Peter Amstutz's activity

From 02/19/2017 to 03/20/2017

03/20/2017

08:08 pm Arvados Feature #11255 (New): [Crunchv2] Option to use host networking for containers
Peter Amstutz
07:39 pm Arvados Feature #11255 (In Progress): [Crunchv2] Option to use host networking for containers
Peter Amstutz
07:32 pm Arvados Bug #11170: Stale squeue processes on c97qk caused by "crunch-dispatch --jobs"
@squeue_jobs@ and @scancel@ should use the block form of @IO.popen()@ so that it is closed automatically. See @stdou... Peter Amstutz
07:04 pm Arvados Revision e20dfe63 (arvados): If API server doesn't publish supported Docker image versions, make ...
error instead of a warning (can be overridden with --force-image-format)
refs #8567
Peter Amstutz
06:34 pm Arvados Revision db7c2ba7 (arvados): Merge branch '8567-docker-migrator' refs #8567
Peter Amstutz
04:56 pm Arvados Revision 9b40808f (arvados-dev): install-arvados-jobs-image: Delete check for Docker image+repo a...
because it incorrectly skips upload in circumstances when the image+repo exists
but associated with the wrong differe...
Peter Amstutz
03:58 pm Arvados Revision 433cd703 (arvados): 8567: Bugfix check for existing repo+tag links.
Peter Amstutz
02:02 pm Arvados Revision 03589784 (arvados): 8567: arv-keepdocker catches EPIPE so it doesn't print backtrace whe...
other commands such as "head". Peter Amstutz
01:36 pm Arvados Revision fd42d69f (arvados): 8567: Add migrate19
Peter Amstutz

03/17/2017

09:54 pm Arvados Revision 2accec1f (arvados): 8567: Better command line UI
Peter Amstutz
08:40 pm Arvados Bug #11288 (Resolved): [Nodemanager] Need reason to set DOWN state
Applied in changeset arvados|commit:de283bd8dd383a4177bb714212cf7c59f38a23d8. Peter Amstutz
05:22 pm Arvados Bug #11288 (Resolved): [Nodemanager] Need reason to set DOWN state
Slurm expects a reason when setting node to DOWN:... Peter Amstutz
08:36 pm Arvados Revision de283bd8 (arvados): Merge branch '11288-slurm-down-reason' closes #11288
Peter Amstutz
05:27 pm Arvados Revision da8c9048 (arvados): 11288: Slurm requires reason to put node in DOWN state.
Peter Amstutz
03:14 pm Arvados Wiki edit: Keep_cache_policy (#1)
Peter Amstutz
02:34 pm Arvados Wiki edit: Proposals (#55)
Peter Amstutz

03/16/2017

08:57 pm Arvados Task #11271 (Resolved): Review 11254-nodemanager-no-actor
Peter Amstutz
08:55 pm Arvados Bug #11254 (Resolved): [Node manager] backtrace on node shutdown
Applied in changeset arvados|commit:996b635700d7270229200a56d2c2b9f7c96a84fb. Peter Amstutz
08:52 pm Arvados Revision 996b6357 (arvados): Merge branch '11254-nodemanager-no-actor' closes #11254
Peter Amstutz
08:49 pm Arvados Revision b60a21fe (arvados): 11254: Refactor _node_states
Peter Amstutz
08:28 pm Arvados Bug #4124: [Crunch] Socket timed out on send/recv operation causes pipeline failure
I don't know if we ever updated our default puppet configuration.
We've seen some unexplained SLURM timeouts on so...
Peter Amstutz
08:11 pm Arvados Revision 2c69d491 (arvados): 11254: Cloud nodes where "actor is None" are considered to be in shu...
only time it should be "None" is the period between a successful shutdown and
when the node disappears from the cloud...
Peter Amstutz

