Ward Vandewege [Fri, 1 Apr 2016 19:16:49 +0000 (15:16 -0400)]
Fix package building by pinning docker-py to version 1.7.2
No issue #
Brett Smith [Fri, 1 Apr 2016 18:47:19 +0000 (14:47 -0400)]
Merge branch '8782-reapchildren-after-signal-wip'
Closes #8782, #8860, #8870.
Brett Smith [Fri, 1 Apr 2016 18:37:34 +0000 (14:37 -0400)]
8782: Remove WIFEXITED check from crunch-job reapchildren.
The intent of this check was to avoid reaping children that got
SIGSTOP. But from the waitpid(2) man page, you must pass specific
flags for waitpid to return those children. Without those flags,
waitpid will only return the pids of children that have terminated.
Meanwhile, WIFEXITED only returns true if the exit code indicates that
the child terminated normally. It returns false if the child was
killed by a signal like SIGINT or SIGKILL. This means children so
killed were not reaped by reapchildren, leading to infinite loops.
Peter Amstutz [Fri, 1 Apr 2016 18:32:14 +0000 (14:32 -0400)]
Merge branch '8857-cwl-job-reuse' closes #8857
Peter Amstutz [Fri, 1 Apr 2016 17:28:03 +0000 (13:28 -0400)]
8816: Handle cloud errors slightly differently from unrecognized errors.
Peter Amstutz [Fri, 1 Apr 2016 17:11:51 +0000 (13:11 -0400)]
8816: ComputeNodeUpdateActor._throttle_errors logs errors instead of re-throwing them.
Ward Vandewege [Fri, 1 Apr 2016 14:59:46 +0000 (10:59 -0400)]
A few more fixes for run-build-packages-python-and-ruby.sh, and a small
safeguard for run-build-packages.sh.
refs #8864
Peter Amstutz [Fri, 1 Apr 2016 14:01:39 +0000 (10:01 -0400)]
Merge branch 'master' into 8857-cwl-job-reuse
Conflicts:
sdk/cwl/arvados_cwl/__init__.py
Ward Vandewege [Fri, 1 Apr 2016 01:38:50 +0000 (21:38 -0400)]
Add build/run-build-packages-python-and-ruby.sh script to handle upload
to pypi and rubygems.
refs #8864
Peter Amstutz [Thu, 31 Mar 2016 22:29:45 +0000 (18:29 -0400)]
Merge branch '8828-which-crunchrunner' closes #8828
Peter Amstutz [Thu, 31 Mar 2016 21:25:05 +0000 (17:25 -0400)]
8828: Fix bind mount point for certificates.
Peter Amstutz [Thu, 31 Mar 2016 19:58:47 +0000 (15:58 -0400)]
8828: Move logic for checking $(which crunchrunner) into script that runs before invoking Docker on the compute node.
Ward Vandewege [Thu, 31 Mar 2016 17:49:54 +0000 (13:49 -0400)]
Build newer cwltool version.
No issue #
Peter Amstutz [Thu, 31 Mar 2016 15:54:40 +0000 (11:54 -0400)]
Merge branch '8840-lock-job-record' closes #8840
Peter Amstutz [Thu, 31 Mar 2016 15:35:49 +0000 (11:35 -0400)]
Merge branch '8654-arv-jobs-cwl-runner' closes #8654
Peter Amstutz [Thu, 31 Mar 2016 15:30:31 +0000 (11:30 -0400)]
8654: Update test because input cwl files changed.
Peter Amstutz [Thu, 31 Mar 2016 15:00:15 +0000 (11:00 -0400)]
8654: Fix versionstring(). Improve help text / comments / style tweaks.
Peter Amstutz [Thu, 31 Mar 2016 14:32:09 +0000 (10:32 -0400)]
Merge branch 'master' into 8654-arv-jobs-cwl-runner
Peter Amstutz [Thu, 31 Mar 2016 14:31:59 +0000 (10:31 -0400)]
8654: Rename tests/inp/ to test/input/
Peter Amstutz [Thu, 31 Mar 2016 14:21:17 +0000 (10:21 -0400)]
8857: Add --ignore-docker-for-reuse option to assist workflow development.
Peter Amstutz [Wed, 30 Mar 2016 19:00:10 +0000 (15:00 -0400)]
8840: Use 'with_lock' instead of 'transaction' in Job.lock method.
