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>
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>
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>
Tom Clegg [Tue, 6 Mar 2018 19:52:29 +0000 (14:52 -0500)]
13078: Ensure compute0 always has all the instancetype=X features.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 6 Mar 2018 18:49:41 +0000 (13:49 -0500)]
Merge branch '13078-cds-noheader' refs #13078
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 6 Mar 2018 18:49:10 +0000 (13:49 -0500)]
13078: Add --noheader to squeue invocation.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 6 Mar 2018 16:44:20 +0000 (13:44 -0300)]
Merge branch '12268-build-fix'
Refs #12268
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 6 Mar 2018 16:43:27 +0000 (13:43 -0300)]
12268: Add comment just in case we need to use a forked libcloud again.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Tue, 6 Mar 2018 16:36:07 +0000 (11:36 -0500)]
12526: Add constant for default priority and check range.
Also fix a-c-r help text refs #12410
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 2 Mar 2018 20:05:47 +0000 (15:05 -0500)]
12526: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 2 Mar 2018 14:53:39 +0000 (09:53 -0500)]
12526: add --priority for --api=containers
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 6 Mar 2018 15:56:52 +0000 (12:56 -0300)]
12268: Fix package build scripts
Libcloud now is built from official sources instead of our fork.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 5 Mar 2018 21:58:17 +0000 (18:58 -0300)]
12268: Fix merge conflict.
Refs #12268
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 5 Mar 2018 21:49:58 +0000 (18:49 -0300)]
Merge branch '12268-libcloud230-official'
Closes #12268
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 5 Mar 2018 21:39:04 +0000 (18:39 -0300)]
13147: Logger call fix.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 5 Mar 2018 21:16:03 +0000 (18:16 -0300)]
12268: Remove libcloud fork installation attempt on run-tests.sh
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 5 Mar 2018 20:20:01 +0000 (17:20 -0300)]
12268: Update nodemanager dependency on libcloud 2.3.0
As we're now using the official release, this update run-test.sh will
try to install from PyPI.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Mon, 5 Mar 2018 18:38:43 +0000 (13:38 -0500)]
Merge branch '13140-cwl-conformance' refs #13140
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Sun, 4 Mar 2018 02:58:06 +0000 (21:58 -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.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Sat, 3 Mar 2018 00:40:40 +0000 (19:40 -0500)]
Stop running sdk/R install if sdk/R is not being tested. It is
really expensive on a clean install (~6 minutes).
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Fri, 2 Mar 2018 21:12:17 +0000 (16:12 -0500)]
13140: Fix call to docker.get_image()
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 2 Mar 2018 19:58:43 +0000 (14:58 -0500)]
12552: Remove superfluous arithmetic.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 2 Mar 2018 19:53:05 +0000 (14:53 -0500)]
12552: Fix starvation in test case.
refs #12552
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 2 Mar 2018 19:22:46 +0000 (16:22 -0300)]
Merge branch '12737-arvados-gem-dependency'
Refs #12737
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Fri, 2 Mar 2018 19:18:10 +0000 (14:18 -0500)]
13140: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Fri, 2 Mar 2018 19:04:11 +0000 (14:04 -0500)]
The crunch-dispatch-slurm binary has a new dependency on the
lib/dispatchcloud directory. Reflect that in the build scripts.
refs #13078
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Lucas Di Pentima [Thu, 1 Mar 2018 19:57:10 +0000 (16:57 -0300)]
12737: Fix activesupport dependency from arvados gem.
Upper version requirement was avoiding gem installation when upgrading rails
to a version >= 4.2.6.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Fri, 2 Mar 2018 15:00:12 +0000 (10:00 -0500)]
13140: Bump cwltool version
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 1 Mar 2018 21:41:07 +0000 (16:41 -0500)]
Merge branch '12552-slurm-priority'
refs #12552
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
jiayong2 [Wed, 28 Feb 2018 17:47:15 +0000 (17:47 +0000)]
Merge branch '11850-singlecontainer-max-requirements'
closes #11850
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jiayong@math.mit.edu>
jiayong2 [Wed, 28 Feb 2018 17:39:42 +0000 (17:39 +0000)]
Merge branch 'master' into 11850-singlecontainer-max-requirements
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jiayong@math.mit.edu>
Tom Clegg [Wed, 28 Feb 2018 16:27:29 +0000 (11:27 -0500)]
Merge branch '13078-slurm-feature-test'
refs #13078
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 28 Feb 2018 16:27:12 +0000 (11:27 -0500)]
12552: Improve PrioritySpread docs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 27 Feb 2018 22:09:20 +0000 (17:09 -0500)]
13078: Accept "no nodes" as an indication that features are OK.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 27 Feb 2018 22:01:19 +0000 (17:01 -0500)]
13078: Use --test-only instead of invalid --gres to check features.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 27 Feb 2018 18:05:13 +0000 (13:05 -0500)]
Merge branch '12315-exclude-child-procs'
closes #12315
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 27 Feb 2018 16:08:19 +0000 (11:08 -0500)]
12315: Tidy up test params.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 26 Feb 2018 21:27:08 +0000 (16:27 -0500)]
