Activity

From 04/29/2015 to 05/28/2015

05/28/2015

09:13 pm Revision 5e0dd2c6 (arvados): 6146: Exit TEMPFAIL early (without failing the job) if worker nodes ...
This is meant to improve the way we handle a couple of edge cases.
1. A worker node doesn't get bootstrapped properl...
Tom Clegg
08:16 pm Revision 36dd29f8 (arvados): 6146: Exit TEMPFAIL early (without failing the job) if worker nodes ...
This is meant to improve the way we handle a couple of edge cases.
1. A worker node doesn't get bootstrapped properl...
Tom Clegg
08:11 pm Story #6089 (Resolved): Write development update blog (first three days of sprint)
Brett Smith
08:05 pm May development review: Project promotion and Keep performance
We want Arvados to be the premier way for bioinformaticians and data scientists to collaborate. And as an open sourc... Brett Smith
06:53 pm Revision 8884a9ff (arvados): Merge branch 'master' into 6087-collection-timing
Radhika Chippada
05:08 pm Bug #6175 (New): [Workbench] Add social sharing buttons to public projects [and other data?]
You know, for Twitter, Facebook, Google+, etc. Brett Smith
02:57 pm Bug #6174 (New): [Workbench] Propagate old search engine meta tags in sync with Open Graph data
We set some very generic meta tags in the header of all Workbench pages. For a more consistent appearance across sea... Brett Smith
02:54 pm Bug #6173 (New): [Workbench] Make public data crawlable
Right now our application layout sets the noindex and nofollow meta tags on every page, telling search engines to not... Brett Smith
02:48 pm Bug #6172 (New): [Workbench] Breadcrumbs can occupy multiple rows when the screen is narrow
This looks bad. If your window actually is small, it can cause the breadcrumbs to take up too much space. Make sure... Brett Smith
02:44 pm Bug #3588 (Duplicate): [Workbench] When looking at a project shared with you (but not owned by yo...
Duplicates #3573. Brett Smith
02:37 pm Story #6171 (Resolved): [FUSE] Document the writable FUSE mount
In an appropriate place in the user documentation, introduce the writable FUSE mount. Discuss how it can be used in ... Brett Smith
02:00 am Bug #6141: [Docs] Don't hardcode https:// in links to workbench
Radhika Chippada wrote:
> Review comments: LGTM
>
> Please note that doc.arvados.org probably needs to update the...
Ward Vandewege

05/27/2015

09:34 pm Bug #6098: [API] slow search? SQL query
After deploying this evening, still slow (though the api server was under very heavy load at the time):... Ward Vandewege
12:58 pm Bug #6098: [API] slow search? SQL query
LGTM
Just one additional comment request: can you please add a comment to the effect "check if search indexes are ...
Radhika Chippada
08:24 pm Story #6089 (In Progress): Write development update blog (first three days of sprint)
Brett Smith
08:10 pm Revision 7a53d874 (arvados): Merge branch '6146-retry-install' refs #6146
Tom Clegg
07:48 pm Revision 1b5c30eb (arvados): 6146: Retry install (max 3 attempts) if install script fails with no...
Also: if install fails, croak() instead of exit(1) so we still get a log file. Tom Clegg
07:38 pm Revision fa9fc5ab (arvados): Merge branch 'master' into 6093-refresh-docs
Conflicts:
doc/user/tutorials/tutorial-submit-job.html.textile.liquid
Radhika Chippada
07:35 pm Story #6057 (Resolved): [Workbench] Provide an attractive index of public projects
Applied in changeset arvados|commit:32038d56fbfe5b635b1c53f247aea9abcca2285c. Radhika Chippada
03:45 pm Story #6057: [Workbench] Provide an attractive index of public projects
At commit:a2eb98f
In the new controller tests, the first assertion is superfluous since it's a strict subset of th...
Tom Clegg
07:28 pm Task #6158 (Resolved): Review 5548-test-cwltool in arvados-dev
Peter Amstutz
05:50 pm Task #6158 (In Progress): Review 5548-test-cwltool in arvados-dev
Nico César
04:31 pm Task #6158 (Resolved): Review 5548-test-cwltool in arvados-dev
Peter Amstutz
07:27 pm Revision 32038d56 (arvados): closes #6057
Merge branch '6057-public-projects-page' Radhika Chippada
07:26 pm Revision c51a3888 (arvados): 6057: few more minor tweaks
Radhika Chippada
07:22 pm Revision a73f5150 (arvados): 6146: Retry install (max 3 attempts) if install script fails with no...
Also: if install fails, croak() instead of exit(1) so we still get a log file. Tom Clegg
07:11 pm Revision 3101fea5 (arvados): Merge branch '6141-doc-workbench-links' refs #6141
Peter Amstutz
07:03 pm Revision 6fed8498 (arvados): Merge branch 'master' into 6057-public-projects-page
Radhika Chippada
07:03 pm Bug #6141: [Docs] Don't hardcode https:// in links to workbench
Review comments: LGTM
Please note that doc.arvados.org probably needs to update the *arvados_workbench_host* attri...
Radhika Chippada
07:00 pm Task #6155 (In Progress): Review 6141-doc-workbench-links
Radhika Chippada
02:28 pm Task #6155 (Resolved): Review 6141-doc-workbench-links
Peter Amstutz
06:40 pm Revision 44eab398 (arvados-dev): Merge branch '5548-test-cwltool' refs #5548
Peter Amstutz
06:40 pm Revision 44eab398 (arvados): Merge branch '5548-test-cwltool' refs #5548
Peter Amstutz
06:31 pm Task #5629 (Resolved): Write test script
Peter Amstutz
04:30 pm Task #5629 (In Progress): Write test script
Peter Amstutz
06:25 pm Story #6138 (Resolved): [Docker] Docker install uses standalone SSO server
Applied in changeset arvados|commit:e73222a8d0c18b159ae3d8b53b54474650bdda16. Peter Amstutz
06:19 pm Story #6138: [Docker] Docker install uses standalone SSO server
checked a7d558d6c2db242a6555c7f397cb4d91618aa13c
looks good to me
Nico César
06:23 pm Task #6128 (Resolved): Test Docker install
Peter Amstutz
06:23 pm Task #6133 (Resolved): Review 6090-docker-use-local-sso
Peter Amstutz
06:23 pm Revision e73222a8 (arvados): Merge branch '6090-docker-use-local-sso' closes #6138
Peter Amstutz
06:18 pm Revision a572ef64 (arvados-dev): 5548: Remove git commands from run-cwl-tests. Remove cwltool fr...
Peter Amstutz
06:18 pm Revision a572ef64 (arvados): 5548: Remove git commands from run-cwl-tests. Remove cwltool from b...
Peter Amstutz
06:07 pm Story #5548: [CWL/OPS] Jenkins runs cwltool tests
reviewing commit:ac6798733ce11d6a3410bf1da639cb3e5a84047f
L160 I see that this logic wont be ever excecuted in jen...
Nico César
04:42 pm Revision d9214af1 (arvados): Add GPG key for RVM installation in the doc.
No issue # Ward Vandewege
04:30 pm Revision ac679873 (arvados-dev): 5548: Script to test, build and upload common workflow language ...
docker images. Peter Amstutz
04:30 pm Revision ac679873 (arvados): 5548: Script to test, build and upload common workflow language pack...
docker images. Peter Amstutz
04:13 pm Bug #6157 (Resolved): [Documentation] Explain extra steps needed when compute hostnames are not fooN
h3. background
Changing slurm config files, and keeping them synchronized across controller+workers, is a bit pain...
Tom Clegg
04:07 pm Bug #6156 (Resolved): [API] Node record accommodates setups where hostnames are set statically by...
h2. Goals
Have the process documented in our "compute node install guide":http://doc.arvados.org/install/install-c...
Tom Clegg
02:51 pm Task #6150 (In Progress): Test correct index usage with "explain analyze"
Tom Clegg
01:09 pm Task #6150 (Closed): Test correct index usage with "explain analyze"
Tom Clegg
02:27 pm Task #6137 (In Progress): Fix documentation links in docker build
Peter Amstutz
02:26 pm Task #6136 (Resolved): review 6135-docker-git-tag
Nico César
02:20 pm Task #6135 (Resolved): 'docker' jenkins jobs has to tag with the git revision on push
Applied in changeset arvados-dev|commit:845e3998bb2b4175e947a20eea4ed530629a778b. Anonymous
02:16 pm Revision 845e3998 (arvados-dev): Merge branch '6135-docker-git-tag'
closes #6135
Conflicts:
jenkins/run-docker-tests.sh
Nico Cesar
02:16 pm Revision 845e3998 (arvados): Merge branch '6135-docker-git-tag'
closes #6135
Conflicts:
jenkins/run-docker-tests.sh
Nico Cesar
01:43 pm Task #6099 (Resolved): Finish fixing tests for draft2-updates
Peter Amstutz
01:43 pm Task #6097 (In Progress): Implement "id" loading
Peter Amstutz
01:23 pm Bug #6153 (Closed): SLURM_JOB_ID environment variable expiration persistence on compute node
A new user ran qr1hi-d1hrv-nfqsgixupqykgok and immediately ran into:
2015-05-27_12:02:56 srun: error: slurm_receiv...
Bryan Cosca
01:20 pm Bug #6152: [Docs] Eliminate `arv` dependency in compute node installer
gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 Peter Amstutz
01:16 pm Bug #6152 (Resolved): [Docs] Eliminate `arv` dependency in compute node installer
The ping script on the compute node install page uses @arv node create@. This adds a dependency on the entire Ruby s... Peter Amstutz
01:09 pm Task #6112 (Resolved): Review 6098-full-text-index 64cfaed
Tom Clegg
12:58 pm Task #6112 (In Progress): Review 6098-full-text-index 64cfaed
Radhika Chippada
01:06 pm Revision 59d68bda (arvados): Merge branch '6098-full-text-index' refs #6098
Tom Clegg
01:05 pm Revision 15009c10 (arvados): 6098: Recreate full text indexes with leading spaces, to persuade Po...
Tom Clegg
12:18 am Revision fc8cdf0a (arvados-dev): make single quotes around reponame optional...
apparently the git client, when using ext:: transports, does not send those
quotes
https://groups.google.com/forum/#...
Sitaram Chamarty
12:18 am Revision 4ed15ad8 (arvados-dev): create command: remove race condition...
Because of the pipe in the create command, 'gitolite git-config' and 'perms
-c' would run simultaneously. The proble...
Sitaram Chamarty

05/26/2015

11:02 pm Bug #6098 (In Progress): [API] slow search? SQL query
Radhika Chippada
07:31 pm Bug #6098: [API] slow search? SQL query
This query takes 1075ms.... Tom Clegg
05:46 pm Bug #6098: [API] slow search? SQL query
Removing the "uuid" field from the full text index (and query) moves my test query time from 1075ms to 4ms. Tom Clegg
03:18 pm Bug #6098: [API] slow search? SQL query
Definitely a full-text search problem ("explain" on the query minus the "@@" condition says 73ms). Presumably the ind... Tom Clegg
11:01 pm Story #6057: [Workbench] Provide an attractive index of public projects
Tom, thanks for the comments. I incorporated all those comments. Also, removed the integration tests and made them co... Radhika Chippada
10:58 pm Revision a2eb98fa (arvados): Merge branch 'master' into 6057-public-projects-page
Radhika Chippada
10:54 pm Revision b3e2782f (arvados): 6057: if /projects/public is accessed when anonymous config is not e...
Radhika Chippada
08:04 pm Revision 53b19718 (arvados): Merge branch 'master' into 6093-refresh-docs
Radhika Chippada
07:58 pm Bug #6149 (Resolved): [Crunch] Install step logs error message from `setup.py egg_info`
In https://cloud.curoverse.com/collections/fefe083539813d3a01108c90fa684f7c+85/qr1hi-8i9sb-74468yxq0cauxbw.log.txt
...
Bryan Cosca
07:57 pm Revision 2578f9c1 (arvados): 6093: one more
Radhika Chippada
07:51 pm Revision 7a47332f (arvados): 6093: a few more updates
Radhika Chippada
07:22 pm Task #6144 (Resolved): Review 6094-install-script-sigpipe @ e010ab7
Tom Clegg
02:31 pm Task #6144 (In Progress): Review 6094-install-script-sigpipe @ e010ab7
Brett Smith
07:21 pm Task #6122 (Resolved): Improve query performance (or prevent clients from doing it?)
Tom Clegg
07:21 pm Task #6106 (Closed): Add a performance test case that exposes the slow query
Tom Clegg
01:56 pm Task #6106 (In Progress): Add a performance test case that exposes the slow query
Tom Clegg
07:18 pm Revision 64cfaed1 (arvados): 6098: Recreate full text indexes with leading spaces, to persuade Po...
Tom Clegg
03:56 pm Revision 6bc89efd (arvados): 6093: some more doc updates.
Radhika Chippada
03:46 pm Revision b6a55136 (arvados): 6035: add support for --upload as an option
refs #6035 Nico Cesar
03:46 pm Revision b6a55136 (arvados-dev): 6035: add support for --upload as an option
refs #6035 Nico Cesar
02:31 pm Revision 9b67268f (arvados): Merge branch '6094-install-script-sigpipe' refs #6094
Tom Clegg
02:31 pm Revision d3fcdc7a (arvados): 6094: Propagate install script stderr+stdout to job log.
Tom Clegg
02:31 pm Bug #6094: [Crunch] Install script exited 141
Tom Clegg wrote:
> Brett Smith wrote:
> > this commit does not assign 1 to vec's lvalue
>
> Whoops, yes, that wa...
Brett Smith
02:26 pm Bug #6094: [Crunch] Install script exited 141
Brett Smith wrote:
> this commit does not assign 1 to vec's lvalue
Whoops, yes, that was an oversight. Amended (n...
Tom Clegg
02:14 pm Bug #6094: [Crunch] Install script exited 141
Reviewing commit:e010ab73 (literally, just that commit)
It looks like you intend to use the recipe in select's per...
Brett Smith
02:18 pm Revision c96f21fc (arvados): 6094: Propagate install script stderr+stdout to job log.
Tom Clegg
12:35 am Task #6117 (Resolved): Review 6095-arv-copy-preserve-object-order-wip
Applied in changeset arvados|commit:872cc3d79d99f5fc4b26b970c3d269ca363ea27c. Brett Smith
12:35 am Bug #6095 (Resolved): [SDKs] Make arv-copy preserve pipeline template component order
Applied in changeset arvados|commit:872cc3d79d99f5fc4b26b970c3d269ca363ea27c. Brett Smith
12:32 am Revision 872cc3d7 (arvados): Merge branch '6095-arv-copy-preserve-object-order-wip'
Closes #6095, #6117. Brett Smith
12:32 am Revision 79564b0a (arvados): 6095: arv-copy preserves order of copied JSON.
This means arv-copy no longer loses the order of pipeline template
components, which makes for a nicer presentation i...
Brett Smith

05/25/2015

10:36 pm Revision 8a2a84af (arvados): 6093: doc updates
Radhika Chippada
09:42 pm Story #6057: [Workbench] Provide an attractive index of public projects
Comments @ commit:1a0ba80
h3. Controller
If Workbench is not configured to serve public projects, I don't think...
Tom Clegg
08:43 pm Task #6115 (In Progress): Review branch: 6057-public-projects-page
Tom Clegg
08:42 pm Bug #6095: [SDKs] Make arv-copy preserve pipeline template component order
LGTM @ commit:2f64531 Tom Clegg
05:52 pm Task #6117 (In Progress): Review 6095-arv-copy-preserve-object-order-wip
Tom Clegg
05:25 pm Revision dab62e90 (arvados): 6087: Add big-manifest tests, with some finer-grained performance nu...
Tom Clegg
02:35 pm Revision ccfa3ebf (arvados): 6087: Use HTTPClient's compression feature (instead of adding the
Content-Encoding header ourselves). Rename config knob to describe
purpose instead of implementation.
Tom Clegg
02:23 pm Revision cc988c81 (arvados): 6087: Compute portable_data_hash only once during check_signatures.
Tom Clegg
02:21 pm Revision 0ded94e1 (arvados): 6087: Use app-configured key by default for blob signing and verific...
Tom Clegg

05/24/2015

10:33 pm Bug #6095: [SDKs] Make arv-copy preserve pipeline template component order
6095-arv-copy-preserve-object-order-wip is up for review. A couple of notes:
* If you look at the original JsonMo...
Brett Smith
10:02 pm Revision 2f64531d (arvados): 6095: arv-copy preserves order of copied JSON.
This means arv-copy no longer loses the order of pipeline template
components, which makes for a nicer presentation i...
Brett Smith

05/23/2015

05:36 pm Bug #6016: No pipeline to run with docker install
Mohammad Zia wrote:
> Hello,
>
> I installed the docker version of Arvados today and tried to follow the tutorial...
Albert Vilella