03/15/2017

08:10 pm Arvados Task #11271 (Resolved): Review 11254-nodemanager-no-actor
Peter Amstutz
07:35 pm Arvados Story #9132: [Crunch2] crunch-run uses official docker client library
Please take over 9132-dockerclient
* Replace API calls to equivalent ones, see https://godoc.org/github.com/docker...
Peter Amstutz
06:54 pm Arvados Bug #11257 (New): [CWL] Fails with $schemas referencing remote resources.
Workflows with external http resources listed in $schemas get into trouble with the code to find and upload local dep... Peter Amstutz
06:53 pm Arvados Bug #11254: [Node manager] backtrace on node shutdown
The backtrace looks like an unintended side effect of #10846.
On further research, we determined the underlying re...
Peter Amstutz
05:20 pm Arvados Task #11141 (Resolved): Review 6520-nodemanager-docs
Peter Amstutz
03:50 pm Arvados Feature #11255 (Resolved): [Crunchv2] Option to use host networking for containers
Docker bridge networking has bugs on certain kernels. Add a flag to crunch-run to instruct containers to use host ne... Peter Amstutz
03:03 pm Arvados Revision 54837bca (arvados): 8567: Add check that admin token is used and ensure that migration l...
created owned by system user. Also fix tests now that arv-keepdocker uses
logging instead of printing directly to sy...
Peter Amstutz

03/14/2017

07:56 pm Arvados Bug #11186 (Duplicate): Priority 0 state shouldn't be labeled "Ready"
See #11250 Peter Amstutz
06:29 pm Arvados Bug #11186: Priority 0 state shouldn't be labeled "Ready"
Suggest "Stopped" Peter Amstutz
07:35 pm Arvados Revision 91118e3a (arvados): Add missing documentation file. refs #6520
Peter Amstutz
07:17 pm Arvados Revision bdaa9de9 (arvados): Merge branch '8567-api-select-docker-fmt' refs #8567
Peter Amstutz
07:17 pm Arvados Revision d363323b (arvados): Merge branch '8567-cwl-docker-img' refs #8567
Peter Amstutz
07:15 pm Arvados Story #11123 (Resolved): Add node manager to install guide
Applied in changeset arvados|commit:449d780f0a470f67d1a28fe1459a8bab79562069. Peter Amstutz
04:02 pm Arvados Story #11123: Add node manager to install guide
Made some updates, if you want to take another quick look: 6520-nodemanager-docs Peter Amstutz
02:57 pm Arvados Story #11123: Add node manager to install guide
Javier Bértoli wrote:
> Question, in *doc/install/install-keepstore.html.textile.liquid*: does it make sense to docu...
Peter Amstutz
07:09 pm Arvados Revision 449d780f (arvados): Merge branch '6520-nodemanager-docs' closes #11123
Peter Amstutz
06:30 pm Arvados Story #11250 (New): [Workbench] Better user-facing terms for container states
* When a container is in the slurm queue, its state is displayed as "Locked". This is confusing to users who don't a... Peter Amstutz
04:44 pm Arvados Revision eabc13f2 (arvados): 8567: Add note about updating API server configuration.
Peter Amstutz
04:39 pm Arvados Revision dee634b2 (arvados): 8567: Add docker19 migration instructions to install guide.
Peter Amstutz
04:30 pm Arvados Revision 2ed5325b (arvados): 8567: Add check for ARVADOS_API_HOST_INSECURE
Peter Amstutz
04:30 pm Arvados Revision f074ef81 (arvados): 8567: Fix migrate links to use PDH instead of UUID.
Better error reporting.
Migrate script cleans up /var/lib/docker inside container.
Peter Amstutz
04:30 pm Arvados Revision 55c719bf (arvados): 8567: Rename docker19-migrate to migrate-docker19 for consistency with
arv-migrate-docker19. Add docstrict to migrate19() function. Peter Amstutz
04:30 pm Arvados Revision 1d7577d0 (arvados): 8567: Add status reporting to migrate script.
Peter Amstutz
04:30 pm Arvados Revision 205b0776 (arvados): 8567: Creates migration links.
Peter Amstutz
04:30 pm Arvados Revision 6058f336 (arvados): 8567: Move out of tools/ into sdk/python and docker/docker19-migrate.
Peter Amstutz
04:30 pm Arvados Revision 0eb52182 (arvados): 8567: Docker image migration WIP.
Peter Amstutz
04:25 pm Arvados Revision 5fffad60 (arvados): 8567: Fix tests now that container_image provides docker repo+tag an...
Peter Amstutz
04:03 pm Arvados Revision 355fe24b (arvados): 8567: If a search_term looks like a PDH, always treat it as one. Al...
correct optional parameter syntax. Peter Amstutz
03:38 pm Arvados Revision 25296def (arvados): 6520: Add page with sample ping script. Improve instructions on cre...
compute node a little bit. Peter Amstutz
03:06 pm Arvados Revision c04608e4 (arvados): 6520: Add node_mem_scaling to documentation.
Peter Amstutz
02:59 pm Arvados Revision 7eb2eff1 (arvados): 6520: Node manager docs WIP
Peter Amstutz
02:59 pm Arvados Revision a1383389 (arvados): 6520: Add information about setting up SLURM to crunchv2 documentation.
Peter Amstutz
02:46 pm Arvados Revision 6ea807b2 (arvados): 8567: Use Docker image repo+tag name instead of PDH so that API serv...
Peter Amstutz