Peter Amstutz [Wed, 30 Mar 2016 18:58:30 +0000 (14:58 -0400)]
8654: Add missing test_submit
Peter Amstutz [Wed, 30 Mar 2016 18:45:12 +0000 (14:45 -0400)]
8654: Add comments
Peter Amstutz [Wed, 30 Mar 2016 18:00:24 +0000 (14:00 -0400)]
8654: Print uuid of uploaded docker image on stderr instead of stdout.
radhika [Wed, 30 Mar 2016 13:47:29 +0000 (09:47 -0400)]
closes #8703
Merge branch '8703-job-components'
radhika [Wed, 30 Mar 2016 13:47:08 +0000 (09:47 -0400)]
Merge branch 'master' into 8703-job-components
Peter Amstutz [Wed, 30 Mar 2016 13:33:49 +0000 (09:33 -0400)]
8654: Update test_with_arvbox.sh
Peter Amstutz [Wed, 30 Mar 2016 01:11:06 +0000 (21:11 -0400)]
crunchrunner crunch script selects between $JOB_PARAMETER_CRUNCHRUNNER
or /usr/local/bin/crunchrunner, refs #8827
Peter Amstutz [Tue, 29 Mar 2016 20:28:27 +0000 (16:28 -0400)]
8654: Pin pyasn1_modules to version that is compatible with pyasn1==0.1.7.
Peter Amstutz [Tue, 29 Mar 2016 20:28:19 +0000 (16:28 -0400)]
8654: Fix version string produced by arvados-cwl-runner.
Peter Amstutz [Tue, 29 Mar 2016 19:34:48 +0000 (15:34 -0400)]
Fix sdk/cwl test refs #8815
Peter Amstutz [Tue, 29 Mar 2016 18:16:58 +0000 (14:16 -0400)]
Merge branch '8815-crunchrunner-everywhere' closes #8815
Peter Amstutz [Tue, 29 Mar 2016 17:34:40 +0000 (13:34 -0400)]
Merge branch '8815-crunchrunner-everywhere' into 8654-arv-jobs-cwl-runner
Conflicts:
sdk/cwl/arvados_cwl/__init__.py
Peter Amstutz [Tue, 29 Mar 2016 17:30:17 +0000 (13:30 -0400)]
8654: Make --submit --wait the default mode.
radhika [Tue, 29 Mar 2016 17:10:49 +0000 (13:10 -0400)]
8703: better organized tests
Peter Amstutz [Tue, 29 Mar 2016 17:06:22 +0000 (13:06 -0400)]
8815: Fix syntax errors.
Peter Amstutz [Tue, 29 Mar 2016 16:18:15 +0000 (12:18 -0400)]
8815: Now expect /usr/local/bin/crunchrunner. Bind mount host certificates to
/etc/arvados/ca-certificates.crt
radhika [Tue, 29 Mar 2016 15:54:01 +0000 (11:54 -0400)]
Merge branch 'master' into 8703-job-components
Ward Vandewege [Tue, 29 Mar 2016 15:24:59 +0000 (11:24 -0400)]
Build a package for crunchrunner.
refs #8815
Peter Amstutz [Tue, 29 Mar 2016 13:38:16 +0000 (09:38 -0400)]
8815: Rely on system-provided crunchrunner. Also use arvados/jobs by default if no docker provided.
Peter Amstutz [Tue, 29 Mar 2016 13:23:51 +0000 (09:23 -0400)]
8815: Crunch-job bind mounts crunchrunner binary and certificates from host.
Updated arvbox to compile and install crunchrunner.
Peter Amstutz [Mon, 28 Mar 2016 14:06:32 +0000 (10:06 -0400)]
8654: Bump cwltool version dependency and print cwl version string in cwl-runner crunch script.
Peter Amstutz [Mon, 28 Mar 2016 13:37:37 +0000 (09:37 -0400)]
Merge branch 'master' into 8654-arv-jobs-cwl-runner
Conflicts:
docker/jobs/Dockerfile
Brett Smith [Sun, 27 Mar 2016 20:47:07 +0000 (16:47 -0400)]
Merge branch '8800-queue-query'
Closes #8800, #8809.
Brett Smith [Sun, 27 Mar 2016 20:43:55 +0000 (16:43 -0400)]
8800: Document the new queue_position implementation.
For the benefit of future readers.
Ward Vandewege [Sun, 27 Mar 2016 02:19:09 +0000 (22:19 -0400)]
Fix package build and test of the arvados-cwl-runner package for
ubuntu1204 and centos6.
refs #8671
Tom Clegg [Fri, 25 Mar 2016 19:59:34 +0000 (15:59 -0400)]
8800: Drop queue_position support.
Ward Vandewege [Sat, 26 Mar 2016 01:50:28 +0000 (21:50 -0400)]
Bump up the iteration for the python-arvados-cwl-runner package so that
it gets rebuilt.
refs #8671
Ward Vandewege [Sat, 26 Mar 2016 01:36:19 +0000 (21:36 -0400)]
Fix a few more dependencies for the python-arvados-cwl-runner package.
refs #8671
Peter Amstutz [Fri, 25 Mar 2016 20:35:10 +0000 (16:35 -0400)]
8654: Passes 100% CWL conformance tests using running cwl-runner in a crunch job!
