Fuad Muhic [Mon, 26 Mar 2018 15:07:07 +0000 (17:07 +0200)]
Merge branch 'master' of git.curoverse.com:arvados into 13076-r-autogen-api
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Mon, 26 Mar 2018 15:07:07 +0000 (17:07 +0200)]
Added project manipulation methods to autogenerated Arvados class.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Ward Vandewege [Sun, 25 Mar 2018 01:16:47 +0000 (21:16 -0400)]
build scripts: only run the package tests on packages built since the
previous time the package test script ran. This speeds up the build
pipeline significantly.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Fri, 23 Mar 2018 18:27:33 +0000 (14:27 -0400)]
Merge branch '13245-cwl-dir-literal' closes #13245
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Mar 2018 18:21:25 +0000 (14:21 -0400)]
Merge branch '13212-unavailable-output-workunit' closes #13212
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 23 Mar 2018 18:18:50 +0000 (14:18 -0400)]
Merge branch '7931-replicas-by-volume'
refs #7931
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 23 Mar 2018 18:11:35 +0000 (14:11 -0400)]
7931: Merge branch 'master' into 7931-replicas-by-volume
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 23 Mar 2018 17:18:50 +0000 (13:18 -0400)]
7931: Update json field tags on trash/pull requests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 23 Mar 2018 17:03:28 +0000 (13:03 -0400)]
13212: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Mar 2018 14:52:44 +0000 (10:52 -0400)]
13212: Replace "Output data not available" with "uuid (Unavailable)"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Mar 2018 14:34:29 +0000 (10:34 -0400)]
Add cookbook examples for uploading and downloading a file from a
Collection in Python, closes #13253
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Mar 2018 14:07:24 +0000 (10:07 -0400)]
Fix cwl extension doc typo. refs #13179
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Mar 2018 13:59:44 +0000 (09:59 -0400)]
Fix cwl extension doc typo. closes #13179
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 22 Mar 2018 20:07:54 +0000 (16:07 -0400)]
13245: Bump cwltool version
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 22 Mar 2018 18:56:21 +0000 (14:56 -0400)]
13245: Sort InitialWorkDir contents to fix conflicts and redundant mounts.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 22 Mar 2018 17:20:32 +0000 (13:20 -0400)]
7931: OTBE, prefer readonly replicas; they can't be trashed anyway.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 22 Mar 2018 16:58:57 +0000 (12:58 -0400)]
7931: Don't bother trying to trash replicas on readonly mounts.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 20 Mar 2018 17:10:38 +0000 (13:10 -0400)]
7931: Fix format/type mismatch.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 19 Mar 2018 17:19:41 +0000 (13:19 -0400)]
7931: Trash excess replicas when a server has more than one.
Previously a given server was classified only as "having" or "not
having" a replica, regardless of how many it reported. With this
change, once there are already enough distinct replicas on other
servers, excess replicas will be trashed -- even if they are on the
same server as a replica that is being retained.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sun, 18 Mar 2018 06:48:43 +0000 (02:48 -0400)]
7931: keep-balance: use keepstore /mounts APIs instead of /index.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Tue, 20 Mar 2018 18:04:00 +0000 (15:04 -0300)]
Merge branch '12167-arvput-log-on-signals'
Refs #12167
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 20 Mar 2018 17:39:49 +0000 (13:39 -0400)]
12167: Stop waiting for arv-put to start up when logs appear.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 19 Mar 2018 17:02:25 +0000 (13:02 -0400)]
Merge branch '13208-permission-performance' refs #13208
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Mar 2018 18:13:37 +0000 (14:13 -0400)]
13208: Refactor permission checking to improve query performance
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 15 Mar 2018 19:36:19 +0000 (15:36 -0400)]
Merge branch '13138-request-error' refs #13138
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 15 Mar 2018 19:01:10 +0000 (16:01 -0300)]
12167: Report request-id when receiving SIGINT on arv-put.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 15 Mar 2018 19:28:02 +0000 (15:28 -0400)]
Fix 'arvbox log' to propagate terminal size, no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 15 Mar 2018 19:12:38 +0000 (15:12 -0400)]
Merge branch '13100-crunch-run-memory'
refs #13100
refs #11583
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 15 Mar 2018 16:45:52 +0000 (12:45 -0400)]
11583: 13100: Fix memory leak in test suite.
Something (an unterminated goroutine?) holds a reference to the keep
client, which (in the test suite) holds a reference to the last block
it wrote. Releasing the reference to the block reduces test suite
memory use by about 2.6 GB.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 15 Mar 2018 14:57:59 +0000 (10:57 -0400)]
13100: Fix memory leak (64MiB per stream in output/log collection).
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 14 Mar 2018 19:10:56 +0000 (15:10 -0400)]
Merge branch '12552-wf-priority'
refs #12552
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 14 Mar 2018 18:46:22 +0000 (14:46 -0400)]
13138: Gather arvados API errors under "RequestError" class.