03/13/2017

09:37 pm Arvados Revision dbb0d22a (arvados): 8567: Tests default to image format v1 to avoid breaking all the tes...
uses the :docker_image collection. Peter Amstutz
09:31 pm Arvados Revision 918e16de (arvados): 8567: Adjust job container resolve test now that images are filtered...
support version. Peter Amstutz
08:40 pm Arvados Revision a7220572 (arvados): 8567: Refactor code that queries migration links into get_compatible...
Peter Amstutz
04:55 pm Arvados Bug #11226: [SDK] Python client tries to cache discovery document at the same local path regardle...
Tom Morris wrote:
> I take it this got instagroomed while I was gone.
>
> Does this mean that #10669 is fixed (an...
Peter Amstutz

03/10/2017

07:06 pm Arvados Revision e1e0bec5 (arvados): 8567: Add & tweak tests for selecting compatible Docker image format.
Peter Amstutz
06:51 pm Arvados Revision f4a7c5e6 (arvados): 8567: find_all_for_docker_image() returns only Docker images compati...
Peter Amstutz
02:38 pm Arvados Task #11233 (Resolved): Review
Peter Amstutz

03/09/2017

10:44 pm Arvados Revision f63c160f (arvados): Bugfix: python Collection class sets _portable_data_hash in _populat...
refs #10956 Peter Amstutz
10:41 pm Arvados Revision 669e7f30 (arvados): 8567: Fix migrate links to use PDH instead of UUID.
Better error reporting.
Migrate script cleans up /var/lib/docker inside container.
Peter Amstutz
08:14 pm Arvados Bug #5036: [FUSE] Provide a unique mount subtype
LGTM. Peter Amstutz
07:50 pm Arvados Bug #11226 (Resolved): [SDK] Python client tries to cache discovery document at the same local pa...
Applied in changeset arvados|commit:82697fea93b1c87cdee27d2b9a76c1b7ac07497e. Peter Amstutz
03:49 pm Arvados Bug #11226: [SDK] Python client tries to cache discovery document at the same local path regardle...
+1 Peter Amstutz
03:45 pm Arvados Bug #11226: [SDK] Python client tries to cache discovery document at the same local path regardle...
Also want to do one of:
a) continue to use httplib2 caching, which is apparently not multithread/multiprocess safe...
Peter Amstutz
03:38 pm Arvados Bug #11226: [SDK] Python client tries to cache discovery document at the same local path regardle...
https://github.com/google/google-api-python-client/pull/127
I think we can use the @cache_discovery@ option to bui...
Peter Amstutz
07:44 pm Arvados Revision 82697fea (arvados): Merge branch '11226-discovery-doc-cache' closes #11226
Peter Amstutz
07:40 pm Arvados Revision a15fc58f (arvados): 11226: Disable google api client discovery doc caching, use only htt...
Google API client has its own caching mechanism. The problem is, by default
this goes to /tmp/google-api-python-clie...
Peter Amstutz
06:11 pm Arvados Revision fe2484ec (arvados): 10401: Bump cwltool pin.
Peter Amstutz
03:55 pm Arvados Task #11233 (Resolved): Review
Peter Amstutz
03:53 pm Arvados Revision ebb0138d (arvados): 8567: Fix docker_migration_pdh to seach head/tail_uuid (PDH doesn't ...
Peter Amstutz