05/22/2015

09:43 pm Task #6144 (Resolved): Review 6094-install-script-sigpipe @ e010ab7
Tom Clegg
09:42 pm Revision 0f125dd5 (arvados): Merge branch '6094-install-script-sigpipe' (early part) refs #6094
Tom Clegg
09:41 pm Task #6111 (Resolved): Review 6094-install-script-sigpipe
Tom Clegg
09:39 pm Revision e010ab73 (arvados): 6094: Propagate install script stderr+stdout to job log.
Tom Clegg
09:29 pm Bug #6094: [Crunch] Install script exited 141
6094-install-script-sigpipe @ commit:b4c2a96 ensures the DATA section gets consumed even in that "don't need to extra... Tom Clegg
07:57 pm Bug #6094: [Crunch] Install script exited 141
I'm satisfied with that explanation, and I'm satisfied with commit:fbcc5ab if it passes testing. Thanks. Brett Smith
07:02 pm Bug #6094: [Crunch] Install script exited 141
This doesn't show the warning message "srun: error: compute32: task 0: Exited with exit code 141" but it does seem pr... Tom Clegg
06:56 pm Bug #6094 (In Progress): [Crunch] Install script exited 141
Brett Smith
03:59 pm Bug #6094: [Crunch] Install script exited 141
I created a tar archived that combines the requested Arvados SDK version and script version. That's 15144960 bytes. ... Brett Smith
09:07 pm Bug #6095 (In Progress): [SDKs] Make arv-copy preserve pipeline template component order
Brett Smith
08:56 pm Task #6136 (In Progress): review 6135-docker-git-tag
Nico César
01:28 pm Task #6136 (Resolved): review 6135-docker-git-tag
Nico César
08:53 pm Task #6135: 'docker' jenkins jobs has to tag with the git revision on push
added --tag support in 6096-docker-git-tag (arvados-dev) Nico César
08:32 pm Task #6135: 'docker' jenkins jobs has to tag with the git revision on push
I think the best place to do this is:
* add a parameter --tags to run-docker-tests
* "docker tag $ID" before t...
Nico César
07:44 pm Task #6135 (In Progress): 'docker' jenkins jobs has to tag with the git revision on push
mental note... Nico César
01:28 pm Task #6135 (Resolved): 'docker' jenkins jobs has to tag with the git revision on push
Nico César
08:52 pm Revision a1fe656e (arvados-dev): added --tags support
refs #6135 Nico Cesar
08:40 pm Revision 1a0ba80d (arvados): Merge branch 'master' into 6057-public-projects-page
Radhika Chippada
08:39 pm Revision 71f1ccba (arvados): 6057: add projects/public page, which lists publicly accessible proj...
Radhika Chippada
08:32 pm Revision a996653c (arvados-dev): 6141: Add https:// to arvados_workbench_host
Peter Amstutz
08:16 pm Bug #6142 (Resolved): [Node Manager] When canceling a SLURM shutdown, check state before resuming...
Node Manager's SLURM dispatcher always tries to resume the node in SLURM when a shutdown is canceled. However, this ... Brett Smith
08:13 pm Revision 80d57cdc (arvados): 6141: Remove hard-coded "https://" from "https://{{site.arvados_work...
Peter Amstutz
07:40 pm Revision fbcc5ab5 (arvados): 6094: Consider arvados_sdk_version (not just script_version) when
deciding there's no need to extract or install anything. Tom Clegg
07:39 pm Revision b4c2a96e (arvados): 6094: Avoid SIGPIPE by consuming DATA section even when it's not nee...
Tom Clegg
07:35 pm Bug #6141 (Resolved): [Docs] Don't hardcode https:// in links to workbench
Peter Amstutz
07:34 pm Story #6138: [Docker] Docker install uses standalone SSO server
Nico Cesar wrote:
> reviewing 6090-docker-use-local-sso commit ae3bb0033a24a38489c49ffc26e5a5e8fd93c160
>
>
> h...
Peter Amstutz
03:35 pm Story #6138: [Docker] Docker install uses standalone SSO server
So I cant really test this in my machine... I have space restrictions and SSD drive is incredible slow. Options here? Nico César
03:18 pm Story #6138: [Docker] Docker install uses standalone SSO server
reviewing 6090-docker-use-local-sso commit ae3bb0033a24a38489c49ffc26e5a5e8fd93c160
h3. docker/arvdock
* line...
Nico César
02:54 pm Story #6138 (Resolved): [Docker] Docker install uses standalone SSO server
Peter Amstutz
07:32 pm Revision a7d558d6 (arvados): 6138: Added --domain to set ARVADOS_DOMAIN. Removed useless comment...
Peter Amstutz
07:32 pm Revision 1e7b6aa1 (arvados): Merge branch '6035-docker-upload-option'
closes #6035 Nico Cesar
07:32 pm Revision 1e7b6aa1 (arvados-dev): Merge branch '6035-docker-upload-option'
closes #6035 Nico Cesar
07:28 pm Story #6057 (In Progress): [Workbench] Provide an attractive index of public projects
Radhika Chippada
05:27 pm Story #6057: [Workbench] Provide an attractive index of public projects
Discussed this with Tom and some highlights:
* Let's do the basic public projects display first. We will look into...
Radhika Chippada
07:18 pm Revision bb480826 (arvados-dev): style and fashion for classy 'if' statements
refs #6035 Nico Cesar
07:18 pm Revision bb480826 (arvados): style and fashion for classy 'if' statements
refs #6035 Nico Cesar
06:56 pm Support #5833: Cannot get Arvados installed
Check ticket_5833.txt
I was unable to reproduce the error in a brand new instance (this is in GCE ) running Ubuntu...
Nico César
06:51 pm Support #5833: Cannot get Arvados installed
By The Way, try a quick ... Nico César
06:07 pm Support #5833: Cannot get Arvados installed
Thanks Darshan for the detailed information, I'll respond inline
Darshan Singh wrote:
(..)
> darshan@Linux2:~$ ...
Nico César
05:41 pm Story #3408: [Keep] Implement Production Data Manager
Okay, I was able to run data manager against my local development instance and get a report.
Scratch one of my pri...
Peter Amstutz
03:20 pm Story #3408: [Keep] Implement Production Data Manager
Also, API server provides microsecond timestamps, but it looks like datamanager is truncating that to whole seconds. ... Peter Amstutz
03:14 pm Story #3408: [Keep] Implement Production Data Manager
I ran it without any arguments and here's what I got:... Peter Amstutz
02:16 pm Story #3408: [Keep] Implement Production Data Manager
More comments.
In @BuildPullLists@, I think the assignment @spl[destination] = pullList@ inside the @if !pullListExi...
Peter Amstutz
03:45 pm Bug #6139: [OPS] Jenkis Job arvados-api-server should create unique databases so it can ran in pa...
Current runs of Jenkins Job 'arvados-api-server' uses 'arvados-test' database. When multiple jobs are running they co... Nico César
03:39 pm Bug #6139 (Duplicate): [OPS] Jenkis Job arvados-api-server should create unique databases so it c...
Nico César
03:00 pm Task #6108 (In Progress): Review data manager
Peter Amstutz
02:57 pm Task #6099 (In Progress): Finish fixing tests for draft2-updates
Peter Amstutz
02:54 pm Task #6133 (In Progress): Review 6090-docker-use-local-sso
Peter Amstutz
02:54 pm Task #6133 (New): Review 6090-docker-use-local-sso
Peter Amstutz
02:18 pm Revision 77bf9668 (arvados-dev): 3408: Tests for datamanager
Peter Amstutz
02:03 pm Revision 3bf22ae1 (arvados): Add installation instructions for compute nodes; update the installa...
instructions for crunch dispatcher.
No issue #
Ward Vandewege
01:39 pm Task #6137 (Resolved): Fix documentation links in docker build
Peter Amstutz
01:30 pm Story #6096: [OPS] Implement a process to regularly deploy a Docker image for running jobs to Arv...
see #6135 . docker images will have tags Nico César
12:57 pm Story #6096: [OPS] Implement a process to regularly deploy a Docker image for running jobs to Arv...
mental note:
from #3847...
Nico César
04:08 am Revision 46b43471 (arvados): 6087: Add big-manifest tests, with some finer-grained performance nu...
Tom Clegg

05/21/2015

10:55 pm Story #6057: [Workbench] Provide an attractive index of public projects
Something like this should get public projects:... Tom Clegg
05:42 pm Story #6057: [Workbench] Provide an attractive index of public projects
In case it's useful, source:apps/workbench/app/views/projects/_show_featured.html.erb and source:apps/workbench/app/a... Tom Clegg
09:15 pm Revision 8b658d96 (arvados): Merge branch '6087-collection-timing' (early part) refs #6087 refs #...
Tom Clegg
09:12 pm Story #3408: [Keep] Implement Production Data Manager
Reviewing commit:5824ee2
* "DefaultReplicationLevel" should come from the "defaultCollectionReplication" key in th...
Peter Amstutz
08:58 pm Task #6133 (In Progress): Review 6090-docker-use-local-sso
Nico César
07:00 pm Task #6133 (Resolved): Review 6090-docker-use-local-sso
Peter Amstutz
08:51 pm Revision 1a2d8a73 (arvados): 6087: Get database time only once per manifest-signing/verifying eve...
Tom Clegg
08:19 pm Story #6096: [OPS] Implement a process to regularly deploy a Docker image for running jobs to Arv...
Ok .. I understand that we can do a new Jenkins job that triggers this update.
I see from "docker" Job:...
Nico César
07:34 pm Story #6096: [OPS] Implement a process to regularly deploy a Docker image for running jobs to Arv...
Nico Cesar wrote:
> As far as I understand this is as simple as:
>
> ...
Brett Smith
07:20 pm Story #6096 (In Progress): [OPS] Implement a process to regularly deploy a Docker image for runni...
As far as I understand this is as simple as:... Nico César
08:06 pm Revision 5d26f7e8 (arvados): Update tutorial pipeline page to match new definition.
No issue #. Brett Smith
07:00 pm Task #6102 (In Progress): IRC support
Peter Amstutz
07:00 pm Task #6128 (In Progress): Test Docker install
Peter Amstutz
07:00 pm Revision ae3bb003 (arvados): 6090: Docker install uses local SSO server instead of auth.curoverse...
clean up references to dev.arvados to use @@ARVADOS_DOMAIN@@. Peter Amstutz
06:52 pm Task #6056 (Resolved): Review puppet branch 3793-docker-image-cleaner-wip
Brett Smith
06:52 pm Bug #3793 (Resolved): [Crunch] Docker containers not removed consistently, filling disk
Ward Vandewege wrote:
> reviewing the puppet branch 3793-docker-image-cleaner-wip:
>
> * I think the compute_dock...
Brett Smith
06:49 pm Task #5870 (Closed): Test scaling performance on exome and whole genome
Bryan Cosca
06:36 pm Revision 6a1a627a (arvados-dev): 6035: add support for --upload as an option
refs #6035 Nico Cesar
06:36 pm Revision 6a1a627a (arvados): 6035: add support for --upload as an option
refs #6035 Nico Cesar
06:23 pm Revision 9b44bba3 (arvados): Update tutorial pipeline template definition.
This helps it run out of the box again.
No issue #.
Brett Smith
05:54 pm Bug #5850: All clients authenticate directly against SSO server without going through API server
I accidentally took a story task and treated it like a bug. Apologies to Tom. Brett Smith
05:53 pm Task #6131 (Resolved): Sort out browser and command line authentication mechanisms
Tom Clegg
04:10 pm Revision 59129909 (arvados): refs #6061
6061: set profiling_enabled to true in workbench application.default.yml for test env. Radhika Chippada
03:45 pm Story #3198: [FUSE] Writable streaming arv-mount
I think conflict filenames should avoid using ":" characters. They have a tendency to confuse programs that know abou... Tom Clegg
03:34 pm Revision 2b9864be (arvados): Merge branch '6061-add-performance-plots' refs #6061
Nico Cesar
03:34 pm Revision 2b9864be (arvados-dev): Merge branch '6061-add-performance-plots' refs #6061
Nico Cesar
03:33 pm Support #6055: [Support] Cannot log into VM
Hi Ward,
I am using the Arvados docker image and not the curoverse installation.
Thanks,
--Mohammad
Mohammad Zia
03:32 pm Revision cc7fb936 (arvados-dev): 3793: Fix how python3 fpm arguments are added.
The previous code would add arguments such that they could be
interpreted as the package version. Avoid this by addi...
Brett Smith
03:32 pm Revision 32f2a67e (arvados): Improve packaging of third-party Python 3 packages.
* Fix the bug where we're passing in "python3" as the vendor argument
to build_and_scp_deb.
* Build more dependenci...
Brett Smith
03:32 pm Revision eae444a7 (arvados): 5766: Remove "remove dependencies" step. Detect existing PyYAML faster.
Tom Clegg
03:32 pm Revision c4d584c5 (arvados): Tidy up sanity checks. Add checks for fuse.h, pyconfig.h, nginx.
Suggest how to fix missing dependencies.
No issue #
Tom Clegg
03:32 pm Revision 32f2a67e (arvados-dev): Improve packaging of third-party Python 3 packages.
* Fix the bug where we're passing in "python3" as the vendor argument
to build_and_scp_deb.
* Build more dependenci...
Brett Smith
03:32 pm Revision c4d584c5 (arvados-dev): Tidy up sanity checks. Add checks for fuse.h, pyconfig.h, nginx.
Suggest how to fix missing dependencies.
No issue #
Tom Clegg
03:32 pm Revision eae444a7 (arvados-dev): 5766: Remove "remove dependencies" step. Detect existing PyYAML ...
Tom Clegg
03:32 pm Revision cc7fb936 (arvados): 3793: Fix how python3 fpm arguments are added.
The previous code would add arguments such that they could be
interpreted as the package version. Avoid this by addi...
Brett Smith
03:32 pm Revision 31e86126 (arvados-dev): 6061: comment cleanup and final version tested. it works
closes #6061 Nico Cesar
03:32 pm Revision 31e86126 (arvados): 6061: comment cleanup and final version tested. it works
closes #6061 Nico Cesar
03:31 pm Revision 0f079375 (arvados-dev): adding 3 more test for the performance suite.
I'm guessing the names, lets see if they are good or not ...
refs #6061
Nico Cesar
03:31 pm Revision 23b42a86 (arvados-dev): 6061: plot data
added create plot data script to exit_cleanly()
3 initial test to use
Matching more generic test names
refs #6061
Nico Cesar
03:31 pm Revision 23b42a86 (arvados): 6061: plot data
added create plot data script to exit_cleanly()
3 initial test to use
Matching more generic test names
refs #6061
Nico Cesar
03:31 pm Revision 0f079375 (arvados): adding 3 more test for the performance suite.
I'm guessing the names, lets see if they are good or not ...
refs #6061
Nico Cesar
03:31 pm Revision 5b7e2250 (arvados): 5416: Terminate connections on the configured test database (not nec...
Tom Clegg
03:31 pm Revision 72c34579 (arvados): 5416: Add --retry flag: when a test suite fails, prompt to try that ...
Tom Clegg
03:31 pm Revision 42234907 (arvados): Be consistent in our package and binary naming:
arv-git-httpd becomes arvados-git-httpd
No issue #
Ward Vandewege
03:31 pm Revision ffa8b415 (arvados-dev): 5416: Support testargs for go bits, like "services/arv-git-httpd...
Tom Clegg
03:31 pm Revision a3465f97 (arvados-dev): 5416: Run keepproxy, arv-git-httpd, and SSL proxy services durin...
Tom Clegg
03:31 pm Revision 4bfcd9f1 (arvados): run-tests.sh can now run the arv-git-httpd tests too.
No issue # Ward Vandewege
03:31 pm Revision 1553f484 (arvados-dev): 5766: Make sure it doesn't try to fetch arvados packages from Py...
we only install the local ones. Peter Amstutz
03:31 pm Revision a3465f97 (arvados): 5416: Run keepproxy, arv-git-httpd, and SSL proxy services during Wo...
Tom Clegg
03:31 pm Revision 72c34579 (arvados-dev): 5416: Add --retry flag: when a test suite fails, prompt to try t...
Tom Clegg
03:31 pm Revision 4bfcd9f1 (arvados-dev): run-tests.sh can now run the arv-git-httpd tests too.
No issue # Ward Vandewege
03:31 pm Revision 123d3d77 (arvados-dev): 3793: Add services/dockercleaner to run-tests.sh.
Brett Smith
03:31 pm Revision ffa8b415 (arvados): 5416: Support testargs for go bits, like "services/arv-git-httpd_tes...
Tom Clegg
03:31 pm Revision 9a4afad1 (arvados-dev): 3793: Build Docker cleaner service in run-build-packages.sh.
Brett Smith
03:31 pm Revision a43a3fb3 (arvados-dev): adding the creation of plot data that jenkins plot pluging will ...
refs #6061 Nico Cesar
03:31 pm Revision 42234907 (arvados-dev): Be consistent in our package and binary naming:
arv-git-httpd becomes arvados-git-httpd
No issue #
Ward Vandewege
03:31 pm Revision 1553f484 (arvados): 5766: Make sure it doesn't try to fetch arvados packages from PyPi, ...
we only install the local ones. Peter Amstutz
03:31 pm Revision a43a3fb3 (arvados): adding the creation of plot data that jenkins plot pluging will be a...
refs #6061 Nico Cesar
03:31 pm Revision 9a4afad1 (arvados): 3793: Build Docker cleaner service in run-build-packages.sh.
Brett Smith
03:31 pm Revision 123d3d77 (arvados): 3793: Add services/dockercleaner to run-tests.sh.
Brett Smith
03:31 pm Revision 5b7e2250 (arvados-dev): 5416: Terminate connections on the configured test database (not...
Tom Clegg
03:31 pm Revision bf95f654 (arvados): 5416: Add arv-git-httpd.
Tom Clegg
03:31 pm Revision bf95f654 (arvados-dev): 5416: Add arv-git-httpd.
Tom Clegg
03:00 pm Revision 49d7df5e (arvados-dev): adding an empty csv in case of error
Nico Cesar
02:48 pm Revision a4b2f2a2 (arvados-dev): no more trailing spaces
Nico Cesar
02:48 pm Bug #6130 (New): [Workbench] Support searching collections by their collection name
!select_all_logs.gif!
For example, I want to remove all the log files, I would like to search for log and get ever...
Bryan Cosca
02:47 pm Revision cfb3c455 (arvados-dev): Merge branch 'master' into 6061-add-performance-plots
Nico Cesar
02:27 pm Revision 2dae0755 (arvados-dev): 6061: comment cleanup and final version tested. it works
closes #6061 Nico Cesar
02:21 pm Revision 0fbece8e (arvados): 3793: Fix how python3 fpm arguments are added.
The previous code would add arguments such that they could be
interpreted as the package version. Avoid this by addi...
Brett Smith
02:21 pm Revision 0fbece8e (arvados-dev): 3793: Fix how python3 fpm arguments are added.
The previous code would add arguments such that they could be
interpreted as the package version. Avoid this by addi...
Brett Smith
02:04 pm Revision 9fa53446 (arvados): Improve packaging of third-party Python 3 packages.
* Fix the bug where we're passing in "python3" as the vendor argument
to build_and_scp_deb.
* Build more dependenci...
Brett Smith
02:04 pm Revision 9fa53446 (arvados-dev): Improve packaging of third-party Python 3 packages.
* Fix the bug where we're passing in "python3" as the vendor argument
to build_and_scp_deb.
* Build more dependenci...
Brett Smith
01:12 pm Revision 08d02e15 (arvados-dev): Merge branch 'more-sanity-check-less-download' refs #5766
Tom Clegg
01:12 pm Revision 08d02e15 (arvados): Merge branch 'more-sanity-check-less-download' refs #5766
Tom Clegg
12:57 pm Revision 42e438d9 (arvados-dev): 5766: Remove "remove dependencies" step. Detect existing PyYAML ...
Tom Clegg
12:57 pm Revision 42e438d9 (arvados): 5766: Remove "remove dependencies" step. Detect existing PyYAML faster.
Tom Clegg
12:51 pm Revision 303a6e2a (arvados): Tidy up sanity checks. Add checks for fuse.h, pyconfig.h, nginx.
Suggest how to fix missing dependencies.
No issue #
Tom Clegg
12:51 pm Revision 303a6e2a (arvados-dev): Tidy up sanity checks. Add checks for fuse.h, pyconfig.h, nginx.
Suggest how to fix missing dependencies.
No issue #
Tom Clegg
12:24 pm Bug #5766: [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, even when alre...
Peter Amstutz wrote:
> tomclegg: If I'm understanding your suggestion, you're suggesting uninstalling everything exc...
Tom Clegg

05/20/2015

09:47 pm Revision 9d3fa25b (arvados-dev): script working better
Nico Cesar
08:58 pm Task #6128 (Resolved): Test Docker install
Peter Amstutz
08:48 pm Revision cb1c4d58 (arvados-dev): Merge branch '6061-add-performance-plots' of git.curoverse.com:a...
Nico Cesar
08:47 pm Revision 63e40231 (arvados-dev): 6011: Matching more generic test names
Nico Cesar
08:47 pm Revision d16c7ef6 (arvados-dev): taking out the tests don-t make sense
Nico Cesar
08:43 pm Revision 08995325 (arvados-dev): taking out the tests don-t make sense
Nico Cesar
08:30 pm Task #6127 (New): Preserve template goal through login->UA->profile->back-to-work process, and th...
Tom Clegg
08:29 pm Task #6126 (New): Decide URL and advice for appropriate next step when in "pipeline goal" mode
Tom Clegg
08:27 pm Task #6125 (New): Enter goal mode when hitting Run on a pipeline template
Tom Clegg
08:27 pm Task #6124 (New): Add "goal mode" infrastructure
Tom Clegg
08:25 pm Task #6123 (Resolved): Determine why still NoMemoryError even with API memory-limiting feature
Tom Clegg
08:24 pm Task #6122 (Resolved): Improve query performance (or prevent clients from doing it?)
Tom Clegg
08:18 pm Task #6119 (Resolved): Review 6096-deploy-jobs-image
Nico César
08:14 pm Task #6117 (Resolved): Review 6095-arv-copy-preserve-object-order-wip
Brett Smith
08:12 pm Task #6116 (Closed): Review 5883-oauth2-update at get-evidence.git
Tom Clegg
08:11 pm Task #6115 (Resolved): Review branch: 6057-public-projects-page
Tom Clegg
08:10 pm Task #6113 (Resolved): Review branch: 6203-collection-perf-api
Tom Clegg
08:10 pm Task #6112 (Resolved): Review 6098-full-text-index 64cfaed
Tom Clegg
08:09 pm Task #6111 (Resolved): Review 6094-install-script-sigpipe
Tom Clegg
08:04 pm Task #6110 (Resolved): Review 6074-collections-index @ 22c8b63
Tom Clegg
08:04 pm Task #6052: Review branch: 5930-smalldocfix
ops... wrong ticket. Nico César
08:03 pm Bug #6086: [API] Creating new job sometimes takes too long
I am currently leaving this on the 2015-06-10 sprint. Currently we believe that #6071 will be enough of a workaround... Brett Smith
08:02 pm Task #6109 (New): Review
Tom Clegg
08:02 pm Task #6108 (Resolved): Review data manager
Peter Amstutz
07:55 pm Task #6107 (Resolved): Fix Docker image search/list
Peter Amstutz
07:54 pm Task #6106 (Closed): Add a performance test case that exposes the slow query
Tom Clegg
07:53 pm Task #6105 (Resolved): Review 5990-arv-run-default-runtime
Peter Amstutz
07:52 pm Task #6104 (Resolved): Review
Peter Amstutz
07:52 pm Task #6103 (Resolved): Review 5790-copy-most-recent-docker-image-wip
Peter Amstutz
07:51 pm Task #6102 (Resolved): IRC support
Peter Amstutz
07:50 pm Task #6100 (Resolved): Improve draft 2 spec docs
Peter Amstutz
07:50 pm Task #6099 (Resolved): Finish fixing tests for draft2-updates
Peter Amstutz
07:50 pm Bug #6098 (Resolved): [API] slow search? SQL query
... Ward Vandewege
07:50 pm Task #6097 (Resolved): Implement "id" loading
Peter Amstutz
07:35 pm Story #6096: [OPS] Implement a process to regularly deploy a Docker image for running jobs to Arv...
mental note: this is a arv-keep docker thing Nico César
07:28 pm Story #6096 (Resolved): [OPS] Implement a process to regularly deploy a Docker image for running ...

