/install-keep-web.html, the note:

Whether you choose to serve collections from their own subdomain or from a single domain, it’s important to keep in mind that they should be served from me same site as Workbench for the inline previews to work.

Please check keep-web’s URL pattern guide to learn more.

https://doc.arvados.org/api/keep-web-urls.html#same-site

Ward Vandewege
@cure
Can you try again @cibinsb ? Problem found and fixed.
Cibin S B
@cibinsb
Thanks @cure, Its working now
Ward Vandewege
@cure
excellent! thanks for confirming. We'll be adding some monitoring of the package repositories to make sure this (missing published packages in the stable repo) does not happen again.
Ryan Golhar
@golharam
Hi all - I'm going through the users guide and discovered a discrepency in steps. Specifically https://doc.arvados.org/v2.2/user/tutorials/wgs-tutorial.html, from step 3a setting up a new project to step 3b working with collections. There is no transition.
EDIT: Nevermind, its there, just wasn't clear as II was reading it.
Peter Amstutz
@tetron:matrix.org
[m]
hi @golharam
Peter Amstutz
@tetron
we'll take that as feedback to improve the tutorial text
we have a ticket of details to polish in the tutorial, I added your comment https://dev.arvados.org/issues/17846
Peter Amstutz
@tetron
@/all the Arvados user group meeting is starting soon: https://meet.google.com/eig-fvsw-xvd
Gudule JR
@GuduleJR_twitter
Hi all... Coming back with Arvados... I would like to know if the "Multi host Arvados" is posible for a provate network, tahts is, to install all of the services for a storage managment, using somne local CA certificates? That's because i have to proove on my staff that Arvados is viable, to have some public ip....
Peter Amstutz
@tetron
yes, you can use a local CA for your certificates
crusoe
@mr-c:matrix.org
[m]
I've seen multiple references to https://gitlab.com/iidsgt/arv-helm but that returns 404 ; where did that get moved to?
Peter Amstutz
@tetron
maybe @osmanwa knows?
Gudule JR
@GuduleJR_twitter
@tetron ok, thank's I supose I have to use salt to autoticaly transfer the certificates to each servers....
Tom Schoonjans
@tschoonj

Hi all,

We are currently setting up a test Arvados cluster and I ran into some unusual behaviour regarding the default replication number: even though I have set this number to 1 in config.yml (Clusters.ClusterID.Collections.DefaultReplication), and this is confirmed in the output of http://ClusterID.our.domain.com/arvados/v1/config, this does not appear to be replicated in the Python SDK:

$ /usr/share/python3/dist/python3-arvados-python-client/bin/python
Python 3.8.10 (default, Jun  2 2021, 10:49:15) 
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import arvados
>>> arvados.api('v1')._rootDesc['defaultCollectionReplication']
2

Any thoughts on why this happens? Thanks in advance!!

Peter Amstutz
@tetron:matrix.org
[m]
good catch, let me see
Tom Schoonjans
@tschoonj
thanks Peter
Peter Amstutz
@tetron:matrix.org
[m]
oh, perhaps you have a cached discovery document?
Tom Schoonjans
@tschoonj
not sure what that is
I actually ran into this problem through arv-put
Peter Amstutz
@tetron:matrix.org
[m]
rm -r ~/.cache/arvados
Tom Schoonjans
@tschoonj
ok
this works!
thanks Peter!!
Peter Amstutz
@tetron:matrix.org
[m]
by the way we have an Arvados use group meeting today in half an hour
Tom Schoonjans
@tschoonj
I know, but won't be able to make it due to childcare :-(
Peter Amstutz
@tetron
@/all The user group video chat is happening soon https://forum.arvados.org/t/arvados-user-group-video-chat/47/8