03/08/2017

10:04 pm Arvados Revision c69d4a2b (arvados): 10401: Fix arvcontainer use of pathmapper.
Peter Amstutz
08:33 pm Arvados Revision c7143dc9 (arvados): Add ability to use "arvbox start test" to re-run tests without teari...
restarting whole container. no issue # Peter Amstutz
08:33 pm Arvados Revision 005595fb (arvados): Arvbox now uses Go websockets server instead of Puma. no issue #
Peter Amstutz
07:31 pm Arvados Bug #11226 (Resolved): [SDK] Python client tries to cache discovery document at the same local pa...
The Python SDK instructs httplib2 to cache the discovery document in @~/.cache/arvados/discovery@. However, the goog... Peter Amstutz
06:43 pm Arvados Task #11225 (In Progress): Update cwltool
Peter Amstutz
06:43 pm Arvados Task #11225 (In Progress): Update cwltool
Peter Amstutz
06:41 pm Arvados Revision 16180e3b (arvados): 10401: Passes unit tests.
Peter Amstutz
06:23 pm Arvados Revision 08bf82bb (arvados): 10401: Allow Arvados extensions to be used in "requirements" not jus...
Peter Amstutz
06:19 pm Arvados Revision dd7710a6 (arvados): 10401: Use use_custom_schema feature for extensions.
Peter Amstutz
06:13 pm Arvados Revision e05dddc4 (arvados): 10401: Bump cwltool & schema salad pins.
Peter Amstutz
03:52 pm Arvados Task #11141 (In Progress): Review 6520-nodemanager-docs
Peter Amstutz
03:01 pm Arvados Task #11224 (In Progress): Update API usage
Peter Amstutz
03:01 pm Arvados Task #11224 (In Progress): Update API usage
Peter Amstutz
02:14 pm Arvados Bug #3624: [API] Remove redundant "updated_at" column
You know, we still have a redundant update_at column... Peter Amstutz