We're now in a place where we install all components via debs.
There's a script in arvados-dev called
jenki...
Brett Smith
07:31 pm Bug #5990: [SDKs] arv-run defaults to using arvados/jobs, without checking that it exists or is r...
Perhaps the default image should have no Arvados SDK, and arv-run should use the version given in the API discovery d... Tom Clegg
07:11 pm Story #5781: [API] [DRAFT] Provide API methods for manipulating and combining collections
Proposed Collection Update API:
https://arvados.org/projects/arvados/wiki/Collection_update_API
Peter Amstutz
07:09 pm Bug #5523 (New): [Crunch] crunchstat should not report errors during normal timing races
Tom Clegg
07:08 pm Bug #5748 (Resolved): [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
Tom Clegg
07:04 pm Feature #5787 (Resolved): [Crunch] Add Crunch support to GATK Queue
Peter Amstutz
06:23 pm Bug #6076: [API] walk api server installations and ensure modified_at for collections is unique +...
Isn't this easy enough to handle at the client level with filters like @modified_at >= current_working_modified_time,... Brett Smith
06:23 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
reviewing the puppet branch 3793-docker-image-cleaner-wip:
* I think the compute_docker_image_quota default should...
Ward Vandewege
06:19 pm Task #6056 (In Progress): Review puppet branch 3793-docker-image-cleaner-wip
Ward Vandewege
06:18 pm Bug #5499: [SDKs] arv-copy fails to create collection after copying many blocks
Is it possible that this was caused by the GCE 10-minute firewall rule, and so duplicates that ticket? Brett Smith
05:58 pm Support #6055: [Support] Cannot log into VM

Hi Mohammed,
Mohammad Zia wrote:
> I have followed the instructions for logging into the VM, specifically, gene...
Ward Vandewege
05:28 pm Revision c4630bce (arvados-dev): added result checking
Nico Cesar
05:27 pm Revision 1341bb72 (arvados-dev): added result checking
Nico Cesar
03:57 pm Bug #6095 (Resolved): [SDKs] Make arv-copy preserve pipeline template component order
Implementation steps:
# Add an OrderedJsonModel class to arvados.api. This is a subclass of googleapiclient.model...
Brett Smith
03:45 pm Bug #5831: [SDKs] CollectionReader.open(filename, 'r') fails (arvados/keep.py 665 in get_from_cac...
This bug appeared again: https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-29d3lxak8gdlo46
Nev...
Sarah Guthrie
03:43 pm Revision 8561679d (arvados-dev): added create plot data script to exit_cleanly()
Nico Cesar
03:29 pm Revision bf0c6769 (arvados): Documentation fix (quoting) for the 'Add an Arvados repository' page.
No issue # Ward Vandewege
03:13 pm Revision 0f3a97b1 (arvados-dev): adding 3 more test for the performance suite.
I'm guessing the names, lets see if they are good or not ...
refs #6061
Nico Cesar
02:54 pm Revision 5151ef79 (arvados): 5748: Remove unused import. refs #5748
Tom Clegg
02:26 pm Bug #6094: [Crunch] Install script exited 141
More errors: qr1hi-d1hrv-oykvsg3tkkvoznt Bryan Cosca
02:23 pm Bug #6094: [Crunch] Install script exited 141
Another instance with this error: qr1hi-d1hrv-96bdqhdlhgopth1 Bryan Cosca
01:30 pm Bug #6094 (Resolved): [Crunch] Install script exited 141
Pipeline qr1hi-d1hrv-yer77lzhezepsui... Peter Amstutz
02:15 pm Revision c6dd0227 (arvados): 5748: Remove runtime.GC() obsoleted by bufferpool. refs #5748
Tom Clegg
01:48 pm Bug #4706: [Workbench] Re-connect to websockets when the connection drops; use "last_log_id" so n...
In addition, we could provide a fallback method that uses log table polling to get events. The Python SDK uses this ... Peter Amstutz
01:45 pm Task #6069 (Resolved): Review branch: 6064-collection-output-of-perf-issue
Radhika Chippada
01:45 pm Bug #6064 (Resolved): [Workbench] [Performance] Collection#show for /collections/qr1hi-4zz18-hqfx...
Applied in changeset arvados|commit:e5c66d135d453a4af4c978590b99a118f65ae12b. Radhika Chippada
01:40 pm Revision e5c66d13 (arvados): closes #6064
Merge branch '6064-collection-output-of-perf-issue' Radhika Chippada
01:10 pm Story #6057: [Workbench] Provide an attractive index of public projects
Brett Smith wrote:
> Would it maybe be a little nicer to manipulate the generated HTML directly? That way you don't...
Tom Clegg
12:13 pm Revision 35c8b0a5 (arvados): integration_performance tests: add comment describing how to run the...
since the tests in this directory will not be part of regular test run because it is not a standard rails test direct... Radhika Chippada
03:00 am Revision d144724e (arvados): 6064: rollback cache update so that it can be done in a separate bra...
Radhika Chippada
02:32 am Revision a5401e34 (arvados): Merge branch 'master' into 6064-collection-output-of-perf-issue
Radhika Chippada

05/19/2015

10:53 pm Feature #5728: ssh port 2222 is blocked on many networks
The workaround is to tunnel ssh from a non-firewalled host. You can (arguably) use a Cloud instance for that. Pjotr Prins
10:09 pm Bug #4706: [Workbench] Re-connect to websockets when the connection drops; use "last_log_id" so n...
This is still an issue, but it may be lower priority: we just realized that #6048 was happening because websockets si... Brett Smith
10:04 pm Story #5623: [Crunch] Specify Crunch2 features and APIs
Assuming no unforeseen wrinkles come up, I would really like to see this done by the end of the 2015-06-10 sprint so ... Brett Smith
09:59 pm Story #6092: [TBD] Improve the performance of the worst-performing collections component
This can't be done until we have results from #6061. Brett Smith
09:54 pm Story #6092 (Resolved): [TBD] Improve the performance of the worst-performing collections component
Brett Smith
09:50 pm Story #6091 (Resolved): Support users and triage their bugs (second half of sprint)
This includes:
* Be the front-line person to answer questions from the science team and other users
* Resolve bug...
Brett Smith
09:46 pm Story #6090 (Resolved): Support users and triage their bugs (first half of sprint)
This includes:
* Be the front-line person to answer questions from the science team and other users
* Resolve bug...
Brett Smith
09:46 pm Story #6089 (Resolved): Write development update blog (first three days of sprint)
Brett Smith
09:45 pm Story #6088 (Resolved): Contribute to CWL specification
Brett Smith
09:11 pm Story #6057: [Workbench] Provide an attractive index of public projects
Tom Clegg wrote:
> Possible first approximation:
> * Use the first non-empty line of the project description as the...
Brett Smith
07:59 pm Story #6057: [Workbench] Provide an attractive index of public projects
Possible first approximation:
* Use the first non-empty line of the project description as the "short description": ...
Tom Clegg
09:08 pm Bug #6064: [Workbench] [Performance] Collection#show for /collections/qr1hi-4zz18-hqfxewp0r3dsaov...
Good catch on the logic for caching. It looks like caching never been used. I wonder what else caching will help wi... Peter Amstutz
08:34 pm Task #6069 (In Progress): Review branch: 6064-collection-output-of-perf-issue
Peter Amstutz
02:11 am Task #6069 (Resolved): Review branch: 6064-collection-output-of-perf-issue
Radhika Chippada
08:31 pm Revision 45d885d5 (arvados): Merge branch '6071-java-sdk-timeouts' closes #6071
Peter Amstutz
08:29 pm Revision 61144008 (arvados): 6071: Bump up timeout to 120 seconds.
Peter Amstutz
08:23 pm Bug #6086 (Closed): [API] Creating new job sometimes takes too long
We have been seeing a lot of timeouts in the java sdk when it is attempting to create a job. The Java SDK uses a def... Peter Amstutz
08:01 pm Bug #5951 (In Progress): GET-Evidence login via google login no longer works - OpenID 2.0 is gone
Tom Clegg
07:49 pm Bug #6048 (Duplicate): Pipeline Instance does not automatically refresh
Duplicates #4706. Brett Smith
07:46 pm Bug #6048: Pipeline Instance does not automatically refresh
Bryan and Ward report that this is happening very consistently when pipelines run.
Sally reports it happens about ...
Brett Smith
07:31 pm Revision 974ab38a (arvados): Merge branch '6073-pycurl-version' refs #6073
Peter Amstutz
07:28 pm Revision 5824ee2e (arvados): More reformatting of unittests to improve readability.
Misha Zatsman
07:26 pm Revision 82f7fcd2 (arvados): refs #6061
Merge branch '6061-intg-perf-tests' Radhika Chippada
07:23 pm Revision 0f6a0017 (arvados): 6061: add workbench integration_performance test folder.
Radhika Chippada
07:20 pm Revision f3c45652 (arvados): 6071: Fix URL
Peter Amstutz
07:10 pm Revision 999c05af (arvados): Modified pull list code to change json output to match the specifica...
Changed PullList type
Renamed PullListEntry to PullRequest to match the type defined in services/keepstore/handlers.g...
Misha Zatsman
07:01 pm Story #3198: [FUSE] Writable streaming arv-mount
Suggest changing "Collection must be writable" error message to "Collection is not writable" or "Collection is read-o... Tom Clegg
06:44 pm Revision 8b3d7b73 (arvados-dev): adding the creation of plot data that jenkins plot pluging will ...
refs #6061 Nico Cesar
05:55 pm Revision 836999ec (arvados): 6071: Refactor project organization a bit.
Peter Amstutz
05:52 pm Revision 3c517a48 (arvados): 6071: Increase default timeout and enable retry support.
Peter Amstutz
05:26 pm Revision b2329e2c (arvados): Fixed compilation errors after merging master.
Misha Zatsman
05:16 pm Revision 6eb3d1fb (arvados): Merge branch 'master' into 3408-production-datamanager
Because it's been a long time. Misha Zatsman
05:09 pm Bug #6076 (New): [API] walk api server installations and ensure modified_at for collections is un...
Until this is done, datamanager needs to ask for groups of collections with overlap. That is not the most efficient, ... Ward Vandewege
04:55 pm Bug #6074 (Resolved): [API] collections are being returned too slowly + NoMemoryError
... Ward Vandewege
04:54 pm Revision 29009a1c (arvados): 6073: Pycurl depends on latest in Arvados SDK setup.py
Peter Amstutz
03:36 pm Task #5711 (In Progress): Requirements / API for Crunch v2
Peter Amstutz
03:19 pm Support #5833: Cannot get Arvados installed
I searched around the issues on arvados, so I ran following commands:
darshan@Linux2:~$ docker info
Containers: 1...
Darshan Singh
03:09 pm Support #5833: Cannot get Arvados installed
I got past the original error.
Now I get following error when I try to login.
Web application could not be start...
Darshan Singh
02:20 pm Feature #5829 (Resolved): [SSO] improve UI for ldap/local account login
Peter Amstutz
02:18 pm Task #6066 (In Progress): Review 3198-writable-fuse
Tom Clegg
01:57 pm Task #5965 (Resolved): Update sso install docs for plain email/password login
Peter Amstutz
01:37 pm Task #5965 (In Progress): Update sso install docs for plain email/password login
Peter Amstutz
01:36 pm Task #5936 (Resolved): Review SSO master
Peter Amstutz
01:17 pm Task #6070 (Resolved): Refactor arv-git-httpd authenticator into a package
Tom Clegg
03:30 am Feature #4717 (Resolved): [API] [SDKs] Read-only flag on keep_services table as hint to clients n...
Applied in changeset arvados|commit:4110970a34689ed526c3365e9b64a784fba7efda. Radhika Chippada
03:26 am Feature #4717: [API] [SDKs] Read-only flag on keep_services table as hint to clients not to try t...
Addressed all comments and merged into master. (Yes, the change method worked for both up and down for this case). Th... Radhika Chippada
03:29 am Task #5776 (Resolved): Review branch: 5720-ajax-loading-error
Radhika Chippada
03:28 am Task #5633 (Resolved): Update Python SDK
Radhika Chippada
03:28 am Task #5634 (Resolved): Update Go SDK
Radhika Chippada
03:27 am Task #6040 (Resolved): Review branch: 4717-read-only-keep-services-flag
Radhika Chippada
03:24 am Revision 4110970a (arvados): closes #4717
Merge branch '4717-read-only-keep-services-flag' Radhika Chippada
03:11 am Revision d5142a69 (arvados): 4717: rename writableRoots as writableLocalRoots.
Radhika Chippada
02:25 am Bug #5720 (Resolved): [Workbench] Search for pipeline templates breaks
Applied in changeset arvados|commit:f1827e2044aff826e63826880b296a59c4a17e2a. Radhika Chippada
02:22 am Revision b085f051 (arvados): Merge branch 'master' into 4717-read-only-keep-services-flag
Radhika Chippada
02:21 am Revision f1827e20 (arvados): closes #5720
Merge branch '5720-ajax-loading-error' Radhika Chippada
02:09 am Revision 100a504e (arvados): 6064: display only 5 objects for which this collection is the output...
Radhika Chippada
12:54 am Revision b9bf39b1 (arvados): Added code for generating pull lists.
Misha Zatsman
12:37 am Revision 5a662d84 (arvados): Made HostPort() an explicit method to print the HostPort, so that St...
Misha Zatsman

05/18/2015

11:54 pm Revision edd979c6 (arvados-dev): 'who-pushed' learns super-efficient 'tip search'
Sitaram Chamarty
09:20 pm Feature #4717: [API] [SDKs] Read-only flag on keep_services table as hint to clients not to try t...
At commit:e41260f
In the Go SDK, WritableRoots and writableRoots seem to mean writableLocalRoots, so should probab...
Tom Clegg
08:50 pm Revision 28e6503a (arvados): Merge branch 'master' into 3198-writable-fuse
Peter Amstutz
08:49 pm Revision 19c43ceb (arvados): 3198: Enable support for event bus based updates in arv-mount.
Peter Amstutz
08:44 pm Task #6040 (In Progress): Review branch: 4717-read-only-keep-services-flag
Tom Clegg
08:38 pm Feature #6034: [Deployment] Add sysvinit script to the keepproxy package
Yes, Go doesn't mind if you have subdirs, so that would also work -- like services/keepproxy/pkg-extras/ cf. IRC
Tom Clegg
08:11 pm Feature #6034: [Deployment] Add sysvinit script to the keepproxy package
Tom Clegg wrote:
> Nico Cesar wrote:
> > is it ok to drop the init file there too?
>
> afaik go tools ignore an...
Ward Vandewege
08:06 pm Feature #6034: [Deployment] Add sysvinit script to the keepproxy package
Nico Cesar wrote:
> is it ok to drop the init file there too?
afaik go tools ignore anything other than *.go
...
Tom Clegg
06:50 pm Feature #6034: [Deployment] Add sysvinit script to the keepproxy package
the code of keepproxy is here:... Nico César
06:59 pm Story #3198: [FUSE] Writable streaming arv-mount
3198-writable-fuse is ready for review. Notes:
* Supports creating, writing, renaming, deleting files in collecti...
Peter Amstutz
06:57 pm Bug #6064 (In Progress): [Workbench] [Performance] Collection#show for /collections/qr1hi-4zz18-h...
In IRC:
tomclegg
1:25 radhika: workbench arvados_base.rb L102 already uses the rails cache to optimize for cases ...
Radhika Chippada
04:04 pm Bug #6064 (Resolved): [Workbench] [Performance] Collection#show for /collections/qr1hi-4zz18-hqfx...
Display of /collections/qr1hi-4zz18-hqfxewp0r3dsaov takes forever.
* The issue seems to be linking all the items ...
Radhika Chippada
06:50 pm Revision faefe8fc (arvados): 3198: VWD syncs collection before loading from API server.
Peter Amstutz
06:50 pm Task #6066 (Resolved): Review 3198-writable-fuse
Peter Amstutz
06:49 pm Task #5895 (Resolved): Ensure vwd.checkin doesn't accidentally commit (or otherwise mess up) when...
Peter Amstutz
06:36 pm Bug #5662: [FUSE] cd/ls sometimes takes too long on su92l
Our current thinking is that #5748 is the main culprit here. We're very interested to hear how things look after the ... Brett Smith
06:36 pm Bug #5713: [FUSE] File access sometimes takes too long on su92l
Our current thinking is that #5748 is the main culprit here. We're very interested to hear how things look after the... Brett Smith
06:27 pm Revision 27616fe7 (arvados): 3198: Add docstring with overview of the architecture. Implement ch...
method wrapper and expand use_counter to every method containing a
llfuse.lock_released block. Add note about big_wr...
Peter Amstutz
06:26 pm Task #5785 (Resolved): Documentation and code cleanup
Peter Amstutz
06:26 pm Task #5630 (Resolved): Write tests
Peter Amstutz
05:41 pm Bug #5720: [Workbench] Search for pipeline templates breaks
5720-ajax-loading-error looks good. I pushed (without actually trying) commit:6702cda to explain what I meant about "... Tom Clegg
05:36 pm Revision 6702cdab (arvados): 5720: Leave existing content in place (and schedule another reload) ...
Tom Clegg
02:10 pm Revision fea4d2ba (arvados): 3198: writeto() notifies with WRITE instead of MOD. WRITE doesn't i...
Move llfuse.lock_released down one level into individual fusefile and fusedir methods.
Add big_writes option, improve...
Peter Amstutz
02:01 pm Story #6058 (New): [Workbench] Provide a guided workflow to new users who want to upload data and...
Imagine that I'm a bioinformatician looking at a public pipeline on an Arvados installation. I don't have an account... Brett Smith
02:00 pm Story #6057 (Resolved): [Workbench] Provide an attractive index of public projects
The index should list basic information about each project, so a user can browse the page and determine whether or no... Brett Smith
01:39 pm Task #6056 (Resolved): Review puppet branch 3793-docker-image-cleaner-wip
Brett Smith
01:39 pm Task #5997 (Resolved): Deploy Docker image cleaner via Puppet
Brett Smith
01:27 pm Support #6055 (Feedback): [Support] Cannot log into VM
Hi,
I have followed the instructions for logging into the VM, specifically, generating a public SSH key and adding...
Mohammad Zia
01:18 am Story #6054 (New): [Workbench] [Performance] Same request performance at different times varies s...
Performance of qr1hi can be quite bad at times.
Attached performance profiles show the times taken for collection#...
Radhika Chippada
01:04 am Story #6053 (Resolved): [Workbench] [Performance] Dashboard display is sluggish
Dashboard display takes several seconds to display. When looked at the workbench console log (pointing to qr1hi API s... Radhika Chippada

05/17/2015

01:40 am Bug #5930: [Documentation] Misc. documentation fixes
Review comments:
* doc/_includes/_tutorial_cluster_name.liquid
** Not sure if we should mention su12l in general ...
Radhika Chippada
01:21 am Bug #5930 (In Progress): [Documentation] Misc. documentation fixes
Radhika Chippada
01:21 am Task #6052 (Closed): Review branch: 5930-smalldocfix
Radhika Chippada

05/16/2015

09:29 pm Revision 858cd939 (arvados): Merge branch '3793-docker-cleaner-wip'
Refs #3793. Closes #6003. Brett Smith
09:29 pm Revision 858cd939 (arvados-dev): Merge branch '3793-docker-cleaner-wip'
Refs #3793. Closes #6003. Brett Smith
09:25 pm Revision 034677aa (arvados-dev): 3793: Build Docker cleaner service in run-build-packages.sh.
Brett Smith
09:25 pm Revision 034677aa (arvados): 3793: Build Docker cleaner service in run-build-packages.sh.
Brett Smith
04:37 am Task #6031 (Resolved): Review 5748-max-buffers-leak
Tom Clegg