Merge branch '13037-composer-link' closes #13037
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
jiayong2 [Mon, 26 Feb 2018 20:11:08 +0000 (20:11 +0000)]
Merge branch 'master' into 11850-singlecontainer-max-requirements
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jiayong@math.mit.edu>
jiayong2 [Mon, 26 Feb 2018 20:06:59 +0000 (20:06 +0000)]
Take sum for outdir requirement in single container
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jiayong@math.mit.edu>
Lucas Di Pentima [Mon, 26 Feb 2018 18:22:44 +0000 (15:22 -0300)]
Merge branch '12707-storage-classes-columns'
Closes #12707
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 26 Feb 2018 17:26:41 +0000 (14:26 -0300)]
12707: Adds default value setting on collection creation.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 26 Feb 2018 16:14:18 +0000 (11:14 -0500)]
12552: Fix accidental textile link syntax.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 14 Feb 2018 16:22:57 +0000 (11:22 -0500)]
13037: Add hidden api_token to Composer button to skip extra login
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 26 Feb 2018 15:42:16 +0000 (10:42 -0500)]
12552: Document PrioritySpread. Default to 10 if not configured.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 26 Feb 2018 14:46:39 +0000 (09:46 -0500)]
12552: Skip extra lookup.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 26 Feb 2018 14:46:31 +0000 (09:46 -0500)]
12552: Add slurm-renice test cases.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 23 Feb 2018 18:09:30 +0000 (15:09 -0300)]
12707: Some fixes and additions on storage classes:
* Remove the unnecessary default values from model.
* Fixes and tests on storage classes columns.
* Adds tests for 'exists' filter on jsonb array columns.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Fri, 23 Feb 2018 21:29:06 +0000 (16:29 -0500)]
12315: Propagate show_children to infinite scroll pages. Fix & add tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Feb 2018 19:31:40 +0000 (14:31 -0500)]
12315: Add abstract show_children query parameter
Can't use requesting_container_uuid filter directly because it breaks
query of jobs and pipelines. Add abstract show_children query
parameter. Default is to hide children processes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Feb 2018 18:28:50 +0000 (13:28 -0500)]
Merge branch 'wtsi/13113-acr-collectioncache-retries' refs #13113
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Feb 2018 18:26:59 +0000 (13:26 -0500)]
Merge branch 'wtsi/13093-crunch-dispatch-slurm-add-mem' refs #13093
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Feb 2018 16:15:44 +0000 (11:15 -0500)]
Merge branch '13064-arv-mount-perf' closes #13064
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 23 Feb 2018 16:15:03 +0000 (11:15 -0500)]
13064: Add comment about has_ref() and in_use() checks
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 16 Feb 2018 23:47:49 +0000 (20:47 -0300)]
12707: Add storage classes attributes to collections.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 22 Feb 2018 20:58:56 +0000 (15:58 -0500)]
13064: Explicitly precompile regexes used in manifest parsing
Seems to improve parsing time roughly 5-10%
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 22 Feb 2018 19:47:42 +0000 (14:47 -0500)]
13064: Add __slots__ to ArvadosFile and FuseArvadosFile
More than 50% decrease in memory footprint for large collections!!!
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 22 Feb 2018 19:09:33 +0000 (14:09 -0500)]
13064: Check has_ref before checking in_use
Kernel behavior seems to be that if a file is referenced, its parents
remain referenced too. This means has_ref() exits early when a
collection is not candidate for eviction.
By contrast, in_use() doesn't increment references on parents, so it
requires a full tree walk to determine if a collection is a candidate
for eviction.
Switching the order of the checks retains correctness but greatly
improves real-world performance.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Joshua C. Randall [Thu, 15 Feb 2018 18:50:19 +0000 (18:50 +0000)]
add ReserveExtraRAM config option to crunch-dispatch-slurm
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Joshua Randall [Wed, 21 Feb 2018 20:51:56 +0000 (20:51 +0000)]
Fix CollectionCache to pass num_retries to CollectionReader
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Peter Amstutz [Wed, 21 Feb 2018 20:46:32 +0000 (15:46 -0500)]
Merge branch '11645-keepstore-storageclasses' closes #11645
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Feb 2018 20:42:48 +0000 (15:42 -0500)]
11645: Add tests that StorageClasses is loaded from config
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Wed, 21 Feb 2018 20:13:02 +0000 (15:13 -0500)]
Fix typos/grammar.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Wed, 21 Feb 2018 17:06:04 +0000 (12:06 -0500)]
Merge branch '13106-keepclient-slot' closes #13106
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Feb 2018 17:05:36 +0000 (12:05 -0500)]
13106: Add note about the test.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Feb 2018 16:56:39 +0000 (11:56 -0500)]
11645: Add support for StorageClasses in volume config.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Feb 2018 01:32:44 +0000 (20:32 -0500)]
13106: Add test confirming deadlock
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 20 Feb 2018 21:29:22 +0000 (16:29 -0500)]
13106: Ensure cache slot is reset on error
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
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