03/07/2017

07:52 pm Arvados Feature #7709: [API] Upgrade API server to Rails 4.2
Release notes: http://guides.rubyonrails.org/ Peter Amstutz
06:59 pm Arvados Bug #10350 (Resolved): [Documentation] Update /api/authentication.html with correct information
Fixed in #10346 Peter Amstutz
06:57 pm Arvados Bug #9702 (Closed): [Crunch2] Five CWL conformance tests are failing with Crunch2
Closing this as it no longer reflects the current state of CWL on crunch v2.
The latest conformance test results c...
Peter Amstutz
06:55 pm Arvados Story #9132 (In Progress): [Crunch2] crunch-run uses official docker client library
Peter Amstutz
06:53 pm Arvados Task #8845 (Resolved): Diagnose
Parent ticket is resolved. Peter Amstutz
06:47 pm Arvados Task #7601 (Resolved): Review 6358-put-rendezvous
Parent ticket is resolved. Peter Amstutz
06:47 pm Arvados Task #6299 (Resolved): Review
Parent ticket is resolved. Peter Amstutz
06:46 pm Arvados Task #5680 (Resolved): Async dispatch hooks from CWL engine
CWL is supported an Arvados. Peter Amstutz
06:45 pm Arvados Task #5449: Update examples to use new Python Collection SDK and add deprecation notes to old APIs
Workflow examples using CWL don't involve the SDK.
Pipeline examples that use the Python SDK are already marked as...
Peter Amstutz
06:41 pm Arvados Feature #4223: [SDKs] arv keep docker --download to get image from Arvados
I still find myself wanting this feature occasionally, although we may want to abandon this particular branch. Peter Amstutz
06:39 pm Arvados Task #5681 (Closed): Task dispatch from CWL job runner
arvados-cwl-runner doesn't use job_tasks (which are specific to crunch v1).
Peter Amstutz
06:37 pm Arvados Task #5679 (Resolved): CWL job runner framework
CWL is supported on Arvados. Peter Amstutz
06:32 pm Arvados Task #2637 (Closed): Add support for filters to generic create API
Parent ticket closed. Peter Amstutz
06:31 pm Arvados Task #2628 (Closed): Write wiki page design for simple joins in REST API
Not currently planned. Peter Amstutz
06:31 pm Arvados Task #3884 (Closed): Review 3605-improved-dashboard
Revisit dashboard in future tickets. Peter Amstutz
06:30 pm Arvados Task #4703 (Resolved): Work on CWL draft 1 spec for tools
CWL supported on Arvados.
Peter Amstutz
06:29 pm Arvados Task #4686 (Resolved): Example wrapping bcbio sub-tool using CWL tool description
bcbio generates CWL that runs on Arvados. Peter Amstutz
06:29 pm Arvados Task #4613 (Resolved): Workbench template for generating UI
Workbench generates input form for CWL workflows. Peter Amstutz
06:28 pm Arvados Task #4612 (Resolved): Start writing user guide page
CWL support in Arvados is documented. Peter Amstutz
06:27 pm Arvados Task #4575 (Resolved): Review 4035-pipeline-support-cwl-tool
CWL is supported in Arvados. Peter Amstutz
06:27 pm Arvados Task #4420 (Resolved): Support user+pass database managed locally by SSO server
Implemented commit:49ab94b9d8d2c6e85c22b0e19171255af66db5e2 Peter Amstutz
06:25 pm Arvados Task #4146 (Closed): Fix crunch-job
Parent ticket closed. Peter Amstutz
06:24 pm Arvados Bug #4028 (Closed): [Crunch] Task stdout appearing in job logs should be labeled "stdout" instead...
Seems unlikely this will be fixed.
Crunch v2 logs distinguish between stdout and stderr.
Peter Amstutz
06:23 pm Arvados Task #4144 (Resolved): Use num_retries on regular collection writer instead of robust_put
Was implemented in commit:1281ecab8f2396739ee9232c36796e46cd551426
Also run-command is nearing end-of-life as it i...
Peter Amstutz
06:20 pm Arvados Task #3887 (Closed): Fix tests
Revisit dashboard / workbench design in future tickets. Peter Amstutz
06:20 pm Arvados Feature #3605 (Closed): [Workbench] improved dashboard page
Will dashboard design in future tickets. Peter Amstutz
06:18 pm Arvados Task #3324 (Closed): Build new docker image, run on qr1hi with test data
Bcbio now generates CWL to run on Arvados. Uses upstream bcbio Docker image. Peter Amstutz
06:17 pm Arvados Feature #3319 (Closed): [Sample Pipelines] Run monolithic bcbio pipeline on tiny dataset. Package...
Bcbio now generates CWL to run on Arvados. Peter Amstutz
06:16 pm Arvados Task #2648 (Closed): Write tests
No longer applicable due to closing of original ticket. Peter Amstutz
06:15 pm Arvados Task #2649 (Closed): Assign collection to project
Obsolete by arv-put --project-uuid Peter Amstutz
06:15 pm Arvados Task #3230 (Closed): Support bcbio parallelization framework
bcbio generates CWL files which are runnable on Arvados. Peter Amstutz
06:14 pm Arvados Task #2647 (Closed): Put files from staging directory into Keep
Obsoleted by enabling arv-put to upload directly to Keep via keepproxy. Peter Amstutz
06:14 pm Arvados Task #2643 (Closed): "Ready to ingest" endpoint (in /actions controller?)
Obsoleted by enabling arv-put to write directly to Keep using keepproxy. Peter Amstutz
06:13 pm Arvados Feature #2176 (Closed): API server supports atomic find_or_create operation
Containers API uses a different approach. Does not have compelling use case in other APIs. Peter Amstutz
06:12 pm Arvados Story #2627 (Closed): Write design for joins in API
Currently no plans to do this. Peter Amstutz
06:07 pm Arvados Story #11139: [Node manager] Expected MemTotal for each cloud node size
Thanks, LGTM Peter Amstutz
02:54 pm Arvados Story #11139: [Node manager] Expected MemTotal for each cloud node size
Can you add a test that shows that changing the configuration parameter changes the server calculator.
Can you add...
Peter Amstutz
06:07 pm Arvados Task #11200 (Resolved): Review 11139-nodemanager-mem-scale-factor
Peter Amstutz
02:46 pm Arvados Task #11200 (In Progress): Review 11139-nodemanager-mem-scale-factor
Peter Amstutz
03:02 pm Arvados Revision fce072c7 (arvados): 8567: Add check for ARVADOS_API_HOST_INSECURE
Peter Amstutz
02:46 pm Arvados Task #11196 (Resolved): Review 11166-log-name-collision
Peter Amstutz
02:27 pm Arvados Task #11196 (In Progress): Review 11166-log-name-collision
Peter Amstutz
02:45 pm Arvados Bug #11166: [Crunch2] crunchrun.go should avoid name collisions when creating log collections
LGTM. Peter Amstutz
02:26 pm Arvados Revision 123251c6 (arvados): 8567: Rename docker19-migrate to migrate-docker19 for consistency with
arv-migrate-docker19. Add docstrict to migrate19() function. Peter Amstutz
02:18 pm Arvados Revision 80d9b40b (arvados): 8567: Docker image migration WIP.
Peter Amstutz
02:18 pm Arvados Revision 09fc7249 (arvados): 8567: Move out of tools/ into sdk/python and docker/docker19-migrate.
Peter Amstutz
02:18 pm Arvados Revision 57fec89d (arvados): 8567: Add status reporting to migrate script.
Peter Amstutz
02:18 pm Arvados Revision b5886da1 (arvados): 8567: Creates migration links.
Peter Amstutz
02:18 pm Arvados Revision 5780b539 (arvados): 9132: WIP switching to using official Docker Go client.
Peter Amstutz