05/15/2015

11:27 pm Story #6050 (New): [Workbench] [Performance] collections/_show_files page performance need to be ...
Showing files in a collection takes an awful lot of time for large collections. For qr1hi-4zz18-tcnxylwkxg0nfhi, it i... Radhika Chippada
11:21 pm Story #6049 (New): [Workbench] [Performance] [API] GET "/collections/<uuid>" is very expensive fo...
Getting a large collection from the API server takes a long time. When observed for the following, it took 20 to 60 s... Radhika Chippada
09:28 pm Support #5833: Cannot get Arvados installed
Darshan,
I just updated arvdock so it takes in account the bridge and autodetects the IP. Please try again with th...
Nico César
09:27 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Thanks, LGTM! Ward Vandewege
09:10 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Ward Vandewege wrote:
> Reviewing 3793-docker-cleaner-wip in the arvados-dev repository:
>
> * I added a commit t...
Brett Smith
07:41 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Reviewing 3793-docker-cleaner-wip in the arvados-dev repository:
* I added a commit to fix a bug (the path to PKG-...
Ward Vandewege
09:24 pm Task #6003 (Resolved): Review arvados-dev branch 3793-docker-cleaner-wip
Ward Vandewege
06:28 pm Task #6003 (In Progress): Review arvados-dev branch 3793-docker-cleaner-wip
Ward Vandewege
09:09 pm Revision eecd9773 (arvados-dev): 3793: Add dependency check for python3-setuptools.
Brett Smith
09:04 pm Revision e41260f6 (arvados): Merge branch '5998-arvdock-bridge-option'
closes #5998 Nico Cesar
08:17 pm Bug #6048 (Duplicate): Pipeline Instance does not automatically refresh
When I run a new pipeline, sometimes it fails to automatically refresh, making me have to manually refresh to see if ... Bryan Cosca
07:34 pm Revision 1ab2da62 (arvados-dev): Fix typo.
refs #3793 Ward Vandewege
07:00 pm Revision d39be4ad (arvados): $start_bridge -> $bridge
options modified
ip command refactored
refs #5998
Nico Cesar
03:28 pm Bug #5947: [Workbench] Provide additional guidance to users running their first pipeline
The "quick fix" doesn't seem so quick because different users will have different levels of familiarity with differen... Brett Smith
03:25 pm Bug #5946: [Workbench] "other collections have the same content" page is confusing
Nancy,
It might help if you could explain a little more what you'd like to see Workbench do in this case. Just be...
Brett Smith
02:53 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
The same setup popup is also used by the "Add new user" button in /users page. Hence, the changes need to agree with ... Radhika Chippada
02:39 pm Story #6043 (New): [Workbench] [Performance] [api] _projects_tree adds seconds of lag
While performance profiling workbench collection#show page, it was noticed that the projects tree display takes 2 to ... Radhika Chippada
02:19 pm Story #6042 (New): [Workbench] [Performance] [API] collection#show page source_summary section is...
While performance profiling the collection#show page for qr1hi-4zz18-tcnxylwkxg0nfhi, it was observed that the source... Radhika Chippada
02:14 pm Story #6041 (New): [Workbench] [Performance] While in a collection page, clicking on any of the o...
Observed this behavior of retrieving collection object and other objects from API server by looking at workbench cons... Radhika Chippada
02:04 pm Story #5624: [API] [Workbench] [Performance] Use object caching to improvement performance (such ...
Currently, when testing in development, you can look at the workbench console log and notice that the same object(s) ... Radhika Chippada
01:46 pm Revision 47b10ff0 (arvados): Check in docker/sso/database.yml.in, forgotten in commit ea7da293b0a...
No issue # Ward Vandewege
01:42 pm Bug #6023 (Closed): Deleting subprojects from my home projects don't stay deleted
Duplicates #4409. Brett Smith
03:11 am Task #6040 (Resolved): Review branch: 4717-read-only-keep-services-flag
Radhika Chippada
03:10 am Task #5633 (In Progress): Update Python SDK
Radhika Chippada
03:10 am Task #5634 (In Progress): Update Go SDK
Radhika Chippada
02:56 am Revision 1f2a1c4d (arvados): Merge branch 'master' into 4717-read-only-keep-services-flag
Radhika Chippada
02:55 am Revision 8eb65b21 (arvados): 4717: use keep_services -> read_only flag in python sdk.
Radhika Chippada
02:11 am Revision a709514c (arvados): Merge branch '5748-max-buffers-leak-TC' refs #5748
Tom Clegg
02:10 am Revision a007e4eb (arvados): 5748: gofmt fixes.
Tom Clegg
02:06 am Revision 92a203c4 (arvados): 5748: Time out leak tests after 20s.
Tom Clegg
01:52 am Revision 9e20ed85 (arvados): 5748: Put() always takes a non-nil buf.
Tom Clegg

05/14/2015

11:04 pm Revision b05c94ff (arvados-dev): Don't overwrite gl-log on each flush in who-pushed
_print always overwrites the target file. Empty the file at the
beginning of the migrate run but subsequently append ...
milki
10:35 pm Bug #5915 (Resolved): [Workbench] Sharing link for public collection still renders after sharing ...
Applied in changeset arvados|commit:b7c7f20d17afc11d2cce7bfee2205a26dc4a4762. Brett Smith
10:23 pm Bug #5915 (In Progress): [Workbench] Sharing link for public collection still renders after shari...
I haven't proven it, but I'm pretty sure this is what happened:
* The first sharing link was created.
* The colle...
Brett Smith
10:32 pm Revision b7c7f20d (arvados): 5915: Workbench tries the anonymous reader token first for collectio...
This is necessary to make sure we provide a usable token to arv-get.
If we don't check the anonymous reader token fir...
Brett Smith
09:32 pm Task #6031 (New): Review 5748-max-buffers-leak
Ward Vandewege
08:43 pm Task #6031 (In Progress): Review 5748-max-buffers-leak
Ward Vandewege
08:04 pm Task #6031 (Resolved): Review 5748-max-buffers-leak
Peter Amstutz
09:30 pm Feature #6034: [Deployment] Add sysvinit script to the keepproxy package
So currently this kind of works: ... Nico César
09:26 pm Feature #6034 (Rejected): [Deployment] Add sysvinit script to the keepproxy package
Functional requirements:
* The script should always be installed somewhere under @/usr/share/doc/keepproxy@.
* On...
Nico César
09:24 pm Bug #5909 (Closed): Cannot see output collection from workbench
Duplicate of #5682. Brett Smith
09:17 pm Bug #5744 (Closed): PermissionDenied error writing job output of pipeline_instance qr1hi-d1hrv-4z...
This bug is effectively a duplicate of #3261. The Arvados SDK in the Docker image does not retain Keep permission to... Brett Smith
09:01 pm Revision 7a7b8ee6 (arvados): 5748: Basic tests to check for bufferpool resource leaks
Peter Amstutz
08:24 pm Revision 2403cd9f (arvados): Merge branch '5748-max-buffers-leak' into 3198-writable-fuse
Peter Amstutz
08:02 pm Revision ae34fb3d (arvados): 5748: Fix leaks in GetBlock error handling and PutBlock use of GetBl...
buffers were not being returned to the buffer pool. Peter Amstutz
07:26 pm Revision 3809452a (arvados): Merge branch 'master' into 3198-writable-fuse
Peter Amstutz
07:21 pm Revision 3d1d497b (arvados): 3198: Support setattr().
Peter Amstutz
07:12 pm Bug #5521 (Closed): [Workbench] Slow download speed from browser
I'm closing this for sort of a combination of reasons. One, we already know that general Workbench download performa... Brett Smith
06:43 pm Revision a04932c2 (arvados): 3198: Renaming collections in projects works. Improved conformance ...
Peter Amstutz
05:32 pm Bug #6027 (Resolved): [Documentation] Update "Working with an Arvados git repository" to document...
http://doc.arvados.org/user/tutorials/git-arvados-guide.html
The bottom demonstrates adding a file. It should add...
Bryan Cosca
05:15 pm Bug #6025 (Closed): [SSO] Authenticate users with OAuth2
Use case: a lab runs their own OAuth2 server. Authenticating users against that is an easy way to bridge the gap bet... Brett Smith
04:39 pm Revision 46b2b920 (arvados): 4717: just a couple minor tweaks
Radhika Chippada
04:32 pm Revision 0aaa4681 (arvados): 4717: writable roots in go sdk
Radhika Chippada
04:12 pm Feature #6024 (New): [FUSE] Edit records in FUSE similar to arv edit
Peter Amstutz
04:00 pm Feature #5645 (Resolved): [Workbench] Social media optimize anonymous collections/projects/pipelines
Applied in changeset arvados|commit:01574a902d99cba21ed53e62cef6bef683bed2a2. Radhika Chippada
03:56 pm Feature #5645: [Workbench] Social media optimize anonymous collections/projects/pipelines
Thanks for reviewing Brett.
* I expanded the comment to include the feature number and the url, which should grea...
Radhika Chippada
02:53 pm Feature #5645: [Workbench] Social media optimize anonymous collections/projects/pipelines
commit:1be4d28 is good to merge. I just see a couple of small opportunities to smooth things over for future readers... Brett Smith
03:59 pm Revision af934d0f (arvados): Merge branch 'master' into 4717-read-only-keep-services-flag
Radhika Chippada
03:58 pm Revision 01574a90 (arvados): closes #5645
Merge branch '5645-open-graph-meta-tags' Radhika Chippada
03:56 pm Revision ad73066c (arvados): 5645: updated comment
Radhika Chippada
03:56 pm Task #6001 (Resolved): Review branch: 5645-open-graph-meta-tags
Radhika Chippada
02:24 pm Task #6001 (In Progress): Review branch: 5645-open-graph-meta-tags
Brett Smith
03:05 pm Bug #6023 (Closed): Deleting subprojects from my home projects don't stay deleted
After removing projects from my home project (hitting the trash can icon), I see the project fade away. Refreshing t... Abram Connelly
02:09 pm Revision 32f8850d (arvados): 3198: Start working on rename() for collections in projects
Peter Amstutz
01:49 pm Revision e9e1bd87 (sso-provider): Merge branch 'master' of git.curoverse.com:sso-provider
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream...
Peter Amstutz
01:48 pm Revision cdacaf67 (sso-provider): Fix :email_domain => "email_domain" in LDAP callback handler.
Peter Amstutz
01:39 pm Revision 0167e284 (sso-provider): Make the error message more polite.
Peter Amstutz
01:23 pm Revision 1be4d281 (arvados): Merge branch 'master' into 5645-open-graph-meta-tags
Radhika Chippada
01:22 pm Revision cfb0f787 (arvados): 5645: add og:site_name to the list of open graph meta tags added to ...
Radhika Chippada
12:38 pm Bug #6021 (Closed): Create Swift Biosciences Pipeline
Bryan Cosca
12:38 pm Bug #6021 (Closed): Create Swift Biosciences Pipeline
Bryan Cosca
03:05 am Bug #6020 (New): [Workbench] The collection information box values for content address and conten...
Ward Vandewege

05/13/2015

09:58 pm Revision 6b093164 (arvados): refs 5930: misc. small documentation fixes
Nancy Ouyang
09:57 pm Bug #5930: [Documentation] Misc. documentation fixes
Branch 5930-smalldocfix now up for review.
Nancy Ouyang
09:56 pm Bug #5930: [Documentation] Misc. documentation fixes
I addressed these points as below
h2. details
> 1a) where to get file var-GS000016015-ASM.tsv.bz2
http://doc...
Nancy Ouyang
09:10 pm Revision ae85b0b3 (arvados): 3198: Support mkdir() and rmdir() to create collections on projects....
for rename() is pending.
All tests that open files are refactored to use multiprocess for syscalls to
avoid deadlocks.
Peter Amstutz
08:30 pm Bug #6019 (Closed): [FUSE] `ls` in a large home directory (4400+ items) takes too long
... Abram Connelly
08:06 pm Bug #5915: [Workbench] Sharing link for public collection still renders after sharing token is re...
Update: Actually, the files seem correct if I am logged into Workbench, but if I log-out or use private browsing mode... Nancy Ouyang
08:02 pm Revision a88e8713 (arvados): 4717: use keep_services -> read_only flag in go sdk.
Radhika Chippada
07:49 pm Bug #5850: All clients authenticate directly against SSO server without going through API server
Ward says that this ticket means that Workbench authenticates users directly against the SSO server without going thr... Brett Smith
07:47 pm Feature #4571 (Resolved): [SSO] Support local user database on SSO server
Ward Vandewege
07:36 pm Revision a5925592 (arvados): 3198: Serialize updates to avoid doing redundant API server calls.
Peter Amstutz
06:33 pm Bug #6016 (New): No pipeline to run with docker install
Hello,
I installed the docker version of Arvados today and tried to follow the tutorial to run a pipeline. However...
Mohammad Zia
06:31 pm Feature #6015 (New): [SSOs] Support authentication against multiple backend LDAP servers
Use case: a lab has their own internal LDAP server, but wants to be able to fall back from that to the company-wide L... Brett Smith
06:00 pm Bug #6014 (Resolved): [Documentation] Document repository creation in the Arvados tutorial
Most of our tutorial was written before users could generate repositories. It's written with the assumption that the... Brett Smith
05:47 pm Bug #5845 (Closed): Pipeline has failed but no jobs are marked as failed
Closing as a duplicate of #5906 (since I already wrote the specification there). Brett Smith
05:44 pm Feature #6013 (Resolved): [Workbench] clean up 'setup user' behavior in the admin interface
h2. Problem.
The user admin page says:
As an admin, you can setup this user. Please input a VM and repository f...
Ward Vandewege
03:55 pm Bug #6010: $ arv-put [eom] should bring up the help manual
A common idiom to accept stdin is to give the '-' as an option to the tool. Abram Connelly
02:42 pm Bug #6010 (New): $ arv-put [eom] should bring up the help manual
currently, arv-put waits for stdin.
> $ arv-put
> 0
it would be less confusing if arv-put alone would function...
Bryan Cosca
03:48 pm Revision 2fc2ce33 (arvados): 3198: FuseMvDirBetweenCollectionsTest works
Peter Amstutz
03:48 pm Feature #6012 (New): Finding locator information for files in keep mounts is more difficult than ...
I have a keep mount. It has a 'shared' and 'home' directory. Finding the portable data hash string for files in tho... Abram Connelly
03:17 pm Bug #5906: [API] crunch-dispatch should mark a job failed when its repository cannot be fetched
This happened because the remote repository URL was ill-specified. I worked with Abram to correct that problem so he... Brett Smith
02:51 pm Revision ec529e13 (sso-provider): Add additional logging.
Peter Amstutz
12:29 pm Revision ac80adf9 (arvados-dev): README.md: clean up usage
Kosma Moczek
12:27 pm Revision 0c2fd243 (arvados-dev): README.md: update email address
Kosma Moczek
11:32 am Revision 5388255e (arvados-dev): README.md: clean up
Kosma Moczek

05/12/2015

11:29 pm Revision aed4d13a (arvados): Removed a comment that was accidentally copied in.
Misha Zatsman
11:27 pm Revision 8a0e311e (arvados): Switched collection_test.go to use the excellent gocheck framework a...
Misha Zatsman
11:14 pm Feature #6009 (New): curover.se/path/to/file should try to download the file if available
Currently it looks like the URL shortner curover.se throws out everything past the UUID. It would be nice if a fully... Abram Connelly
09:13 pm Revision 06d87aa4 (arvados): 3198: Support efficient moving preserving inode, writing to unlinked...
Peter Amstutz
09:05 pm Feature #6004 (New): Project Description should have textile quick help or help link
The project description should have either a link or some sort of dropdown that has some common textile syntax. Many... Abram Connelly
09:03 pm Task #6003 (Resolved): Review arvados-dev branch 3793-docker-cleaner-wip
Brett Smith
09:03 pm Task #5996 (Resolved): Test Docker image cleaner in run-tests.sh
Brett Smith
09:01 pm Revision 301f99d1 (arvados-dev): 3793: Build Docker cleaner service in run-build-packages.sh.
Brett Smith
08:05 pm Bug #5902: [Workbench] collection#show is unresponsive for a large collection
Large collection problems do not only extend to workbench, they also can cause tasks reading in these collections to ... Sarah Guthrie
08:00 pm Task #5632 (Resolved): Update API server
Added read_only column to keep_services and exposed it as an api_accessible attribute.
Verified in workbench that ...
Radhika Chippada
07:22 pm Task #5632 (In Progress): Update API server
Radhika Chippada
07:55 pm Revision 731547ae (arvados): 4717: add read_only column for keep_services data model.
Radhika Chippada
07:31 pm Revision 37fe7a30 (arvados): Merge branch 'master' into 5998-arvdock-bridge-option
Nico Cesar
07:28 pm Bug #5967: Editing a file within a collection in workbench
Related: Abram has a feature request about editing files in git. Brett Smith
07:24 pm Revision 77f11805 (arvados): trailing whitespaces
Nico Cesar
07:22 pm Revision 60460bc7 (arvados): fixing some trailing whitespaces
Nico Cesar
07:20 pm Feature #4717 (In Progress): [API] [SDKs] Read-only flag on keep_services table as hint to client...
Radhika Chippada
07:12 pm Revision ea7da293 (arvados): Fix sso docker container build, and enable local account creation for
this sso container uses.
No issue #
Ward Vandewege
07:08 pm Revision 311dc34b (arvados): initial version to have a --bridge parameter
also improves:
grep: The -P option is not supported if libpcre.so.3 is not available // Replaced -E making compatible
Nico Cesar
06:57 pm Revision acdfc466 (arvados-dev): 3793: Add services/dockercleaner to run-tests.sh.
Brett Smith
06:57 pm Revision acdfc466 (arvados): 3793: Add services/dockercleaner to run-tests.sh.
Brett Smith
05:54 pm Bug #5720: [Workbench] Search for pipeline templates breaks
* Reverted the "skip" logic and using error message "Cancelled" when "jqxhr.readyState == 0 || jqxhr.status == 0". We... Radhika Chippada
05:50 pm Revision d14dd75b (arvados): Merge branch 'master' into 5720-ajax-loading-error
Radhika Chippada
05:46 pm Revision 17fb6bca (arvados): 5720: when jqxhr readyState == 0 or status == 0, instead of skippin...
Radhika Chippada
05:39 pm Revision 7e78bad9 (arvados): 5720: when jqxhr readyState == 0 or status == 0, instead of skipping...
Radhika Chippada
05:06 pm Feature #5645 (In Progress): [Workbench] Social media optimize anonymous collections/projects/pip...
Radhika Chippada
05:04 pm Feature #5645: [Workbench] Social media optimize anonymous collections/projects/pipelines
Implementation notes:
* Tested using google testing tool at https://developers.google.com/structured-data/testing-...
Radhika Chippada
05:04 pm Feature #5645: [Workbench] Social media optimize anonymous collections/projects/pipelines
Discussed this with Ward this morning and we agreed that:
* Add open graph meta tags to our pages
* Add these t...
Radhika Chippada
05:06 pm Task #6001 (Resolved): Review branch: 5645-open-graph-meta-tags
Radhika Chippada
05:05 pm Revision 682dd5b6 (arvados): Merge branch 'master' into 3198-writable-fuse
Conflicts:
sdk/python/arvados/arvfile.py
sdk/python/arvados/keep.py
services/fuse/arvados_fuse/__init__.py
Peter Amstutz
05:05 pm Revision d2e7d7e1 (arvados): 5645: added open graph meta tags to page
Radhika Chippada
04:54 pm Bug #5736: [Node Manager] Reuse node records after shutting down the cloud node set up with them
Addressing the harder case (where we boot a node, it fails to bootstrap, and we need to recycle the node record we se... Brett Smith
04:51 pm Revision 2b43d35b (arvados): Add instructions to generate assets to SSO installation page.
No issue # Ward Vandewege
03:19 pm Revision 74b090ca (sso-provider): Add
uuid_prefix: ~
to application.yml.example
No issue #
Ward Vandewege
03:17 pm Revision d2f24639 (arvados): Reorder SSO install documentation so that the rake db:setup call does
not fail because uuid_prefix and secret_token are not set yet.
No issue #
Ward Vandewege
03:04 pm Revision 6cac5109 (sso-provider): Remove now unused secret_token.rb.example
No issue # Ward Vandewege
02:48 pm Revision 1c9a733f (sso-provider): Sanitize the default database configuration.
No issue # Ward Vandewege
02:48 pm Revision e6e3ecfd (arvados): Even more SSO server install instructions.
No issue # Ward Vandewege
02:27 pm Revision 4799a403 (arvados): Update SSO server documentation to match current reality.
No issue # Ward Vandewege
01:57 pm Feature #5829: [SSO] improve UI for ldap/local account login
* Improve LDAP configuration formatting to be less error prone
*...
Peter Amstutz
11:10 am Revision fc06dd15 (arvados-dev): release 1.1
Kosma Moczek
11:10 am Revision cdb582b0 (arvados-dev): runit-docker.c: simplify + handle Ctrl-C
Kosma Moczek
09:40 am Revision 10dcfdb2 (arvados-dev): yay for generic Makefiles
Kosma Moczek
08:29 am Revision 1fa8e169 (arvados-dev): make who-pushed more efficient...
- add (commented out) values to LOG_DEST in the default rc file to allow
'repo-log' as a destination
- make g...
Sitaram Chamarty