Don't print stack trace for RequestError, because they are expected
conditions when there is an error in the request.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 14 Mar 2018 18:15:15 +0000 (14:15 -0400)]
12552: Merge branch 'master' into 12552-wf-priority
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 14 Mar 2018 18:13:11 +0000 (14:13 -0400)]
12552: Fix workflow parent priority test.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 14 Mar 2018 15:09:20 +0000 (11:09 -0400)]
Merge branch '13135-cwl-secrets' closes #13135
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 14 Mar 2018 14:48:58 +0000 (10:48 -0400)]
13135: Code cleanup & comments.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 13 Mar 2018 20:23:17 +0000 (16:23 -0400)]
Fix arvbox workbench for updated passenger, refs #12737
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 13 Mar 2018 14:44:15 +0000 (10:44 -0400)]
12552: Prioritize containers according to top-level requests.
This change ensures:
* a high-priority container and all of its descendants are prioritized
ahead of lower-priority containers and their descendants.
* when two top-level containers are requested using equal priority,
the earlier-submitted container has higher priority.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 13 Mar 2018 17:31:36 +0000 (13:31 -0400)]
13135: Fix test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 13 Mar 2018 14:05:19 +0000 (10:05 -0400)]
13135: Update docs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 12 Mar 2018 20:45:39 +0000 (16:45 -0400)]
13135: Add secrets test to arvados-tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 12 Mar 2018 19:18:50 +0000 (15:18 -0400)]
13135: Secrets not supported with --api=jobs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 12 Mar 2018 18:37:56 +0000 (14:37 -0400)]
13135: Update tests for secret_mounts
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 12 Mar 2018 17:48:57 +0000 (13:48 -0400)]
13135: Remove testing workarounds
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Mar 2018 21:57:42 +0000 (16:57 -0500)]
13135: Handle secrets in file literals.
Also check for secrets leaking into command line or environment, and
fail if detected.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Mar 2018 21:32:35 +0000 (16:32 -0500)]
13135: Secrets support WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 13 Mar 2018 19:32:14 +0000 (15:32 -0400)]
Merge branch '13134-secret-mounts' closes #13134
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 13 Mar 2018 15:37:03 +0000 (11:37 -0400)]
13134: Check for conflicts between secret mounts and regular mounts
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 12 Mar 2018 20:25:08 +0000 (16:25 -0400)]
13134: Use the container token to fetch secret_mounts
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 12 Mar 2018 17:46:46 +0000 (13:46 -0400)]
13134: Get secret_mounts from separate API endpoint. Update tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Mar 2018 19:11:28 +0000 (14:11 -0500)]
13134: Support for secret mounts in crunch-run.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 13 Mar 2018 17:08:29 +0000 (13:08 -0400)]
Merge branch '13143-secret-mounts'
refs #13143
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Mar 2018 16:18:08 +0000 (13:18 -0300)]
Merge branch '12737-update-rails-wb'
Refs #12737
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Mar 2018 16:03:50 +0000 (13:03 -0300)]
Merge branch '12369-fuse-driver-doc-updates'
Closes #12369
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Mar 2018 16:02:51 +0000 (13:02 -0300)]
12369: Grammar fix
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 13 Mar 2018 14:47:43 +0000 (10:47 -0400)]
13143: Update find_reusable() invocation in test suite.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fuad Muhic [Tue, 13 Mar 2018 14:28:47 +0000 (15:28 +0100)]
Added listAll utility function which will always fetch all resources.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Lucas Di Pentima [Mon, 12 Mar 2018 20:52:40 +0000 (17:52 -0300)]
12369: Add fuse driver installation notes & update arv-mount tutorial.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 19:57:43 +0000 (15:57 -0400)]
13143: Decode request body secret_mounts properly.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 17:35:53 +0000 (13:35 -0400)]
13143: Remove superfluous check for null hash.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 17:07:51 +0000 (13:07 -0400)]
13143: Add missing "secret_mounts scrubbed" test.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 15:44:19 +0000 (11:44 -0400)]
13143: Fix same/different-secret_mounts tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 15:43:22 +0000 (11:43 -0400)]
13143: Sort hash keys for more realistic fixture md5.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 15:43:03 +0000 (11:43 -0400)]
13143: Ignore secret_mounts_md5 from fixtures, too.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 15:23:48 +0000 (11:23 -0400)]
13143: Prohibit identical path in mounts + secret_mounts.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 14:43:26 +0000 (10:43 -0400)]
13143: Merge branch 'master' into 13143-secret-mounts
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 14:42:33 +0000 (10:42 -0400)]
13143: Skip some unneeded deep_dup.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 14:42:01 +0000 (10:42 -0400)]
13143: Don't advertise secret_* columns in discovery doc.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 14:24:08 +0000 (10:24 -0400)]
13143: Don't load secret_mounts from test fixtures.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Mar 2018 14:32:09 +0000 (10:32 -0400)]