03/06/2017

07:52 pm Arvados Revision 58342141 (arvados): 8567: Move out of tools/ into sdk/python and docker/docker19-migrate.
Peter Amstutz
07:31 pm Arvados Revision f2c45e2c (arvados): 8567: Add status reporting to migrate script.
Peter Amstutz
03:39 pm Arvados Revision 93384273 (arvados): 8567: Creates migration links.
Peter Amstutz
03:23 pm Arvados Revision cee1c18c (arvados): 8567: Docker image migration WIP.
Peter Amstutz

03/03/2017

06:22 pm Arvados Bug #11168: [API] Use JSON instead of YAML for serialized fields in database
... Peter Amstutz
05:02 pm Arvados Bug #11168: [API] Use JSON instead of YAML for serialized fields in database
... Peter Amstutz
04:59 pm Arvados Bug #11168: [API] Use JSON instead of YAML for serialized fields in database
... Peter Amstutz
04:45 pm Arvados Bug #11168: [API] Use JSON instead of YAML for serialized fields in database
Hold on, now I'm having trouble starting the API server in arvbox. I don't know if something is just corrupted/confu... Peter Amstutz
04:30 pm Arvados Bug #11168: [API] Use JSON instead of YAML for serialized fields in database
LGTM @ commit:594e00f Peter Amstutz
04:31 pm Arvados Task #11195 (Resolved): Review 11168-serialize-json
Peter Amstutz

03/02/2017

08:48 pm Arvados Story #11177: [GA4GH] Participate in interoperability challenge
https://www.synapse.org/#!Synapse:syn8080249/wiki/415165 Peter Amstutz
05:43 pm Arvados Story #11177 (Resolved): [GA4GH] Participate in interoperability challenge
Peter Amstutz
05:43 pm Arvados Task #11193 (Resolved): Submit writeup
Peter Amstutz
03:42 pm Arvados Bug #11168: [API] Use JSON instead of YAML for serialized fields in database
11168-serialize-json @ commit:766ddd6
I notice that a couple of places have been switched to use SafeJSON, but the...
Peter Amstutz
02:33 pm Arvados Task #11195 (In Progress): Review 11168-serialize-json
Peter Amstutz

