Arvados

Story

Resolved

Sprint Impediments

7533

[OPS] migrate su92l to Azure

Ward Vandewege

impediments

-c-a

8422

[Microsoft] [M1] Organize input data

Jiayong Li

303

impediments

-c-a

8529

[Microsoft] [M1] Generate CWL pipelines using bcbio

Bryan Cosca

189

impediments

-c-a

8530

[Microsoft] [M1] Generate SNAP-based CWL pipelines using bcbio

Sarah Guthrie

184

impediments

-c-a

8576

[OPS] convert wx7k5 to blob storage

Nico César

288

impediments

-c-a

8577

[Microsoft] [M1] Create collection with necessary reference data needed by bcbio

Bryan Cosca

189

impediments

-c-a

8702

[Keep] HEAD request should do a checksum of the blob without sending it

impediments

-c-a

8720

[OPS] Upgrade non-customer Curoverse clusters to a recent Arvados version

Nico César

288

impediments

-c-a

8819

[Microsoft] [M1] bcbio/bcbio docker image contains GATK

Brad Chapman

188

impediments

-c-a

8855

[Microsoft] Add explicit sort in postprocess_alignment, recreate, and reupload the bcbio docker image

Brad Chapman

188

impediments

-c-a

8893 8893 Brett Smith Brett Smith 79 [Crunch] Invalid `docker run` syntax when crunchrunner is not installed Resolved Resolved 3 0.5 0.5 0.5 8893 36 79 132 1 0.5	8895 8895 Review 8893-crunch-job-crunchrunner-quoting-wip Brett Smith 79 0 8893 3 36 -c-a 5 8921 8921 Review 8893-crunch-job-volumes-array-wip Brett Smith 79 0 8893 3 36 -c-a 5
8724 8724 Radhika Chippada Radhika Chippada 72 [Keep] Block validation script Resolved Resolved 3 2.0 2.0 2.0 8724 36 72 132 6 2.0	8854 8854 Review branch: 8724-keep-block-check-script Radhika Chippada 72 0 8724 3 36 -c-a 5
8913 8913 Brett Smith Brett Smith 79 [Nodemanager] On GCE: 'unicode' object has no attribute 'id', where we should have a NodeSize Resolved Resolved 3 8913 36 79 132 1	8923 8923 Review 8912-node-manager-patch-nodes-wip Peter Amstutz 47 0 8913 3 36 -c-a 5
7658 7658 Radhika Chippada Radhika Chippada 72 SDKs 54 SDKs [SDK] Python websockets reconnect on unexpected close Resolved Resolved 3 2.0 2.0 2.0 7658 36 72 132 6 2.0	8853 8853 Review branch: 7658-websockets-reconnect-on-close Peter Amstutz 47 0 7658 3 36 -c-a 5
8799 8799 Peter Amstutz Peter Amstutz 47 [Node manager] nodes in slurm drained state are counted as "up" but not candidates for shut down Resolved Resolved 3 8799 36 47 132 1	8890 8890 Review 8799-make-drained-nodes-idle Peter Amstutz 47 0 8799 3 36 -c-a 5 8889 8889 Re-enable nodes in drained state Peter Amstutz 47 0 8799 3 36 -c-a 5
8904 8904 Brett Smith Brett Smith 79 Make test suite work on debian 7 (wheezy) by using pip<8 for python3 Resolved Resolved 3 8904 36 79 132 1	8922 8922 Review 8904-wheezy-docker-py-wip Tom Clegg 3 0 8904 3 36 -c-a 5
8872 8872 Brett Smith Brett Smith 79 Node Manager 66 Node Manager [Node Manager] On node creation, node search fails, and unhandled exceptions cascade up to the Daemon Actor Resolved Resolved 3 8872 36 79 132 1	8900 8900 Review 8872-node-manager-create-search-handling-wip Brett Smith 79 0 8872 3 36 -c-a 5
8911 8911 [crunchstat-summary] package as deb/rpm Resolved Resolved 3 8911 36 132 2
8879 8879 Brett Smith Brett Smith 79 [CWL Runner] arvados-cwl-runner --submit --project-uuid does not place new job in specified project Resolved Resolved 3 0.5 0.5 0.5 8879 36 79 132 1 0.5	8887 8887 Review 8879-cwl-runner-job-owner-wip Brett Smith 79 0 8879 3 36 -c-a 5
8810 8810 Brett Smith Brett Smith 79 [Crunch] `docker load` fails to connect to endpoint; srun exits 0 Resolved Resolved 3 8810 36 79 132 1	8888 8888 Review 8810-crunch-improve-docker-loading-wip Brett Smith 79 0 8810 3 36 -c-a 5
8712 8712 Peter Amstutz Peter Amstutz 47 FUSE 69 FUSE [FUSE] Read-only collections appear empty after they are evicted from the cache Resolved Resolved 3 0.5 0.5 0.5 8712 36 47 132 1 0.5	8744 8744 Investigate Peter Amstutz 47 0 8712 3 36 -c-a 5 8745 8745 Review 8712-fuse-cache-reload-bug Nico César 288 0 8712 3 36 -c-a 5
8811 8811 Brett Smith Brett Smith 79 [Crunch] `srun --nodes=1` reports "Unable to create job step: Required node not available (down or drained)" and exits 1 Resolved Resolved 3 0.5 0.5 0.5 8811 36 79 132 1 0.5	8862 8862 Review 8811-srun-sync-tempfail-wip Peter Amstutz 47 0 8811 3 36 -c-a 5
8857 8857 Peter Amstutz Peter Amstutz 47 [CWL] arvados-cwl-runner additional options for job reuse Resolved Resolved 3 0.5 0.5 0.5 8857 36 47 132 6 0.5	8858 8858 Review 8857-cwl-job-reuse Sarah Guthrie 184 0 8857 3 36 -c-a 5
8828 8828 Peter Amstutz Peter Amstutz 47 [Crunch] be more resilient when crunchrunner is not available; also don't test for crunchrunner on api server Resolved Resolved 3 8828 36 47 132 1	8861 8861 Review 8828-which-crunchrunner Peter Amstutz 47 0 8828 3 36 -c-a 5
8840 8840 Peter Amstutz Peter Amstutz 47 [API] Locking job doesn't lock record Resolved Resolved 3 0.5 0.5 0.5 8840 36 47 132 1 0.5	8856 8856 Review 8840 branch Brett Smith 79 0 8840 3 36 -c-a 5