05/11/2015

09:54 pm Task #5997 (Resolved): Deploy Docker image cleaner via Puppet
Brett Smith
09:53 pm Task #5996 (Resolved): Test Docker image cleaner in run-tests.sh
Brett Smith
09:50 pm Revision f116df2e (arvados): Merge branch '5736-node-manager-easy-slot-cleanup-wip'
Refs #5736. Closes #5995. Brett Smith
09:48 pm Revision b5d3c559 (arvados): 5736: Node Manager cleans node records after shutting down a paired ...
This is an easy case to handle, and helps avoid exhausting SLURM
slot numbers.
Brett Smith
09:48 pm Revision 44684242 (arvados): 5736: Fix typo in Node Manager test comments.
Brett Smith
09:47 pm Bug #5736: [Node Manager] Reuse node records after shutting down the cloud node set up with them
Test run clean, LGTM. Ward Vandewege
08:54 pm Bug #5736: [Node Manager] Reuse node records after shutting down the cloud node set up with them
5736-node-manager-easy-slot-cleanup-wip is up for review. It teaches Node Manager to clean up node records after shu... Brett Smith
09:47 pm Task #5995 (Resolved): Review 5736-node-manager-easy-slot-cleanup-wip
Ward Vandewege
09:46 pm Task #5995 (In Progress): Review 5736-node-manager-easy-slot-cleanup-wip
Ward Vandewege
08:52 pm Task #5995 (Resolved): Review 5736-node-manager-easy-slot-cleanup-wip
Brett Smith
09:40 pm Task #5857 (Resolved): Review 3793-clean-docker-images-wip
Applied in changeset arvados|commit:7e80f468042fd4caa78f69fb66efce1b89035d45. Brett Smith
09:36 pm Revision 7e80f468 (arvados): Merge branch '3793-clean-docker-images-wip'
Refs #3793. Closes #5857. Brett Smith
09:24 pm Revision 4d3b8d2e (arvados): 3793: Add Docker image cleaner service for compute nodes.
This service monitors Docker events. When a container is destroyed,
it deletes any images that are unused and exceed...
Brett Smith
09:12 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
On further testing, I see it working now. No further comments. Please merge #3793 Peter Amstutz
06:03 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
I can change the executable bit and the flag name. Let me take a moment to address some of the points that have come... Brett Smith
02:15 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
I can help you with a tcpdump capture maybe we can get better clues Nico César
02:06 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Here's the traceback after waiting ~5 minutes with no indication that it is doing anything, and then hitting ^C:
<...
Peter Amstutz
02:02 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Nico Cesar wrote:
> Does adding this at the beginning of the script make sense?
>
> ...
Peter Amstutz
02:02 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
I am running it now and it doesn't fail, but it doesn't appear to be doing anything either:... Peter Amstutz
01:58 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Does adding this at the beginning of the script make sense?
if sys.version_info[0] < 3:
##exit gracefully...
Nico César
01:54 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Finally I should note that the original story was about removing _containers_ and not images, it may be necessary to ... Peter Amstutz
01:51 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
My fault, I ran it with Python 2.7 instead of Python3.
However I note that @cleaner.py@ has a @#!/usr/bin/env pyth...
Peter Amstutz
01:47 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
docker_py-1.2.1-py3.4.egg Peter Amstutz
01:43 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Minor comment, suggest renaming the command line options from "--keep" to something else (maybe "--limit"), since "ke... Peter Amstutz
09:11 pm Revision dd5deb94 (arvados): Merge branch '5992-keep-proxy-ignore-locator-hints' closes #5992
Peter Amstutz
08:51 pm Revision c042e30c (arvados): 5736: Node Manager cleans node records after shutting down a paired ...
This is an easy case to handle, and helps avoid exhausting SLURM
slot numbers.
Brett Smith
08:38 pm Revision ea8c2900 (arvados): 5992: keepproxy strips +K@{5} hints from locators before trying GET....
locators are preserved. Peter Amstutz
08:09 pm Bug #5915: [Workbench] Sharing link for public collection still renders after sharing token is re...
Fixed ga4gh HGVM wiki link as listed above Nancy Ouyang
05:58 pm Bug #5915: [Workbench] Sharing link for public collection still renders after sharing token is re...
This is also referenced under the wiki https://github.com/ga4gh/schemas/wiki/Human-Genome-Variation-Map-%28HGVM%29-Pi... Abram Connelly
06:57 pm Revision e3a091de (arvados): 5736: Fix typo in Node Manager test comments.
Brett Smith
05:40 pm Feature #3454 (Resolved): [API] Assign a system-default default docker image (instead of using th...
Applied in changeset arvados|commit:1cea19230b490876f99194ea4d84970d6330ae12. Radhika Chippada
05:38 pm Feature #3454: [API] Assign a system-default default docker image (instead of using the non-docke...
I observed that making the job invalid when "no default config + runtime_constraints not including docker image" is a... Radhika Chippada
02:13 pm Feature #3454: [API] Assign a system-default default docker image (instead of using the non-docke...
* If @Rails.configuration.default_docker_image_for_jobs@ is false, and @docker_image@ is not set in the job, that sho... Peter Amstutz
05:39 pm Task #5942 (Resolved): Review branch: 3454-default-docker-image
Radhika Chippada
02:10 pm Task #5942 (In Progress): Review branch: 3454-default-docker-image
Peter Amstutz
05:33 pm Revision 1cea1923 (arvados): closes #3454
Merge branch '3454-default-docker-image' Radhika Chippada
04:07 pm Task #5725 (Resolved): Review 3198-inode-cache
Peter Amstutz
03:57 pm Revision c5909318 (arvados): Merge branch '3198-inode-cache' refs #3198
Peter Amstutz
03:37 pm Story #3198: [FUSE] Writable streaming arv-mount
The test failure I mentioned on IRC was a false alarm, caused by bad database state due to a badly-timed ^C. No worr... Brett Smith
03:17 pm Story #3198: [FUSE] Writable streaming arv-mount
Brett Smith wrote:
> A few thoughts about these:
>
> * The tests repeatedly set @entN.return_value.in_use@ - sh...
Peter Amstutz
02:45 pm Story #3198: [FUSE] Writable streaming arv-mount
commit:0c01dc22 is good to merge. A few final thoughts.
Peter Amstutz wrote:
> Brett Smith wrote:
> > Reviewing...
Brett Smith
03:33 pm Task #5948 (Resolved): Review branch: 5682-download-file-error
Radhika Chippada
02:15 pm Task #5948 (In Progress): Review branch: 5682-download-file-error
Peter Amstutz
03:32 pm Task #5916 (Resolved): Review branch: 4467-project-contents-select-all
Radhika Chippada
02:09 pm Task #5916 (In Progress): Review branch: 4467-project-contents-select-all
Peter Amstutz
02:09 pm Task #5916 (Resolved): Review branch: 4467-project-contents-select-all
Peter Amstutz
03:26 pm Bug #5991 (New): [Workbench] Document "serve_static_assets: true" and/or other methods for servin...
By default, in the "production" configuration has @serve_static_assets: false@. This means in production configurati... Peter Amstutz
03:17 pm Revision 67f0d86c (arvados): Merge branch 'master' into 3454-default-docker-image
Radhika Chippada
03:14 pm Revision 184dabe0 (arvados): 3198: Fix Operation(inode_cache) init. Break up tests into a few sm...
tests. Added comment about how collection size is calculated. Peter Amstutz
03:10 pm Bug #5682 (Resolved): [Workbench] Can't view/download files under subdirectories in stream
Applied in changeset arvados|commit:559d26fd819f477fed75201fa952fed19de77f7e. Radhika Chippada
02:44 pm Bug #5682: [Workbench] Can't view/download files under subdirectories in stream
commit:6c63fcb LGTM
I noticed that this also fixes the rendering (files are nested in their folders instead of hav...
Peter Amstutz
03:05 pm Revision fdd2d805 (arvados): refs #5682 : update arvados gem version
Radhika Chippada
03:05 pm Feature #4467 (Resolved): [Workbench] Add "select all" button to project content panes
Applied in changeset arvados|commit:dc0237c289882a058a0d5c91b720a4b37917bc9d. Radhika Chippada
02:33 pm Feature #4467: [Workbench] Add "select all" button to project content panes
commit:58997b4 LGTM Peter Amstutz
03:02 pm Revision 559d26fd (arvados): closes #5682
Merge branch '5682-download-file-error' Radhika Chippada
03:01 pm Revision a06f90e1 (arvados): Merge branch 'master' into 5682-download-file-error
Radhika Chippada
03:00 pm Revision dc0237c2 (arvados): closes #4467
Merge branch '4467-project-contents-select-all' Radhika Chippada
02:21 pm Support #5833 (Feedback): Cannot get Arvados installed
Nico César
01:43 pm Bug #5990 (Resolved): [SDKs] arv-run defaults to using arvados/jobs, without checking that it exi...
This can lead to pipeline failures that are mysterious to users, if arvados/jobs does not exist or has an SDK that's ... Brett Smith
01:34 pm Bug #5959 (Closed): Failed Jobs on 5/7 (Docker issues?)
Duplicate of #5956. Brett Smith
01:34 pm Bug #5956 (New): [Deployment] Docker configuration changes restart Docker on compute nodes, inter...
This happened because of a Docker configuration change (to fix a bug reported by another user). Right now our config... Brett Smith
01:30 pm Bug #5956 (Closed): [Deployment] Docker configuration changes restart Docker on compute nodes, in...
Brett Smith
12:56 pm Revision b6175cc8 (arvados-dev): Update README.md
Kosma Moczek
12:33 pm Revision abf25e13 (arvados-dev): debianize
Kosma Moczek
12:32 pm Revision 0d3f1856 (arvados-dev): Makefile: install: create directories
Kosma Moczek
12:29 pm Revision 9832172b (arvados-dev): Makefile: install to DESTDIR/
Kosma Moczek
12:17 pm Revision 4d31c3a3 (arvados-dev): README.md: more typos
Kosma Moczek
12:17 pm Revision f3db68c5 (arvados-dev): README.md: typos goddammit
Kosma Moczek
12:11 pm Revision 9b8ea270 (arvados-dev): rename init-runit-docker -> runit-docker so that it fits on dock...
Kosma Moczek
12:01 pm Revision 6f2ad810 (arvados-dev): initial commit
Kosma Moczek
10:46 am Revision 5216f1f2 (arvados-dev): Initial commit
Kosma Moczek
08:42 am Revision cbce2f05 (arvados-dev): change the usage() semantics slightly...
to better accommodate additional custom help messages Sitaram Chamarty
08:41 am Revision 47a8b3c4 (arvados-dev): gitolite query-rc --dump (or -d)
Sitaram Chamarty

05/10/2015

02:00 am Bug #5989 (Resolved): [API] API server repositories permissions list doesn't list repositories wi...
bug 1: it does not create the 'auto' subdirectory if it does not exist yet:... Ward Vandewege

05/09/2015

01:50 am Bug #5988 (Resolved): [API] can not create arvados repository
Applied in changeset arvados|commit:340d6a03a20592e3ba1c69340dbdf70070e43e82. Ward Vandewege
01:40 am Bug #5988 (Resolved): [API] can not create arvados repository
The instructions at http://doc.arvados.org/install/create-standard-objects.html no longer work:... Ward Vandewege
01:47 am Revision 340d6a03 (arvados): Fix install instructions: create arvados repository.
closes #5988 Ward Vandewege

05/08/2015

08:13 pm Bug #5720: [Workbench] Search for pipeline templates breaks
(following up on IRC comments)
In tab_panes.js
* if @$pane.attr('data-loaded-at') > 0@ then there is already vali...
Tom Clegg
07:26 pm Bug #5720: [Workbench] Search for pipeline templates breaks
At commit:acf8433
In tab_panes.js, the early "return" skips the @$pane.removeClass('pane-loading').addClass('pane-...
Tom Clegg
02:32 pm Bug #5720: [Workbench] Search for pipeline templates breaks
> In IRC:
>
> tom@curoverse.com
> 5:06 if (jqxhr.readyState == 0 || jqxhr.status == 0) {
> message = "Cancelled...
Radhika Chippada
06:52 pm Task #5776 (In Progress): Review branch: 5720-ajax-loading-error
Tom Clegg
02:33 pm Task #5776 (New): Review branch: 5720-ajax-loading-error
Radhika Chippada
06:51 pm Bug #5748 (In Progress): [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a...
aside from above comments LGTM, please merge Peter Amstutz
06:49 pm Bug #5748 (Feedback): [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
Tom Clegg
06:09 pm Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
Peter Amstutz wrote:
> That's true, it's easy enough to configure the usage, the important thing will be to communic...
Tom Clegg
05:27 pm Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
Tom Clegg wrote:
> I figured it would be better to err on the "too big" side because the sysadmin story "keepstore...
Peter Amstutz
05:00 pm Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
Peter Amstutz wrote:
> Reviewing 5748-max-buffers commit:978afd4
>
> * The default @maxBuffers = 128@ seems exces...
Tom Clegg
02:22 pm Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
Reviewing 5748-max-buffers commit:978afd4
* The default @maxBuffers = 128@ seems excessive (that's 8 GiB). With @...
Peter Amstutz
06:49 pm Task #5950 (Resolved): review 5748-max-buffers
Tom Clegg
01:37 pm Task #5950 (In Progress): review 5748-max-buffers
Peter Amstutz
06:09 pm Revision 7ea61e9c (arvados): Merge branch '5748-max-buffers' refs #5748
Tom Clegg
06:08 pm Revision 852325b0 (arvados): 5748: Update keepstore install docs (-max-buffers, -blob-signing-key).
Tom Clegg
06:07 pm Revision 4e26efd8 (arvados): 5748: Check for errors when writing pidfile. Keep it locked while ru...
* Handle SIGINT (the same way as SIGTERM)
* Improve startup/shutdown logs
Tom Clegg
06:07 pm Revision 14a27997 (arvados): 5748: Use a buffer pool instead of calling runtime.GC() during each ...
Tom Clegg
06:07 pm Revision a7af112f (arvados): 5748: Log clock time for each request.
For successful responses, log the standard HTTP status text for the
response code (instead of logging "OK" for any st...
Tom Clegg
06:07 pm Revision b25f82e5 (arvados): 5748: Return the real decoder error for unparseable trash and pull r...
Tom Clegg
05:59 pm Revision 460973c0 (arvados): 5748: Update keepstore install docs.
Tom Clegg
05:51 pm Bug #5967 (New): Editing a file within a collection in workbench
Say you have some configuration script, say HaplotypeCaller.scala. You have that in keep in a collection in your proj... Bryan Cosca
05:46 pm Task #5965 (Resolved): Update sso install docs for plain email/password login
Peter Amstutz
05:35 pm Feature #5962 (New): [Keep] Use bufferpool in keepproxy to limit memory use when there are many c...
keepstore lets you specify -max-buffers. keepproxy should have this feature too, for PUT requests. services/keepstore... Tom Clegg
05:12 pm Story #5781: [API] [DRAFT] Provide API methods for manipulating and combining collections
Pointed my workbench in dev to production and accessed:
collections/qr1hi-4zz18-tcnxylwkxg0nfhi?pp=full-backtrace...
Radhika Chippada
03:08 pm Story #5781: [API] [DRAFT] Provide API methods for manipulating and combining collections
On IRC:
tom 4:42 definitely look up the flamegraph gem and try putting &pp=flamegraph at the end of a (dev) workbe...
Radhika Chippada
03:39 pm Bug #5951: GET-Evidence login via google login no longer works - OpenID 2.0 is gone
Tom has a blog post about OpenID to OAuth 2.0 migration:
https://arvados.org/blogs/30
Piddling around I found i...
Abram Connelly
02:55 pm Feature #5960 (New): [API] Support transactional update of collections by multiple writers
To be able to reliably use the fuse mount as a writable shared drive, it is necessary to be able to have multiple wri... Peter Amstutz
02:25 pm Revision acf84339 (arvados): 5720: when jqxhr readyState == 0 or status == 0, it could be that th...
Radhika Chippada
02:17 pm Support #5833: Cannot get Arvados installed
Darshan Singh wrote:
> It did not work
(..)
> /usr/bin/docker run -d -p 172.17.42.1:53:53/udp --name skydns crosb...
Nico César
02:08 pm Bug #5959 (Closed): Failed Jobs on 5/7 (Docker issues?)
From qr1hi-8i9sb-bfc0bxbl6tuyd1a, qr1hi-8i9sb-4jqk0i8zsma5sma
stderr time="2015-05-07T23:15:49Z" level=fatal msg="...
Bryan Cosca
06:45 am Bug #4882 (Resolved): [Crunch] crunchstat reports surprising CPU usage when container appears and...
Applied in changeset arvados|commit:31d8ece649c63b008ed79a930a5b237ec795ff22. Tom Clegg
06:42 am Revision 31d8ece6 (arvados): Merge branch '4882-no-host-when-container' closes #4882
Tom Clegg
06:41 am Revision 81d100b1 (arvados): 4882: If -cgroup-cid flag is given, only read container stats. If no...
Tom Clegg
06:41 am Task #5932 (Resolved): Review 4882-no-host-when-container
Tom Clegg
05:17 am Revision 2ddfdc07 (arvados): 5748: Log clock time for each request.
For successful responses, log the standard HTTP status text for the
response code (instead of logging "OK" for any st...
Tom Clegg
12:18 am Bug #5956 (Duplicate): [Deployment] Docker configuration changes restart Docker on compute nodes,...
Two types of errors causing long-running pipeline jobs to fail. The jobs fail on different inputs. The priority here ... Sarah Guthrie