03/01/2017

08:51 pm Arvados Task #11198 (New): Review
Peter Amstutz
08:50 pm Arvados Task #11194 (New): Review
Peter Amstutz
08:49 pm Arvados Task #11193 (Resolved): Submit writeup
Peter Amstutz
08:49 pm Arvados Task #11192 (New): Review
Peter Amstutz
08:48 pm Arvados Task #11191 (New): Review
Peter Amstutz
08:43 pm Arvados Bug #10729: [Crunch2] Propagate error messages if sbatch command succeeds but crunch-run can't ru...
We can also try running "srun" with the same flags, since it is more likely to return useful errors from the subproce... Peter Amstutz
08:22 pm Arvados Task #11164 (Resolved): Review 9277-container-output
Peter Amstutz
08:11 pm Arvados Bug #10035 (In Progress): [FUSE] Determine why bcl2fastq doesn't work with writable keep mount
Peter Amstutz
08:11 pm Arvados Bug #10035 (Resolved): [FUSE] Determine why bcl2fastq doesn't work with writable keep mount
Peter Amstutz
08:11 pm Arvados Feature #6520 (Resolved): [Node Manager] [Crunch2] Take queued containers into account when compu...
Peter Amstutz
08:03 pm Arvados Bug #11186 (Duplicate): Priority 0 state shouldn't be labeled "Ready"
Peter Amstutz
07:00 pm Arvados Story #10401 (In Progress): [CWL] Limit expansion of Directory inputs
Peter Amstutz

02/28/2017

07:08 pm Arvados Story #11139: [Node manager] Expected MemTotal for each cloud node size
Based on discussion: reduce the predicted RAM available for node by 5% Peter Amstutz

02/27/2017

07:17 pm Arvados Story #11177 (Resolved): [GA4GH] Participate in interoperability challenge
https://www.synapse.org/#!Synapse:syn8080249/wiki/412159
# Get tool & test data
# Import / run it on Arvados
# D...
Peter Amstutz
03:30 pm Arvados Story #11171 (New): [Nodemanager] Packaging for compute node setup scripts
All software installed into compute node images, including setup scripts, should be packaged so that documentation fo... Peter Amstutz

02/24/2017

07:30 pm Arvados Bug #10629 (Resolved): [FUSE] slow enumerating files by collection uuid
Applied in changeset arvados|commit:9b2aa42213a7d333bbe93e040c2d152a70e9b5af. Peter Amstutz
07:25 pm Arvados Story #9277 (Resolved): [Crunch2] System-owned container outputs should be garbage-collected
Applied in changeset arvados|commit:cca78a112d6a2aa4f76c1956cfe8ec2d43a68759. Peter Amstutz
04:12 pm Arvados Story #9277: [Crunch2] System-owned container outputs should be garbage-collected
Additional fixes on 9277-container-output
Tests:
https://ci.curoverse.com/job/developer-run-tests/178/
Peter Amstutz
07:24 pm Arvados Task #11114 (Resolved): Review 10629-fuse-listing-perf
Peter Amstutz
07:24 pm Arvados Revision 9b2aa422 (arvados): Merge branch '10629-fuse-listing-perf' closes #10629
Peter Amstutz
07:22 pm Arvados Task #11041 (Resolved): Review 11002-arvput-crash-fix
Peter Amstutz
07:21 pm Arvados Revision cca78a11 (arvados): Merge branch '9277-container-output' closes #9277
Peter Amstutz
07:20 pm Arvados Revision b86728d2 (arvados): 9277: Add test that setting trashed, unreable collection is disallowed.
Peter Amstutz
06:53 pm Arvados Story #11167 (New): [Workbench] Remove arv-get file download fallback
Currently, if keep-web isn't configured, Workbench will fallback to arv-get and Rails streaming to serve files. Howe... Peter Amstutz
06:14 pm Arvados Bug #11002: [arv-put] crash in arvfile on upload NoneType object has no attribute 'closed'
Rest LGTM. Peter Amstutz
05:02 pm Arvados Bug #11002: [arv-put] crash in arvfile on upload NoneType object has no attribute 'closed'
From IRC: make a note around line L454 that because we catch signals, we expect a SystemExit, not KeyboardInterrupt.
...
Peter Amstutz
04:12 pm Arvados Task #11164 (Resolved): Review 9277-container-output
Peter Amstutz
04:10 pm Arvados Story #11163 (New): [GA4GH] Participate in workflow interoperability activities
Peter Amstutz
04:04 pm Arvados Story #11162 (New): [GA4GH] Support workflow execution API
Peter Amstutz
04:03 pm Arvados Story #11161 (New): [GA4GH] Support task execution API using crunch v2 containers
Peter Amstutz
04:02 pm Arvados Story #11160 (New): [GA4GH] Expose workflow records via tool registry API
Peter Amstutz
04:02 pm Arvados Story #11159 (New): [GA4GH] Import from tool registry API
Support import of tools from tool registry API.
https://github.com/ga4gh/tool-registry-schemas
Initial capabili...
Peter Amstutz
04:01 pm Arvados Revision a04b28a6 (arvados): 9277: arvados-cwl-runner sets "is_trashed" when directly setting out...
Peter Amstutz
03:53 pm Arvados Revision a6e4bccc (arvados): 9277: Container output check must be unscoped to include trashed col...
Peter Amstutz