13143: Skip some unneeded database resets.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 12 Mar 2018 13:43:40 +0000 (09:43 -0400)]
Fix "priority" KeyError in crunch1 refs #12526
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 9 Mar 2018 21:47:19 +0000 (16:47 -0500)]
13143: Do not try to select container secret_mounts column.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 9 Mar 2018 21:21:52 +0000 (18:21 -0300)]
12737: Try pinning all testing gems
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Fri, 9 Mar 2018 20:52:16 +0000 (15:52 -0500)]
13143: Add secret_mounts field to containers and container requests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 9 Mar 2018 20:29:22 +0000 (15:29 -0500)]
Fix packaging for python-cwltest. refs #13140
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 9 Mar 2018 19:38:11 +0000 (16:38 -0300)]
12737: Avoid upgrading to selenium 3.x
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 9 Mar 2018 18:49:03 +0000 (15:49 -0300)]
12737: Fix benchmark & integration tests
Minitest & angularjs-rails gems seem to have incompatible changes
on newer versions.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 7 Mar 2018 14:18:35 +0000 (11:18 -0300)]
12737: Update workbench rails to 4.1.16 (latest 4.1.x)
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 9 Mar 2018 15:49:56 +0000 (12:49 -0300)]
Merge branch '12737-update-rails-api'
Refs #12737
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Fuad Muhic [Fri, 9 Mar 2018 14:05:38 +0000 (15:05 +0100)]
Removed all autogenerated Arvados classes and updated rest of the code to reflect that
change.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Fri, 9 Mar 2018 06:40:53 +0000 (01:40 -0500)]
Merge branch '13078-badconstraints'
refs #13078
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 8 Mar 2018 20:04:38 +0000 (17:04 -0300)]
Merge branch '13147-arvput-request-id'
Closes #13147
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Ward Vandewege [Thu, 8 Mar 2018 18:32:07 +0000 (13:32 -0500)]
When running inside a virtualenv, pip still uses the ~/.cache/pip cache
directory, unless it is explicitly overridden with XDG_CACHE_HOME.
In the test script, stop using pip's cache directory altogether (part 2).
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Thu, 8 Mar 2018 16:14:35 +0000 (11:14 -0500)]
Fix arvados-cwl-runner --version argument (again) refs #12526
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 8 Mar 2018 15:34:16 +0000 (12:34 -0300)]
13147: X-Request-Id logging updates when running arv-put.
Remove the initial request-id logging when starting the run.
Update the custom formatter so that it shows the request-id only once.
Add related tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 8 Mar 2018 15:17:11 +0000 (10:17 -0500)]
Fix arvados-cwl-runner --version argument refs #12526
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 8 Mar 2018 14:55:25 +0000 (09:55 -0500)]
Update version of cwltest package refs #13140
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 7 Mar 2018 22:54:35 +0000 (17:54 -0500)]
13078: Add test case for "release job held because BadConstraints".
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Wed, 7 Mar 2018 19:40:36 +0000 (14:40 -0500)]
Documention: fix spelling of --tempdir argument to arv-migrate-docker19
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 7 Mar 2018 19:35:51 +0000 (14:35 -0500)]
Python sdk: do not try to do a bitwise operation on a float.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Tom Clegg [Wed, 7 Mar 2018 15:09:20 +0000 (10:09 -0500)]
13078: Update comment.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 7 Mar 2018 14:43:28 +0000 (09:43 -0500)]
13078: Reduce "feature kludge" poll interval.
Whenever a new node comes online, "scontrol reconfigure" invalidates
all jobs that could be scheduled onto that node *or any other node* so
it's worthwhile to recover from this quickly.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 7 Mar 2018 14:19:40 +0000 (09:19 -0500)]
13078: Fix jobs stuck in "held" state in old SLURM versions.
In SLURM 14 and 15, if a queued job has feature constraints which
become invalid (e.g., when "scontrol reconfigure" clears all node
features), the job is put on hold with priority=0, and it stays in
this state even after the features reappear. "scontrol release"
recovers a job from this state.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fuad Muhic [Wed, 7 Mar 2018 16:29:30 +0000 (17:29 +0100)]
Refactored autoGenApi to be more readable
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Wed, 7 Mar 2018 14:17:56 +0000 (09:17 -0500)]
13078: Fix ignoring queued jobs with reason=BadConstraints.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 7 Mar 2018 01:07:33 +0000 (20:07 -0500)]
Merge branch '12526-cwl-priority' closes #12526
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 20 Feb 2018 19:16:09 +0000 (16:16 -0300)]
12737: Update API server to rails 4.2.10
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 6 Mar 2018 22:14:24 +0000 (17:14 -0500)]
13078: Ignore held jobs with priority=0 (e.g., SLURM 15.x).
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 6 Mar 2018 22:11:35 +0000 (17:11 -0500)]
13078: Remove debug log.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Tue, 6 Mar 2018 20:29:14 +0000 (17:29 -0300)]
13147: Append X-Request-Id on error & debug log messages.
Set up a custom formatter that replaces the standard arvados one
when running arv-put, so that it appends the Req-Id on errors.
Replacing 'arvados' log formatter makes all loggers below it (arv_put and
api in this case) use the same format.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
projects / arvados.git / log