05/07/2015

10:18 pm Bug #5952 (New): Slow to log-in to Workbench
Workbench is a little sluggish overall, but my main concern is everything between clicking "login" to being able to c... Nancy Ouyang
10:15 pm Bug #5523 (In Progress): [Crunch] crunchstat should not report errors during normal timing races
Reopening to add TODO from #4882.
Tom Clegg
03:50 pm Bug #5523 (Resolved): [Crunch] crunchstat should not report errors during normal timing races
Applied in changeset arvados|commit:200f7004f921a68ec40b407dfe31f1db95e98fb9. Tom Clegg
03:34 pm Bug #5523: [Crunch] crunchstat should not report errors during normal timing races
commit:ae6b514 5523-stats-error LGTM Peter Amstutz
10:13 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Peter Amstutz wrote:
> I see, that is unfortunate. So if I understand correctly, there is a potential race between ...
Brett Smith
02:10 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Brett Smith wrote:
> > * What happens if an image has been loaded but has not yet used? Is it a candidate for imm...
Peter Amstutz
10:11 pm Revision b15e6c65 (arvados): 3793: Log uncleaned images.
Brett Smith
10:11 pm Revision a6495af8 (arvados): 3793: Always keep one Docker image.
Brett Smith
10:01 pm Bug #5951 (Closed): GET-Evidence login via google login no longer works - OpenID 2.0 is gone
Currently unable to login to GET-Evidence, which is blocking editing variants. The error page you get directed to is ... Sarah Guthrie
09:59 pm Task #5924 (Resolved): review 5745-serialize-content-only
Tom Clegg
02:17 pm Task #5924 (In Progress): review 5745-serialize-content-only
Peter Amstutz
09:57 pm Task #5933 (Resolved): Configurable limit on block buffers allocated at a given time
Tom Clegg
08:31 am Task #5933 (In Progress): Configurable limit on block buffers allocated at a given time
Tom Clegg
02:57 am Task #5933 (Resolved): Configurable limit on block buffers allocated at a given time
Tom Clegg
09:57 pm Task #5950 (Resolved): review 5748-max-buffers
Tom Clegg
09:55 pm Bug #5949 (Closed): [DRAFT] [Workbench] Users can be notified about changes to important pipelines
Things to consider:
* There's a lot of ways a pipeline could change: changes in git, changes to source collections...
Brett Smith
09:55 pm Revision 10c7a157 (arvados): 5748: Check for errors when writing pidfile. Keep it locked while ru...
* Handle SIGINT (the same way as SIGTERM)
* Improve startup/shutdown logs
Tom Clegg
09:40 pm Revision 1003636e (arvados): 5748: Use a buffer pool instead of calling runtime.GC() during each ...
Tom Clegg
09:40 pm Revision 8522f4fd (arvados): 5748: Return the real decoder error for unparseable trash and pull r...
Tom Clegg
09:36 pm Task #5948 (Resolved): Review branch: 5682-download-file-error
Radhika Chippada
09:35 pm Bug #5682: [Workbench] Can't view/download files under subdirectories in stream
Moved the logic that checks if a filename has '/' character into each_file_spec method from files method. Radhika Chippada
09:12 pm Bug #5682 (In Progress): [Workbench] Can't view/download files under subdirectories in stream
Radhika Chippada
07:22 pm Bug #5682 (New): [Workbench] Can't view/download files under subdirectories in stream
This is not fixed. #5179 only updated the way Keep::Manifest#files works. Workbench uses #has_file? to check whethe... Brett Smith
09:33 pm Bug #5947 (New): [Workbench] Provide additional guidance to users running their first pipeline
Nico says that, after exiting the tutorial, when he clicked "run a pipeline", he encountered a list of 20 pipelines a... Nancy Ouyang
09:18 pm Revision 3180bb6f (arvados): 3793: Always keep one Docker image.
Brett Smith
09:15 pm Revision 6c63fcb0 (arvados): 5682: update workbench arvados gem version
Radhika Chippada
09:11 pm Revision d2f68bd1 (arvados): Merge branch '3198-inode-cache' into 3198-writable-fuse, fix tests.
Conflicts:
services/fuse/arvados_fuse/__init__.py
services/fuse/arvados_fuse/fresh.py
services/fuse/tests/test_mou...
Peter Amstutz
09:06 pm Revision b8467da4 (arvados): 5682: move logic to check if '/' in filename into each_file_spec met...
Radhika Chippada
08:59 pm Bug #5720: [Workbench] Search for pipeline templates breaks
+1 to note-9. <code class="javascript">$container.data('infinite-serial')</code> can hold any js object... like a Dat... Tom Clegg
08:54 pm Bug #5946 (New): [Workbench] "other collections have the same content" page is confusing
URL; https://workbench.qr1hi.arvadosapi.com/collections/d41d8cd98f00b204e9800998ecf8427e+0
When a pipeline create...
Nancy Ouyang
08:21 pm Revision 80e1bb8d (arvados): 3793: Add unused image polling, per code review.
Brett Smith
08:14 pm Story #3198: [FUSE] Writable streaming arv-mount
Brett Smith wrote:
> Reviewing 3198-inode-cache at commit:2139ee84
>
> * Any chance of getting tests for this? I...
Peter Amstutz
08:07 pm Revision 0c01dc22 (arvados): 3198: Add --file-cache and --directory-cache to arv-mount to specify...
cache limits. Peter Amstutz
08:05 pm Bug #5945 (Closed): arv-get is slow for this collection
... Abram Connelly
08:01 pm Feature #5928: Syntax highlighting of viewing source in workbench
Client side opens up a lot of possibilities:
* https://highlightjs.org/usage/
* https://craig.is/making/rainbows
...
Abram Connelly
07:20 pm Feature #5928: Syntax highlighting of viewing source in workbench
Preferably something that doesn't fork from passenger. Perhaps coderay, or do it client-side with https://github.com/... Tom Clegg
06:47 pm Feature #5928: Syntax highlighting of viewing source in workbench
http://pygments.org/docs/cmdline/
for example:
hello.c:...
Abram Connelly
07:47 pm Revision fa4c5476 (arvados): 3198: Inodes() and Operations() take InodeCache() object directly. ...
number of entries to retain is configurable. Added unit test of inode cache. Peter Amstutz
07:43 pm Feature #4467: [Workbench] Add "select all" button to project content panes
Peter: yes, moving into js and reusing this code is a good idea. Updated accordingly. Thanks. Radhika Chippada
05:43 pm Feature #4467: [Workbench] Add "select all" button to project content panes
The @onclick@ methods are named @select_all_files()@ and @unselect_all_files()@, however they are not selecting files... Peter Amstutz
07:21 pm Revision 58997b45 (arvados): 4467: Move select_all_items and unselect_all_items methods into sele...
Radhika Chippada
07:21 pm Feature #5944 (Rejected): [Workbench] Syntax highlighting for repository-browsing
Tom Clegg
07:10 pm Feature #5944 (Rejected): [Workbench] Syntax highlighting for repository-browsing
Something like this... Tom Clegg
07:09 pm Bug #5943 (New): User uuid changed during a pipeline run
qr1hi-d1hrv-bgj6vtddg9cmyyt looks like it failed due to nodes down:
2015-05-07_18:33:05 salloc: error: Failed to a...
Bryan Cosca
06:40 pm Task #5942 (Resolved): Review branch: 3454-default-docker-image
Radhika Chippada
06:39 pm Feature #3454 (In Progress): [API] Assign a system-default default docker image (instead of using...
Radhika Chippada
06:38 pm Feature #5941 (New): When creating a new collection that is a subset of a previous collection, th...
For example, Created from collection hash and uuid Bryan Cosca
06:37 pm Feature #5940 (New): Rerunning a pipeline should keep as much metadata from the original template...
!descriptionforinstances.png!
I really like this description. But when I re-run the pipeline I lose this descripti...
Bryan Cosca
06:29 pm Revision dc00995b (arvados): Merge branch 'master' into 4467-project-contents-select-all
Radhika Chippada
06:17 pm Revision f820c0ee (arvados): 3454: use configured default docker image when none found in a job's...
Radhika Chippada
05:58 pm Bug #4882: [Crunch] crunchstat reports surprising CPU usage when container appears and disappears
Peter Amstutz wrote:
> It seems likely that there will be spurious "stats not available" messages during container s...
Tom Clegg
05:20 pm Bug #4882: [Crunch] crunchstat reports surprising CPU usage when container appears and disappears
It seems likely that there will be spurious "stats not available" messages during container startup and teardown, it ... Peter Amstutz
02:55 am Bug #4882 (In Progress): [Crunch] crunchstat reports surprising CPU usage when container appears ...
Tom Clegg
05:50 pm Bug #5745 (Resolved): [Keep] keepstore should serialize file reads/writes, but not directory look...
Applied in changeset arvados|commit:fde21d34d011af2123668983c559632221390fd4. Tom Clegg
03:21 pm Bug #5745: [Keep] keepstore should serialize file reads/writes, but not directory lookups, when -...
commit:867263b 5745-serialize-content-only LGTM Peter Amstutz
05:48 pm Revision d38f970a (arvados): 5748: Use a buffer pool instead of calling runtime.GC() during each ...
Tom Clegg
05:48 pm Revision 649ff5c9 (arvados): 5748: Return the real decoder error for unparseable trash and pull r...
Tom Clegg
05:47 pm Revision fde21d34 (arvados): Merge branch '5745-serialize-content-only' closes #5745
Tom Clegg
05:34 pm Task #5938 (New): Handle normal container startup and shutdown races without logging an error/not...
Tom Clegg
05:25 pm Task #5916 (In Progress): Review branch: 4467-project-contents-select-all
Peter Amstutz
05:12 pm Revision 80fe29b4 (arvados): 5748: Use a buffer pool instead of calling runtime.GC() during each ...
Tom Clegg
05:12 pm Revision 978afd40 (arvados): 5748: Return the real decoder error for unparseable trash and pull r...
Tom Clegg
04:48 pm Revision e6c90436 (arvados): 5745: Fix test order dependency (restore mocked methods), tidy up te...
Tom Clegg
04:45 pm Revision cc303a0e (arvados): 5745: Serialize writes and data reads, but allow concurrent requests
to do read-only non-data operations (like finding existing blocks and
checking free disk space) which are likely to b...
Tom Clegg
03:59 pm Revision 929a1068 (arvados): 4882: If -cgroup-cid flag is given, only read container stats. If no...
Tom Clegg
03:47 pm Revision 200f7004 (arvados): Merge branch '5523-stats-error' closes #5523
Tom Clegg
03:46 pm Task #5918 (Resolved): Review 5523-stats-error
Tom Clegg
03:23 pm Task #5918 (In Progress): Review 5523-stats-error
Peter Amstutz
03:35 pm Task #5932 (In Progress): Review 4882-no-host-when-container
Peter Amstutz
02:56 am Task #5932 (Resolved): Review 4882-no-host-when-container
Tom Clegg
03:23 pm Bug #5937 (Duplicate): Log graph shoes up with no log
!loggraphnolog.png!
qr1hi-8i9sb-xs9n42ugaysw5mj
Also I have to keep refreshing to get progress done
Bryan Cosca
03:19 pm Task #5936 (Resolved): Review SSO master
Peter Amstutz
03:01 pm Feature #5935 (New): In workbench, when viewing pipeline instances, there should be an indication...
Sometimes it's useful to know which jobs in the pipeline got re-used. Workbench should give some indication of this ... Abram Connelly
02:15 pm Task #5877 (Resolved): Review 5787-run-command-checkin
Peter Amstutz
12:23 pm Support #5833: Cannot get Arvados installed
It did not work
$ ./arvdock stop
doc_server
api_server
workbench_server
skydock
skydns
keep_server_0
keep_s...
Darshan Singh
03:21 am Support #5833: Cannot get Arvados installed
Darshan Singh wrote:
> This is what I get:
> tcp 0 0 127.0.1.1:53 0.0.0.0:* L...
Ward Vandewege
03:00 am Revision 867263b6 (arvados): 5745: Merge branch 'master' into 5745-serialize-content-only
Tom Clegg
02:57 am Revision 4adea935 (arvados): 4882: If -cgroup-cid flag is given, only read container stats. If no...
Tom Clegg
02:56 am Task #5925 (Resolved): Review 5748-keepstore-leak
Tom Clegg

05/06/2015

09:32 pm Revision 02e1074d (arvados): Fix docker image build for SSO server after refactoring work in #5829.
refs #5829 Ward Vandewege
09:28 pm Revision b6f54ccb (arvados): refs #5493: Merge branch '5493-fix-yellow-gif'
Nancy Ouyang
09:28 pm Revision 3774f7fa (sso-provider): Clean up a bit more after the switch to application.yml
No issue # Ward Vandewege
09:27 pm Revision d0f98546 (arvados): 5493: fix yellow gif
Nancy Ouyang
09:13 pm Revision e7a2db3f (arvados): Merge branch '5748-keepstore-leak' refs #5748
Tom Clegg
09:11 pm Revision b9024e06 (arvados): 5748: Clean up comments and variable names.
Tom Clegg
09:11 pm Revision 6bd5a4e0 (arvados): 5748: Write index data to http.ResponseWriter, instead of using string
concatenation to buffer the entire response. Tom Clegg
09:00 pm Task #5931 (Resolved): Review 5842-node-manager-tighten-successful-boot-criteria-wip
Applied in changeset arvados|commit:88b0204247e448ba5f715cb01adba4597bb6aae7. Brett Smith
08:14 pm Task #5931 (Resolved): Review 5842-node-manager-tighten-successful-boot-criteria-wip
Brett Smith
09:00 pm Bug #5842 (Resolved): [Node Manager] Too many nodes being started
Applied in changeset arvados|commit:88b0204247e448ba5f715cb01adba4597bb6aae7. Brett Smith
08:52 pm Bug #5842: [Node Manager] Too many nodes being started
@_nodes_excess()@ also returns different (and now correct) numbers now that booting nodes are not counted in @_nodes_... Tom Clegg
05:33 pm Bug #5842 (In Progress): [Node Manager] Too many nodes being started
Brett Smith
02:49 pm Bug #5842: [Node Manager] Too many nodes being started
Tackling now per discussion with Ward. Brett Smith
08:57 pm Revision 88b02042 (arvados): Merge branch '5842-node-manager-tighten-successful-boot-criteria-wip'
Closes #5842, #5931. Brett Smith
08:57 pm Revision 42b7aeb0 (arvados): 5842: Node Manager shuts down booted nodes if they can't do compute ...
If a booted node is not able to do work (it's not idle or busy),
consider that a bootstrapping failure and shut it do...
Brett Smith
08:57 pm Revision e81a3e9b (arvados): 5842: Node Manager only considers nodes busy if they're working.
Previously, Node Manager considered any non-idle node as busy,
including down nodes. This causes it to boot replacem...
Brett Smith
08:40 pm Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
Reviewing commit:4d53c7e. This is good, just a couple cleanliness things.
* There are a couple of references to o...
Brett Smith
07:31 pm Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
h3. a memory use bug
Currently, keepstore will allocate as many buffers as it has clients. There is no limit on th...
Tom Clegg
05:43 pm Bug #5748 (In Progress): [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a...
Tom Clegg
08:21 pm Task #5929 (Resolved): review 5926-parameterize-max-slots
Ward Vandewege
07:49 pm Task #5929 (Resolved): review 5926-parameterize-max-slots
Ward Vandewege
08:20 pm Feature #5926 (Resolved): [API] MAX_SLOTS should be a configuration value (app/models/node.rb)
Applied in changeset arvados|commit:e7e61999bf577b3ba5308c747dda4a0011516aa7. Ward Vandewege
08:00 pm Feature #5926: [API] MAX_SLOTS should be a configuration value (app/models/node.rb)
at commit:0358074
_Might_ be worth mentioning in config comment something like: "After this limit is reduced, any ...
Tom Clegg
07:38 pm Feature #5926 (In Progress): [API] MAX_SLOTS should be a configuration value (app/models/node.rb)
Ward Vandewege
07:28 pm Feature #5926 (Resolved): [API] MAX_SLOTS should be a configuration value (app/models/node.rb)
Ward Vandewege
08:19 pm Task #5925 (In Progress): Review 5748-keepstore-leak
Brett Smith
05:42 pm Task #5925 (Resolved): Review 5748-keepstore-leak
Tom Clegg
08:17 pm Revision e7e61999 (arvados): Merge branch '5926-parameterize-max-slots'
closes #5926 Ward Vandewege
08:16 pm Revision b988327f (arvados): Improve comment in application.default.yml based on review feedback.
refs #5926 Ward Vandewege
08:08 pm Revision d52af99c (arvados): 5842: Node Manager shuts down booted nodes if they can't do compute ...
If a booted node is not able to do work (it's not idle or busy),
consider that a bootstrapping failure and shut it do...
Brett Smith
08:08 pm Revision cf08eb6a (arvados): 5842: Node Manager only considers nodes busy if they're working.
Previously, Node Manager considered any non-idle node as busy,
including down nodes. This causes it to boot replacem...
Brett Smith
08:07 pm Bug #5930 (Resolved): [Documentation] Misc. documentation fixes
As listed by Nico:
* Order of upload and download data is wrong.
http://doc.arvados.org/user/tutorials/tutorial-k...
Nancy Ouyang
07:57 pm Feature #5382: [Documentation] arvados VM simulator, demonstrating how it looks to use Arvados fr...
A +1 from Nico, who writes
> "I just want to play" type of instructions:
> something very hands on like https:/...
Nancy Ouyang
07:46 pm Revision 03580741 (arvados): Make MAX_SLOTS a configurable parameter, and rename it to max_comput...
refs #5926 Ward Vandewege
07:36 pm Feature #5928 (Closed): Syntax highlighting of viewing source in workbench
Abram Connelly
07:36 pm Feature #5927 (New): In place editing of source files in workbench for Curoverse/Arvados hosted g...
I would be nice to have in place editing of source files for Arvados/Curoverse repositories in workbench. Abram Connelly
05:36 pm Revision 4d53c7ea (arvados): 5748: Write index data to http.ResponseWriter, instead of using string
concatenation to buffer the entire response. Tom Clegg
05:31 pm Bug #5745 (In Progress): [Keep] keepstore should serialize file reads/writes, but not directory l...
Tom Clegg
05:30 pm Task #5924 (Resolved): review 5745-serialize-content-only
Tom Clegg
05:28 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
Nico Cesar wrote:
> same with docker 1.6.0
The branch set @--memory-swap@ to make the node's entire swap availabl...
Brett Smith
05:25 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
same with docker 1.6.0... Nico César
05:24 pm Bug #5917 (Closed): Node Manager did not spin up enough nodes when I set min_nodes = 20
Closing as a sort of duplicate. This situation is caused by two bugs we already have filed, #4129 and #5824. #5824 ... Brett Smith
03:04 am Bug #5917 (Closed): Node Manager did not spin up enough nodes when I set min_nodes = 20
!nodemanagerdidnotspinupenoughnodes.png!
Job qr1hi-8i9sb-6hfkeo7gvpexcjw has been queued for 6.5 hours. When I log...
Bryan Cosca
04:56 pm Revision 666eb6b6 (arvados): 5745: Serialize writes and data reads, but allow concurrent requests
to do read-only non-data operations (like finding existing blocks and
checking free disk space) which are likely to b...
Tom Clegg
04:49 pm Bug #5923 (Closed): Fiddlesticks when trying to view a log file
https://cloud.curoverse.com/jobs/qr1hi-8i9sb-8rp82pposgfl99y#Log
I think this is because I removed a bunch of log ...
Bryan Cosca
02:37 pm Bug #5920 (New): Clicking on the commit hash on a job brings you to the commit page instead of th...
To actually see the script used to run the job, I need to click on repository and then the script. I would like to cl... Bryan Cosca
02:15 pm Bug #5919 (Closed): Keep errors
https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-bn1dzf48g4jtzgq#Log
2015-05-06_13:23:07 qr1hi-8i9sb-led...
Bryan Cosca
02:09 pm Revision ae6b514a (arvados): 5523: Say "notice" instead of "error" when stats file changes/appear...
Tom Clegg
02:08 pm Task #5918 (Resolved): Review 5523-stats-error
Tom Clegg
02:08 pm Bug #5523 (In Progress): [Crunch] crunchstat should not report errors during normal timing races
Tom Clegg
01:03 am Feature #4467 (In Progress): [Workbench] Add "select all" button to project content panes
Radhika Chippada
12:54 am Task #5916 (Resolved): Review branch: 4467-project-contents-select-all
Radhika Chippada
12:49 am Revision 3e48f1c6 (arvados): 4467: add test for "Select all" and "Unselect all" buttions in proje...
Radhika Chippada