02/23/2017

06:18 pm Arvados Story #9277 (Feedback): [Crunch2] System-owned container outputs should be garbage-collected
... Peter Amstutz

02/22/2017

09:41 pm Arvados Bug #10629: [FUSE] slow enumerating files by collection uuid
10629-fuse-listing-perf ready for review. Peter Amstutz
08:35 pm Arvados Bug #10629 (In Progress): [FUSE] slow enumerating files by collection uuid
... Peter Amstutz
04:16 pm Arvados Bug #10629: [FUSE] slow enumerating files by collection uuid
... Peter Amstutz
09:28 pm Arvados Revision aedb62c7 (arvados): 10629: Don't flush dirhandles.
Peter Amstutz
09:08 pm Arvados Revision fe85406f (arvados): 10629: Make tracking and dirtying of _committed flag efficient.
Peter Amstutz
08:40 pm Arvados Revision 04fb9a14 (arvados): 10629: improve debug logging
--debug includes Keep logging.
--logfile includes timestamps.
Peter Amstutz

02/21/2017

06:49 pm Arvados Bug #11002: [arv-put] crash in arvfile on upload NoneType object has no attribute 'closed'
From our conversations on IRC, I think KeyboardInterrupt should skip checkpointing but shouldn't log anything. Howev... Peter Amstutz
04:07 pm Arvados Bug #11002: [arv-put] crash in arvfile on upload NoneType object has no attribute 'closed'
So if I'm following along, the problem is that it is in repack_small_blocks() which creates a new, un-owned bufferblo... Peter Amstutz
06:44 pm Arvados Bug #11093: "arv keep_service create" should go to an editor.
You want "arv create keep_service"
or do you mean the default behavior should be more user friendly? :-)
Peter Amstutz
04:33 pm Arvados Story #11123 (In Progress): Add node manager to install guide
Peter Amstutz
04:32 pm Arvados Task #11041 (In Progress): Review 11002-arvput-crash-fix
Peter Amstutz

02/20/2017

09:32 pm Arvados Task #11141 (Resolved): Review 6520-nodemanager-docs
Peter Amstutz
09:18 pm Arvados Revision 8b75947e (arvados): Merge branch '6520-pending-reason' refs #6520
Peter Amstutz
09:17 pm Arvados Revision 4bd54c4c (arvados): 6520: Add ReqNodeNotAvail to list of reasons (along with "Resources"...
Peter Amstutz
09:13 pm Arvados Revision 53887579 (arvados): 6520: Add information about setting up SLURM to crunchv2 documentation.
Peter Amstutz
07:47 pm Arvados Story #11139: [Node manager] Expected MemTotal for each cloud node size
This can be fixed entirely through configuration by overriding the "ram" field for each size. However, we need deter... Peter Amstutz
07:07 pm Arvados Story #11139: [Node manager] Expected MemTotal for each cloud node size
GCP... Peter Amstutz
06:20 pm Arvados Story #11139 (Resolved): [Node manager] Expected MemTotal for each cloud node size
There's a discrepancy between the RAM of a VM used to choose what size node to boot for a job, and the actual amount ... Peter Amstutz
 

Also available in: Atom