05/05/2015

10:54 pm Bug #3843 (Resolved): [Crunchstat] Report CPU accounting numbers accurately.
Fixed by 3b0de2173e005deacc22d083a4aea23f9a648865 during #3826. Tom Clegg
09:16 pm Bug #5915 (Resolved): [Workbench] Sharing link for public collection still renders after sharing ...
To replicate: Go to https://workbench.qr1hi.arvadosapi.com/collections/download/qr1hi-4zz18-7zk4muy5grnaqpv/4qji0cfum... Nancy Ouyang
08:47 pm Bug #5913: [Workbench] Should validate that a job's repository actually exists before rendering t...
The pipeline failed because I gave the incorrect repository ('abram' as opposed to 'abram/gffpairwiseconcordance'). ... Abram Connelly
08:31 pm Bug #5913 (New): [Workbench] Should validate that a job's repository actually exists before rende...
When trying to access my repository @abram/gffpairwiseconcordance@ from pipeline su92l-d1hrv-ctxni10ap6vztks I get a ... Abram Connelly
08:37 pm Revision 2e270dde (sso-provider): 5829: Add missing erb partial for rendering buttons for links t...
service actions. Peter Amstutz
08:35 pm Revision 92e4fb52 (sso-provider): 5829: Redirect to :user_return_to after login.
Peter Amstutz
08:35 pm Story #5914 (New): [DRAFT] Provide one clear way for users to get data from an external source in...
h2. Background
Users frequently want to work with data available from public sites. It's important that it be eas...
Brett Smith
08:20 pm Feature #4456: [Workbench] Provide more feedback about when a queued job is likely to start.
Possible ways/places to present this information:
* Pipeline instance #show &rarr; Components
** If component state...
Tom Clegg
02:56 pm Feature #4456: [Workbench] Provide more feedback about when a queued job is likely to start.
Some system states that could be translated to a start-time prediction:
* All worker nodes are busy. Nodemanager wil...
Tom Clegg
08:10 pm Revision e3298ea0 (sso-provider): 5829: Add application.yml to .gitignore
Peter Amstutz
08:05 pm Revision 9cd526a5 (sso-provider): 5829: Committed application.yml by accident.
Peter Amstutz
08:03 pm Revision 4e2319ce (arvados): 4467: add "select all" and "unselect all" buttons to project contents.
Radhika Chippada
07:58 pm Revision 3f69ca6a (sso-provider): 5829: Registration and account management of built-in accounts ...
Peter Amstutz
07:45 pm Bug #5905: [SDKs] Improve certificate validation in Python SDK
I removed this recently (#5562) from source:sdk/python/arvados/keep.py in commit:7ab494e42b35b3769a326a16b7e90f1d2014... Tom Clegg
07:40 pm Feature #5735 (Resolved): [Workbench] Edit box for project description should be bigger
Applied in changeset arvados|commit:cb41817568900d52d3768a91f703f04696f6b702. Radhika Chippada
07:29 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Converted tiptitle to nonhtml_option. Radhika Chippada
06:58 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Reviewing commit:6e10831. This seems really great. Thanks for sticking it through. Just one small thing from here:... Brett Smith
06:19 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Brett: added a new "nonhtml_options" parameter to render_editable_attribute method definition and moved all the btn* ... Radhika Chippada
07:35 pm Revision cb418175 (arvados): closes #5735
Merge branch '5735-edit-description-box-size' Radhika Chippada
07:30 pm Task #5891 (Resolved): Review branch: 5735-edit-description-box-size
Radhika Chippada
07:26 pm Revision 8ac0683e (arvados): 5735: move tiptitle into nonhtml_options
Radhika Chippada
07:02 pm Bug #5713: [FUSE] File access sometimes takes too long on su92l
... Abram Connelly
06:23 pm Story #5781 (In Progress): [API] [DRAFT] Provide API methods for manipulating and combining colle...
Radhika Chippada
06:23 pm Bug #5842: [Node Manager] Too many nodes being started
Here's a log snippet that just happened that I think supports my hypothesis. We start just as a new cloud node comes... Brett Smith
06:16 pm Revision 6e10831b (arvados): Merge branch 'master' into 5735-edit-description-box-size
Radhika Chippada
06:12 pm Revision fe7d9a6c (arvados): 5735: add comment
Radhika Chippada
06:09 pm Bug #5909 (Closed): Cannot see output collection from workbench
Trying to access the output collection of the second portion of the job https://workbench.su92l.arvadosapi.com/pipel... Abram Connelly
05:53 pm Revision bd2023d1 (arvados): 5735: add a new nonhtml_options parameter to render_editable_attribu...
which can be used to pass any non data-* custom attributes that are useful in
customizing the rendering of the editab...
Radhika Chippada
05:16 pm Revision e89c415a (sso-provider): 5829: Add registration page with email confirmation. Use consi...
various login pages. Peter Amstutz
04:54 pm Bug #5908: [Workbench] collection#show performing too many unnecessary API server requests when a...
I pointed my workbench to qr1hi api server and accessed /collections/qr1hi-4zz18-zn1m6s2le7dqjfs. I noticed in the wo... Radhika Chippada
04:37 pm Bug #5908 (Closed): [Workbench] collection#show performing too many unnecessary API server reques...
Radhika Chippada
04:16 pm Story #5837 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
04:14 pm April development review: Workbench makes it easy
Over the last month, we've made it easier than ever to get started with Arvados. You'll literally see the results as... Brett Smith
03:34 pm Task #5880 (Resolved): Review 5724-blob-signature-ttl
Tom Clegg
03:20 pm Revision 49ab94b9 (sso-provider): Merge branch 'login_via_email_and_password'
Peter Amstutz
03:19 pm Revision f1b13f48 (sso-provider): 5829: Better login pages for regular login and LDAP.
Peter Amstutz
02:58 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Peter Amstutz wrote:
> commit:4dc84fd
>
> * Per office conversation, remove @if self.images.any_users(): return@ f...
Brett Smith
02:56 pm Bug #5907 (New): [SDKs] PySDK's internal decorators lose method metadata
Try, e.g., @pydoc arvados.collection.Collection.copy@. The arguments aren't named on the method signature, even thou... Brett Smith
02:38 pm Bug #5906 (New): [API] crunch-dispatch should mark a job failed when its repository cannot be fet...
h2. Development story
If you build a pipeline that refers to a remote repository that cannot be fetched (e.g., typ...
Abram Connelly
02:24 pm Revision df5a73a8 (arvados): 3793: Fixups from code review.
Brett Smith

05/04/2015

11:59 pm Revision 7d12bf89 (arvados): 5735: use data- for button text and button class custom attributes.
Radhika Chippada
11:11 pm Revision cb55d2c0 (arvados): 5735: exclude btn* attributes from span tag.
Radhika Chippada
10:02 pm Bug #5905 (Closed): [SDKs] Improve certificate validation in Python SDK
h2. Development story
Many users are seeing a warning from urllib3 letting them know that certificates can't actua...
Abram Connelly
09:18 pm Bug #5842: [Node Manager] Too many nodes being started
Theory: this is caused or exacerbated by a gap in time between when nodes ping Arvados and when they're resumed in SL... Brett Smith
09:05 pm Bug #5724 (Resolved): [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on def...
Applied in changeset arvados|commit:9d4bc458b767e4c05024dfe02207283745e1ba06. Tom Clegg
08:21 pm Bug #5724: [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on default_trash_...
Radhika Chippada wrote:
> Comments with the latest in branch (da57a997):
>
> * Since you are renaming variables, ...
Tom Clegg
04:25 pm Bug #5724: [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on default_trash_...
Comments with the latest in branch (da57a997):
* Since you are renaming variables, I was wondering if we want to c...
Radhika Chippada
02:17 pm Bug #5724: [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on default_trash_...
Comments for branch 5724-blob-signature-ttl at 6fc44a6:
Should the comment at line 234 in application.default.yml ...
Radhika Chippada
09:00 pm Bug #5898: [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepProxyTestCas...
Suggest a wait loop in run_test_servers.py&rarr;_start_keep() and _start_keep_proxy() that waits up to X milliseconds... Tom Clegg
03:31 pm Bug #5898 (Resolved): [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepP...
Tom Clegg
08:46 pm Revision 9d4bc458 (arvados): Merge branch '5724-blob-signature-ttl' closes #5724
Tom Clegg
08:39 pm Bug #5902: [Workbench] collection#show is unresponsive for a large collection
Also, this collection might have been copied from tb05z and might not have any provenance in terms of pipelines creat... Abram Connelly
08:37 pm Bug #5902: [Workbench] collection#show is unresponsive for a large collection
UPDATE: The project name looks to be not owned by be but by Sally Guthrie (I see it under her directory on the keep m... Abram Connelly
08:34 pm Bug #5902 (New): [Workbench] collection#show is unresponsive for a large collection
When trying to view collection su92l-4zz18-qww94nsw428dm7o, it bogs down Firefox and eventually brings up a 'Warning:... Abram Connelly
08:24 pm Bug #5901 (New): [API] Improve performance of large requests in parallel
Attached are two files. The first is a simple Python script that uses threads to fetch the same collection object fr... Brett Smith
08:17 pm Task #5891 (In Progress): Review branch: 5735-edit-description-box-size
Brett Smith
07:59 pm Task #5891 (Resolved): Review branch: 5735-edit-description-box-size
Radhika Chippada
03:18 pm Task #5891 (In Progress): Review branch: 5735-edit-description-box-size
Brett Smith
08:16 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Reviewing commit:e146ad3. The changes address the previous issues, so thanks much for that.
The span tag is gener...
Brett Smith
08:00 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Thanks Brett. Yes, limiting the inline css config to description is a good idea and I made those updates. Radhika Chippada
03:34 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Reviewing commit:13e4bac
The new CSS will set 98% width for any inline X-Editable component. I'm concerned that t...
Brett Smith
07:50 pm Revision e146ad30 (arvados): Merge branch 'master' into 5735-edit-description-box-size
Radhika Chippada
07:48 pm Revision 71ebe5f5 (arvados): 5735: use the inline css for description only so that any future inl...
Radhika Chippada
05:27 pm Feature #5900 (Closed): [SDK] Implement arvados.gettaskparam(*args) to match arvados.getjobparam(...
Since get_task_param_mount and get_job_param_mount both exist, it would be useful to also have the ability to get bot... Sarah Guthrie
05:10 pm Task #5881 (Resolved): Review 5752-arv-copy-preserve-docker-timestamps-wip
Applied in changeset arvados|commit:73c9a44b85ba72e881c5133422fcabe3f1322142. Brett Smith
03:18 pm Task #5881 (In Progress): Review 5752-arv-copy-preserve-docker-timestamps-wip
Tom Clegg
05:10 pm Bug #5752 (Resolved): [SDKs] Fix unreliable image timestamp recording in arv keep docker
Applied in changeset arvados|commit:73c9a44b85ba72e881c5133422fcabe3f1322142. Brett Smith
03:23 pm Bug #5752: [SDKs] Fix unreliable image timestamp recording in arv keep docker
commit:c19ed0b lgtm, thanks Tom Clegg
05:07 pm Revision 73c9a44b (arvados): Merge branch '5752-arv-copy-preserve-docker-timestamps-wip'
Closes #5752, #5881. Brett Smith
05:07 pm Revision 83164dbf (arvados): 5752: arv-copy preserves properties of docker_image links.
The properties include the image_timestamp, which tells Arvados when
the source image was created, rather than the co...
Brett Smith
04:28 pm Revision 47f4f1b2 (arvados): Merge branch 'master' into 5735-edit-description-box-size
Radhika Chippada
04:19 pm Task #5880 (In Progress): Review 5724-blob-signature-ttl
Radhika Chippada
03:40 pm Revision ffadd5d8 (arvados): Merge branch '5787-run-command-checkin' refs #5787
Peter Amstutz
03:30 pm Bug #5893 (Resolved): [Workbench] Fix unreliable repository browsing
Applied in changeset arvados|commit:eb3303340c51d13512397c3d83c955af9f516f47. Tom Clegg
03:11 pm Bug #5893: [Workbench] Fix unreliable repository browsing
commit:6fcd070 is good to merge. Thanks. Brett Smith
03:24 pm Revision b02d9627 (arvados): 5787: Change caught_error to last_error in vwd.py to return last exc...
Peter Amstutz
03:23 pm Task #5894 (Resolved): Review 5893-helper-stdin
Tom Clegg
02:14 pm Task #5894 (In Progress): Review 5893-helper-stdin
Brett Smith
03:19 pm Task #5869 (Resolved): Review 3145-missing-content-length-error
Peter Amstutz
03:18 pm Revision eb330334 (arvados): Merge branch '5893-helper-stdin' closes #5893
Tom Clegg
03:07 pm Bug #5897 (Closed): [FUSE] Catch and recover from any API client exceptions
#5896 caused an API client error (timeout) to be raised in arv-mount. This exception was ultimately uncaught, and ca... Brett Smith
03:04 pm Bug #5896 (New): [FUSE] Ensure all I/O errors properly distinguish "not found" and other API errors
A user is trying to work with a collection so large that, as of now, the API server can't return it—nginx returns a 5... Brett Smith
03:03 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
commit:4dc84fd
* Per office conversation, remove @if self.images.any_users(): return@ from @clean_images()@ since ...
Peter Amstutz
02:57 pm Revision eb03fb3a (arvados): Merge branch '5724-blob-signature-ttl' commit '6fc44a6' refs #5724
Tom Clegg
02:55 pm Task #5879 (Resolved): Review 5724-blob-signature-ttl at 6fc44a6
Tom Clegg
02:12 pm Task #5879 (In Progress): Review 5724-blob-signature-ttl at 6fc44a6
Radhika Chippada
02:49 pm Task #5895 (Resolved): Ensure vwd.checkin doesn't accidentally commit (or otherwise mess up) when...
see #5787 Tom Clegg
02:45 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Peter Amstutz wrote:
> You're right. Now the task will fail on IOError or OSError (but it will still try to write a...
Tom Clegg
02:27 pm Revision 066efa83 (arvados): 5724: Update reference to keepstore flag, now -blob-signature-ttl.
Tom Clegg
01:27 pm Task #5868 (Resolved): Review 5562-pycurl-upload
Peter Amstutz
01:10 pm Bug #5562 (Resolved): [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Applied in changeset arvados|commit:fc16c2ebbb92d9b0e52b6435b717f26b9680c7e6. Peter Amstutz
01:07 pm Revision fc16c2eb (arvados): Merge branch '5562-pycurl-upload' closes #5562
Peter Amstutz

05/03/2015

02:07 pm Revision 8bef6711 (arvados-dev): (minor) fix typo
Tony Xue

05/02/2015

06:59 am Task #5894 (Resolved): Review 5893-helper-stdin
Tom Clegg
06:58 am Bug #5893 (In Progress): [Workbench] Fix unreliable repository browsing
Tom Clegg
06:51 am Bug #5893 (Resolved): [Workbench] Fix unreliable repository browsing
Sometimes, after getting 401 from arv-git-httpd and asking the credential helper for a password, git exits non-zero i... Tom Clegg
06:49 am Revision 6fcd0706 (arvados): 5893: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:49 am Revision e343f081 (arvados): 5416: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:41 am Revision 57d5f07d (arvados): 5416: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:41 am Revision c311c447 (arvados): 5416: gofmt fixes. Fix some logs to print as strings, not byte arrays.
Tom Clegg
06:41 am Revision 33235ab1 (arvados): 5416: Use git credential helpers for arv-git-httpd tests. Fix workbe...
The sporadic "git exited 128" errors -- very common in git2 and rare
in git1 -- seem to have been caused by git getti...
Tom Clegg
06:41 am Revision 42b4e23e (arvados): 5416: Add realm="git" to WWW-Authenticate header, cf. rfc2617
Tom Clegg
06:41 am Revision 32254a99 (arvados): 5893: Add realm="git" to WWW-Authenticate header, cf. rfc2617
Tom Clegg
06:41 am Revision 33b41435 (arvados): 5893: Use git credential helpers for arv-git-httpd tests. Fix workbe...
The sporadic "git exited 128" errors -- very common in git2 and rare
in git1 -- seem to have been caused by git getti...
Tom Clegg
06:41 am Revision 49a76fac (arvados): 5893: gofmt fixes. Fix some logs to print as strings, not byte arrays.
Tom Clegg
06:34 am Revision 00121a24 (arvados): 5416: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:17 am Revision 0f1d3aca (arvados): 5416: Use git credential helpers for arv-git-httpd tests. Fix workbe...
The sporadic "git exited 128" errors -- very common in git2 and rare
in git1 -- seem to have been caused by git getti...
Tom Clegg
06:09 am Revision c0a80b0a (arvados): 5416: gofmt fixes. Fix some logs to print as strings, not byte arrays.
Tom Clegg
06:07 am Revision 9019ae81 (arvados): 5416: Add realm="git" to WWW-Authenticate header, cf. rfc2617
Tom Clegg
12:25 am Support #5833 (In Progress): Cannot get Arvados installed
Ward Vandewege
12:17 am Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
This doesn't appear to be related to r/o disks, I have seen it happen on tb05z as well, where all disks can be writte... Ward Vandewege

05/01/2015

09:35 pm Story #5837 (In Progress): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
06:15 pm Story #5837: [Documentation] (recurring) Write blog post in first three days of sprint
Stealing per discussion. Brett Smith
09:24 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
commit:bde53a1 LGTM, thanks Tom Clegg
09:15 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Tom Clegg wrote:
> Now at commit:0a87aad
>
> typo "necessay" in vwd.py
Fixed.
> > Also catches exceptions n...
Peter Amstutz
08:47 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Now at commit:0a87aad
typo "necessay" in vwd.py
> Also catches exceptions now.
Hm. This looks like "if can't...
Tom Clegg
06:44 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Tom Clegg wrote:
> Looking at commit:f6fcf9f on 5787-run-command-checkin
>
> The checkin docstring says "Symlinks...
Peter Amstutz
05:34 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Looking at commit:f6fcf9f on 5787-run-command-checkin
The checkin docstring says "Symlinks into the keep mount in ...
Tom Clegg
09:07 pm Revision 8b689efa (arvados): 5787: Fix syntax error
Peter Amstutz
09:02 pm Revision 5b970a6c (arvados): 5787: Error writing output will cause task to fail. Tweak documenta...
Peter Amstutz
08:55 pm Task #5871 (Resolved): Review 5834-api-max-response-size-wip
Applied in changeset arvados|commit:e8f91c87ef238ddf6bd96914a196d2d90825e8ee. Brett Smith
06:50 pm Task #5871 (In Progress): Review 5834-api-max-response-size-wip
Peter Amstutz
08:55 pm Bug #5834 (Resolved): [API] Be careful about memory usage when responding to collections#index qu...
Applied in changeset arvados|commit:e8f91c87ef238ddf6bd96914a196d2d90825e8ee. Brett Smith
08:18 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
commit:f87f91c
per the spec:
"max_response_size should be documented in application.default.yml with a note tha...
Peter Amstutz
08:49 pm Revision e8f91c87 (arvados): Merge branch '5834-api-max-response-size-wip'
Closes #5834, #5871. Brett Smith
08:48 pm Task #5859 (Resolved): Update default config, add to discovery doc
Tom Clegg
08:45 pm Revision 3f51fa48 (arvados): 5834: Limit how much manifest text data API server will load for index.
This prevents situations where clients cause the API server to balloon
in memory use by requesting an index including...
Brett Smith
08:21 pm Task #5857 (In Progress): Review 3793-clean-docker-images-wip
Peter Amstutz
08:07 pm Bug #5892 (Closed): [Workbench] collections#index returns 504 Gateway Timeout
504 Gateway Time-out
nginx/1.6.2
Tried 3x on https://workbench.su92l.arvadosapi.com/collections
qr1hi seems to...
Nancy Ouyang
08:06 pm Task #5867 (Resolved): Review branch: 4458-breadcrumbs-in-small-screens
Radhika Chippada
02:21 pm Task #5867 (In Progress): Review branch: 4458-breadcrumbs-in-small-screens
Brett Smith
08:06 pm Task #5858 (Resolved): Review branch: 5843-subproject-deletion-owner-name-constraint
Radhika Chippada
01:40 pm Task #5858 (In Progress): Review branch: 5843-subproject-deletion-owner-name-constraint
Brett Smith
08:04 pm Feature #5735 (In Progress): [Workbench] Edit box for project description should be bigger
Radhika Chippada
07:54 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Notes about the update:
* The edit button for project description is now displayed on top of textarea; uses btn-pr...
Radhika Chippada
07:55 pm Task #5891 (Resolved): Review branch: 5735-edit-description-box-size
Radhika Chippada
07:43 pm Revision 13e4bacf (arvados): 5735: use inline editing for project description x-editable textarea.
Radhika Chippada
06:43 pm Revision 0a87aad4 (arvados): 5787: Write files that are pointed to by symlinks that are outside o...
Catch exceptions. Update documentation. Peter Amstutz
06:10 pm Bug #5752: [SDKs] Fix unreliable image timestamp recording in arv keep docker
After investigation, arv-copy seems like a more likely culprit. I found a family of images on su92l which all had th... Brett Smith
06:07 pm Task #5881 (Resolved): Review 5752-arv-copy-preserve-docker-timestamps-wip
Brett Smith
06:07 pm Revision c19ed0b4 (arvados): 5752: arv-copy preserves properties of docker_image links.
The properties include the image_timestamp, which tells Arvados when
the source image was created, rather than the co...
Brett Smith
05:36 pm Task #5880 (Resolved): Review 5724-blob-signature-ttl
Tom Clegg
05:35 pm Task #5879 (Resolved): Review 5724-blob-signature-ttl at 6fc44a6
Tom Clegg
05:15 pm Task #5877 (In Progress): Review 5787-run-command-checkin
Tom Clegg
03:35 pm Task #5877 (Resolved): Review 5787-run-command-checkin
Peter Amstutz
03:54 pm Bug #5835 (Closed): [SDK] arv-copy breaks with namespaced git repository names
Peter reports at standup that this was a problem in his local deployment and not an arv-copy bug. Brett Smith
03:40 pm Bug #4458 (Resolved): [Workbench] Replace e-mail address in menu bar with user icon and make sure...
Applied in changeset arvados|commit:91c467665ad493108b69c660d5424c77cce5668f. Radhika Chippada
03:33 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
commit:02676af9 is good to merge. Thanks. Brett Smith
03:36 pm Revision 91c46766 (arvados): closes #4458
Merge branch '4458-breadcrumbs-in-small-screens' Radhika Chippada
03:35 pm Bug #5878 (Closed): [Workbench] PipelineInstancesTest#test_Create_and_run_a_pipeline is not reliable
One run gave me this error:... Brett Smith
03:35 pm Revision 6a7271ad (arvados): Merge branch 'master' into 4458-breadcrumbs-in-small-screens
Radhika Chippada
03:27 pm Revision f6fcf9f5 (arvados): 5787: Copy to the right destination name, add docstring, fix syntax ...
Peter Amstutz
03:22 pm Bug #5876 (Closed): [Docker] Needs smarter dependency ordering when restarting existing containers
I did this:
* I had a functional Docker cluster going with @arvdock start@.
* I stopped it with @arvdock stop@.
...
Brett Smith
02:35 pm Bug #5875 (Closed): [Workbench] Mobile menus lack contrast (gray text on aubergine)
Brett Smith
02:34 pm Bug #5875 (Closed): [Workbench] Mobile menus lack contrast (gray text on aubergine)
See "this screenshot":https://arvados.org/attachments/download/520/4458-lack-of-dashboard.png from #4458. I think we... Brett Smith
02:34 pm Bug #5874 (New): [Workbench] Mobile menus lack contrast (gray text on aubergine)
See "this screenshot":https://arvados.org/attachments/download/520/4458-lack-of-dashboard.png from #4458. I think we... Brett Smith
02:32 pm Revision 1281ecab (arvados): 5787: run-command uploading uses new collection API and supports sym...
Peter Amstutz
02:30 pm Bug #5843 (Resolved): [Workbench] Undeleteable sub-project
Applied in changeset arvados|commit:ee8d5b171e2c30ddc3fe829ba4388778e6a78b27. Radhika Chippada
02:20 pm Bug #5843: [Workbench] Undeleteable sub-project
commit:ec359b6 is good to merge. Thanks. Brett Smith
02:26 pm Revision ee8d5b17 (arvados): closes #5843
Merge branch '5843-subproject-deletion-owner-name-constraint' Radhika Chippada
02:26 pm Revision f81a5a1a (arvados): Merge branch 'master' into 5843-subproject-deletion-owner-name-const...
Radhika Chippada
01:44 pm Support #5833: Cannot get Arvados installed
This is what I get:
tcp 0 0 127.0.1.1:53 0.0.0.0:* LISTEN -
...
Darshan Singh
07:13 am Revision da57a997 (arvados): 5724: gofmt fixes.
Tom Clegg
07:11 am Revision 5bf77ec1 (arvados): 5724: Rename -permission-* flags to -blob-sign* to match apiserver. ...
Tom Clegg
04:59 am Revision 6fc44a67 (arvados): 5724: Add blobSignatureTtl to discovery doc. Add config comment/expl...
Tom Clegg

04/30/2015

10:24 pm Task #5871 (Resolved): Review 5834-api-max-response-size-wip
Brett Smith
10:23 pm Revision f87f91cb (arvados): 5834: Limit how much manifest text data API server will load for index.
This prevents situations where clients cause the API server to balloon
in memory use by requesting an index including...
Brett Smith
09:41 pm Revision 085bacc5 (arvados): 5493: fixed colorspace leading to yellow gif
Nancy Ouyang
09:15 pm Revision 0a173299 (arvados): Merge branch 'master' of git://git.curoverse.com/arvados into 5493-f...
Nancy Ouyang
09:14 pm Revision bde53a1d (arvados): 5562: keepstub sends "100 Continue" to client. Fix test_write_three...
to return a valid response body instead of None. Peter Amstutz
09:05 pm Revision 97ddb4b8 (arvados): 5493: fix yellow mouse-moves gif
Nancy Ouyang
08:52 pm Bug #5724 (In Progress): [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on ...
Tom Clegg
08:38 pm Revision db195a54 (arvados): run-command list correct directory to be uploaded when $(task.cwd) !...
no issue # Peter Amstutz
08:21 pm Revision 6083e432 (arvados): 5562: Use cStringIO module which is more efficient than StringIO.
Peter Amstutz
08:21 pm Revision 11253aff (arvados): 5562: Add comment about UPLOAD
Peter Amstutz
08:14 pm Revision 2826ad75 (arvados): 5562: Add support for "Expect: 100-Continue" flow for PUT.
This tells cURL to wait for a "go ahead" from the Keep server (in the form of a
HTTP/1.1 "100 Continue" response) ins...
Peter Amstutz
08:10 pm Feature #3145 (Resolved): [Keep] keepstore supports read-only flag for each volume, for cases lik...
Applied in changeset arvados|commit:7990a7778f70c243b50ea878787ea83689f5b07e. Peter Amstutz
07:53 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
commit:e94da792 lgtm, thanks.
Nice work on the HTTP status codes that are already defined to mean exactly what we ...
Tom Clegg
06:48 pm Feature #3145 (Feedback): [Keep] keepstore supports read-only flag for each volume, for cases lik...
Peter Amstutz
06:47 pm Feature #3145 (In Progress): [Keep] keepstore supports read-only flag for each volume, for cases ...
Peter Amstutz
02:25 pm Feature #3145 (Resolved): [Keep] keepstore supports read-only flag for each volume, for cases lik...
Applied in changeset arvados|commit:624c5c8d13d6c2e21a80379928387944bedae2a3. Tom Clegg
02:20 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
Peter Amstutz wrote:
> 3145-close-early LGTM
>
> We should use pycurl.UPLOAD in KeepClient (refs #5562)
>
> ht...
Tom Clegg
02:04 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
3145-close-early LGTM
We should use pycurl.UPLOAD in KeepClient (refs #5562)
http://curl.haxx.se/libcurl/c/CURL...
Peter Amstutz
08:07 pm Revision 7990a777 (arvados): Merge branch '3145-missing-content-length-error' closes #3145
Peter Amstutz
07:44 pm Task #5869 (In Progress): Review 3145-missing-content-length-error
Tom Clegg
06:48 pm Task #5869 (Resolved): Review 3145-missing-content-length-error
Peter Amstutz
07:44 pm Task #5859 (In Progress): Update default config, add to discovery doc
Tom Clegg
03:36 pm Task #5859 (Resolved): Update default config, add to discovery doc
Tom Clegg
07:43 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
On 5562-pycurl-upload at commit:589e0f3c (after merging master to deal with pycurl version problems) I get:... Tom Clegg
01:29 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Peter Amstutz wrote:
> On the compute node, pycurl is presumably using this package:
>
> /usr/lib/pymodules/pytho...
Tom Clegg
01:13 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
On the compute node, pycurl is presumably using this package:
/usr/lib/pymodules/python2.7/pycurl-7.19.0.egg-info
Peter Amstutz
01:10 pm Bug #5562 (Feedback): [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
... Peter Amstutz
07:24 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
(03:06:25 PM) Me: tomclegg: Do you want any compensation for the fact that the manifest_text in the database will be ... Brett Smith
06:09 pm Bug #5834 (In Progress): [API] Be careful about memory usage when responding to collections#index...
Brett Smith
07:05 pm Task #5870 (In Progress): Test scaling performance on exome and whole genome
Peter Amstutz
07:05 pm Task #5870 (Closed): Test scaling performance on exome and whole genome
Peter Amstutz
06:46 pm Task #5864 (Resolved): Review 5856-read-exact
Peter Amstutz
05:39 pm Task #5864 (In Progress): Review 5856-read-exact
Brett Smith
04:44 pm Task #5864 (Resolved): Review 5856-read-exact
Peter Amstutz
06:45 pm Task #5868 (In Progress): Review 5562-pycurl-upload
Tom Clegg
06:44 pm Task #5868 (Resolved): Review 5562-pycurl-upload
Tom Clegg
06:39 pm Revision 589e0f3c (arvados): 5562: Use cStringIO module which is more efficient than StringIO.
Peter Amstutz
06:30 pm Revision dffb8b5e (arvados): Merge branch '5856-read-exact' closes #5856
Peter Amstutz
06:29 pm Bug #5856: gzip.open(f) sometimes throws struct.error (unpack requires a string argument of lengt...
commit:c42ccd1f is good to merge. Thanks. Brett Smith
06:22 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
Brett Smith wrote:
> Reviewing commit:4570521
>
> I'm not sure it makes much sense for the tests to manipulate @s...
Peter Amstutz
05:25 pm Bug #5856: gzip.open(f) sometimes throws struct.error (unpack requires a string argument of lengt...
Reviewing commit:4570521
I'm not sure it makes much sense for the tests to manipulate @sfile.arvadosfile@ directly...
Brett Smith
05:02 pm Bug #5856 (In Progress): gzip.open(f) sometimes throws struct.error (unpack requires a string arg...
Peter Amstutz
04:45 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
Applied in changeset arvados|commit:4570521e9d639806b1f25c93822d5cf0dbfe42d0. Peter Amstutz
04:42 pm Bug #5856 (In Progress): gzip.open(f) sometimes throws struct.error (unpack requires a string arg...
Peter Amstutz
03:30 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
Applied in changeset arvados|commit:c807aef7059b253512ba5da5d535e89e800b9c11. Peter Amstutz
06:25 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
* Breadcrumbs are now visible in the page even when it small
** The breadcrumbs do disappears as you keep reducing t...
Radhika Chippada
03:34 pm Bug #4458 (In Progress): [Workbench] Replace e-mail address in menu bar with user icon and make s...
Radhika Chippada
06:21 pm Revision c42ccd1f (arvados): 5856: Tweak tests. Fix typo.
Peter Amstutz
06:21 pm Task #5867 (Resolved): Review branch: 4458-breadcrumbs-in-small-screens
Radhika Chippada
06:19 pm Revision 02676af9 (arvados): 4458: breadcrumbs now visible in small window sizes; also, use user ...
Radhika Chippada
06:08 pm Feature #5866 (New): Document the 'arv' tool
The command line 'arv' tool is very useful when trying to automate tasks that communicate with the Arvados API server... Abram Connelly
06:02 pm Bug #5845: Pipeline has failed but no jobs are marked as failed
The bug is not that the job failed but that workbench is not displaying the failure.
The job failed because I mis-...
Abram Connelly
05:00 pm Bug #5845: Pipeline has failed but no jobs are marked as failed
From the pipeline instance logs:
Error creating job for component RefreshReport: Repository not found: '$USER'
Jo...
Bryan Cosca
05:59 pm Revision e94da792 (arvados): Return error if Content-Length header is missing instead of panicing.
Peter Amstutz
05:55 pm Revision 94129ac4 (arvados): Use pycurl.UPLOAD instead of CUSTOMREQUEST 'PUT'. Set INFILESIZE an...
READFUNCTION. Peter Amstutz
05:41 pm Task #5857 (New): Review 3793-clean-docker-images-wip
Brett Smith
01:25 pm Task #5857 (In Progress): Review 3793-clean-docker-images-wip
Brett Smith
01:25 pm Task #5857 (Resolved): Review 3793-clean-docker-images-wip
Brett Smith
05:09 pm Story #5865 (New): [Crunch] Run a local job using a docker image directly from the shell VM (with...
The objective is to make this development cycle much quicker:
* Edit Dockerfile.
* Rebuild docker image.
* Run job...
Tom Clegg
04:41 pm Revision 4570521e (arvados): ArvadosFileReader object always tries to return the exact amount of ...
This is to avoid breaking stuff like gzip that assumes it always gets the exact
amount of data unless EOF. (From the...
Peter Amstutz
04:03 pm Feature #5863 (New): API documentation updates
The "Arvados API documentation":http://doc.arvados.org/api/methods.html is difficult to understand. Here are a two p... Abram Connelly
03:39 pm Task #5862 (New): Fill in component params from pipeline params in a-r-p-i
Tom Clegg
03:39 pm Task #5861 (New): Allow editing pipeline parameters in workbench
Tom Clegg
03:38 pm Task #5860 (New): Provide detail about expected information/presentation
Tom Clegg
03:37 pm Bug #5835: [SDK] arv-copy breaks with namespaced git repository names
I'm having trouble reproducing. Given this pipeline template:... Brett Smith
03:30 pm Revision f94d59e8 (arvados): Merge branch '5562-pycurl' refs #5562
Tom Clegg
03:30 pm Revision 3da2281b (arvados): 5562: Use static method. Fix "TypeError: _socket_open() takes exactl...
Tom Clegg
03:29 pm Revision c807aef7 (arvados): ArvadosFileReader object always tries to return the exact amount of ...
This is to avoid breaking stuff like gzip that assumes it always gets the exact
amount of data unless EOF. (From the...
Peter Amstutz
03:16 pm Revision caaa8219 (arvados): 5562: Use static method. Fixes "TypeError: _socket_open() takes exac...
Tom Clegg
03:05 pm Task #5858 (Resolved): Review branch: 5843-subproject-deletion-owner-name-constraint
Radhika Chippada
02:59 pm Revision ec359b66 (arvados): 5843: rename objects that contain xx_owner_uuid_name_unique constrai...
Radhika Chippada
02:48 pm Task #5693 (Closed): Review 5692-pysdk-signed-manifest-locator
Tom Clegg
02:45 pm Task #5693 (Resolved): Review 5692-pysdk-signed-manifest-locator
Tom Clegg
02:39 pm Task #5795 (Resolved): Review branch: 5780-sharing-popup-message
Tom Clegg
02:25 pm Revision 624c5c8d (arvados): Merge branch '3145-close-early' closes #3145
Tom Clegg
02:25 pm Bug #5836 (Resolved): [API] Remote API error messages should make it clear that they are remote.
Applied in changeset arvados|commit:a4211acb465bd42869bf2a2f9fad6ff2c5e518e0. Tom Clegg
02:24 pm Revision a4211acb (arvados): Merge branch '5836-remote-api-server-errors-made-obvious' closes #5836
Tom Clegg
02:16 pm Task #5849 (Resolved): Review 3145-close-early
Peter Amstutz
01:53 pm Revision 6c9dde5e (arvados): 5562: Use WRITEFUNCTION instead of WRITEDATA for compatibility with ...
Tom Clegg
01:34 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
3793-clean-docker-images-wip is up for review. A few notes:
* *THIS IS PYTHON 3*. I asked Ward if this was okay ...
Brett Smith
01:24 pm Revision 4dc84fdc (arvados): 3793: Add Docker image cleaner service for compute nodes.
This service monitors Docker events. When no containers are active,
it arranges to keep the most recently used image...
Brett Smith
01:47 am Support #5833: Cannot get Arvados installed
Interesting - it looks like you either already have a skydns container running, or maybe you have another dns resolve... Ward Vandewege

04/29/2015

09:53 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
One of the tasks from https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-pfu68urmcrq00mo failed wi... Sarah Guthrie
09:27 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
That sounds like a great solution Tom. The data manager doesn't really care how many results it gets, as long as it g... Misha Zatsman
08:50 pm Bug #5766 (Resolved): [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, eve...
Applied in changeset arvados-dev|commit:274c7abf3aee7dee8bfe648f485087a5a0ab59ed. Peter Amstutz
08:50 pm Feature #5412 (Resolved): [SSO] Support LDAP-only configuration
Applied in changeset sso-provider|commit:80acc50a1d23b6378682a4729726772d1d616e3d. Peter Amstutz
08:46 pm Task #5710 (Resolved): Review 5692-pysdk-manifest-text-flush
Peter Amstutz
08:46 pm Task #5786 (Resolved): Review 5766-pip-sdk-install in arvados-dev
Peter Amstutz
08:46 pm Revision 274c7abf (arvados): Merge branch '5766-pip-sdk-install' closes #5766
Peter Amstutz
08:46 pm Revision 274c7abf (arvados-dev): Merge branch '5766-pip-sdk-install' closes #5766
Peter Amstutz
08:44 pm Revision 80acc50a (sso-provider): Merge branch '5412-ldap-support' closes #5412
Peter Amstutz
08:18 pm Support #5832: [Support] how to include a bioboxes docker image as a new pipeline?
Hi Albert,
You can use `arv keep docker` to download docker images from the docker registry.
There's a little m...
Ward Vandewege
08:14 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
This will also solve the overlay problem (menu bar makes breadcrumbs bar invisible) between main and mobile view. Ward Vandewege
08:08 pm Task #5855 (New): Add Workbench support
Tom Clegg
08:08 pm Task #5854 (New): Add default display_order on server side
Tom Clegg
07:46 pm Task #5853 (New): Document pipeline parameters API
Tom Clegg
07:39 pm Task #5852 (Resolved): Write install docs
Tom Clegg
07:38 pm Task #5851 (Resolved): Write integration tests
Tom Clegg
07:36 pm Bug #5850 (Closed): All clients authenticate directly against SSO server without going through AP...
Tom Clegg
07:35 pm Task #3844 (Resolved): Agressively close PUT connections when there are no writable volumes.
Tom Clegg
07:28 pm Bug #5836 (In Progress): [API] Remote API error messages should make it clear that they are remote.
Tom Clegg
07:09 pm Task #5849 (Resolved): Review 3145-close-early
Tom Clegg
07:07 pm Task #5847 (Resolved): Review 5562-pycurl
Tom Clegg
02:06 pm Task #5847 (Resolved): Review 5562-pycurl
Tom Clegg
06:56 pm Revision 8af4c5ff (arvados): 3145: Respond to PUT without reading request body if no volumes are ...
Tom Clegg
06:10 pm Bug #5562 (Resolved): [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Applied in changeset arvados|commit:acc7d4a40ae78e866c983624ec36b7bae3b918a9. Tom Clegg
03:55 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
(From IRC: agreed that when talking to a Keep node, the timeout should already be 20 seconds, so setting LOW_SPEED_TI... Peter Amstutz
03:40 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
http://curl.haxx.se/docs/faq.html#I_want_a_different_time_out
We should set http://curl.haxx.se/libcurl/c/CURLOPT_...
Peter Amstutz
02:54 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
* In @KeepService.get()@ it looks like a 404 response will be treated as an error and cause the connection to be rese... Peter Amstutz
02:13 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Test package is here, and /tmp/arvados-python-client-0.1.20150429043929.tar.gz on shell.q... Tom Clegg
06:08 pm Bug #5843 (In Progress): [Workbench] Undeleteable sub-project
Radhika Chippada
06:07 pm Bug #5843: [Workbench] Undeleteable sub-project
Collections, groups, and pipeline_templates have the owner_uuid_name_unique constraint.
Currently, when a collecti...
Radhika Chippada
02:51 pm Bug #5843: [Workbench] Undeleteable sub-project
I think there was another subproject in Home project with that same name and hence the deletion (moving into Home pro... Radhika Chippada
05:45 pm Revision acc7d4a4 (arvados): Merge branch '5562-pycurl' closes #5562
Tom Clegg
05:38 pm Revision ea7c7efb (arvados): 5562: Return UA to pool if it worked well enough to get an HTTP status.
Tom Clegg
05:38 pm Revision 213ace8b (arvados): 5562: Enable TCP Keepalive for Keep requests. refs #5822
Tom Clegg
04:31 pm Revision e2494026 (arvados): Renamed RemoteApiServerError to APIServerError and NewRemoteApiServe...
Reworked error messages to feature error details more prominently.
These changes were requested by code review at
ht...
Misha Zatsman
03:10 pm Revision 4008f2a6 (arvados): 5562: Return UA to pool if it worked well enough to get an HTTP status.
Tom Clegg
02:57 pm Revision cfcefb3d (arvados): 5562: Enable TCP Keepalive for Keep requests. refs #5822
Tom Clegg
02:05 pm Task #5789 (Resolved): Test somehow
Tom Clegg
01:28 pm Feature #5846 (New): [Workbench] [Fiddlesticks] Live job log should show recent history
Jobs can get in this state if the arv-put process that crunch-job ran to create the log fails. See, e.g., qr1hi-8i9s... Peter Amstutz
01:10 pm Bug #5826 (Resolved): [Workbench] Pipeline Instance input tab should be more verbose
Applied in changeset arvados|commit:61d399a57fd1e867cc243a0dab0fad73d9689734. Radhika Chippada
01:07 pm Revision 61d399a5 (arvados): closes #5826
Merge branch '5826-unreadable-inputs-error' Radhika Chippada
12:44 pm Revision e01762a0 (arvados): 5826: use present? instead of !empty?
Radhika Chippada
04:39 am Revision 20b988d5 (arvados): 5562: Add fake keepstore server with configurable problems.
Tom Clegg
04:39 am Revision 7ab494e4 (arvados): 5562: Use pycurl library (instead of requests) for Keep transactions.
Tom Clegg
 

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