Peter Amstutz [Fri, 25 Mar 2016 17:54:29 +0000 (13:54 -0400)]
8654: --version reports versions for arvados-cwl-runner, arvados-python-client,
and cwltool.
Tom Clegg [Thu, 24 Mar 2016 19:38:07 +0000 (15:38 -0400)]
8556: Update method signature for current SDK version.
refs #8556
radhika [Thu, 24 Mar 2016 18:05:25 +0000 (14:05 -0400)]
8703: add "components" hash to job.
Tom Clegg [Thu, 24 Mar 2016 17:58:21 +0000 (13:58 -0400)]
Merge branch '8767-items-available'
refs #8767
Tom Clegg [Tue, 22 Mar 2016 20:31:56 +0000 (16:31 -0400)]
8767: Make offset work properly in ApiClientAuthorizationsController#index.
Before this, #index was ignoring the "offset" request param and was
not providing an "items_available" attribute in the response. This
made Workbench's "get all pages" routine an infinite loop.
Peter Amstutz [Wed, 23 Mar 2016 20:32:15 +0000 (16:32 -0400)]
Don't retry slurm subprocess calls that raise OSError, no issue #
Peter Amstutz [Wed, 23 Mar 2016 19:42:21 +0000 (15:42 -0400)]
Fix merge conflict. refs #8766
Peter Amstutz [Wed, 23 Mar 2016 18:56:48 +0000 (14:56 -0400)]
8654: Add value for quiet to args.
Peter Amstutz [Wed, 23 Mar 2016 18:00:32 +0000 (14:00 -0400)]
Merge branch '8766-cwl-collection-project'
Peter Amstutz [Wed, 23 Mar 2016 18:00:21 +0000 (14:00 -0400)]
Merge branch 'master' into 8766-cwl-collection-project
Conflicts:
sdk/cwl/tests/test_job.py
Ward Vandewege [Wed, 23 Mar 2016 15:15:17 +0000 (11:15 -0400)]
Build script fix: make sure that run-build-docker-jobs-image.sh always
rebuilds the jobs image when the git commit passed in via --tags
changes.
No issue #
Peter Amstutz [Wed, 23 Mar 2016 14:52:38 +0000 (10:52 -0400)]
Merge branch '8766-cwl-collection-project' into 8654-arv-jobs-cwl-runner
Conflicts:
sdk/cwl/arvados_cwl/__init__.py
Peter Amstutz [Wed, 23 Mar 2016 14:41:30 +0000 (10:41 -0400)]
8766: Refactor logic to copy output collection and add tests.
Ward Vandewege [Wed, 23 Mar 2016 00:58:16 +0000 (20:58 -0400)]
Fix sdk/cwl tests after commit
9df4d7da24ef8be639af1ab806cf833ee544fb45
refs #8426
Peter Amstutz [Tue, 22 Mar 2016 20:41:19 +0000 (16:41 -0400)]
8766: Port logic from arv-run-pipeline-instance for copy collection to parent
project.
Peter Amstutz [Tue, 22 Mar 2016 20:23:48 +0000 (16:23 -0400)]
8654: Bump cwltool version
Peter Amstutz [Tue, 22 Mar 2016 20:22:53 +0000 (16:22 -0400)]
8654: Use iterator instead of readlines() when going through job log file.
Ward Vandewege [Tue, 22 Mar 2016 19:55:21 +0000 (15:55 -0400)]
Clean up build/run-build-docker-jobs-image.sh a bit.
No issue #
Peter Amstutz [Tue, 22 Mar 2016 16:24:02 +0000 (12:24 -0400)]
Merge branch 'master' into 8654-arv-jobs-cwl-runner
Tom Clegg [Tue, 22 Mar 2016 16:09:27 +0000 (12:09 -0400)]
Merge branch '8747-fix-crash-on-update'
refs #8747
Tom Clegg [Thu, 10 Mar 2016 20:25:41 +0000 (15:25 -0500)]
8345: Do not crash when update() called without an obj.
Peter Amstutz [Tue, 22 Mar 2016 14:04:36 +0000 (10:04 -0400)]
Crunchrunner fix connect os.Stderr to cmd.Stderr & update crunchrunner
collection ref in arvados-cwl-runner refs #8426
Peter Amstutz [Tue, 22 Mar 2016 03:02:19 +0000 (23:02 -0400)]
8654: Remove print statements.
Peter Amstutz [Tue, 22 Mar 2016 03:01:38 +0000 (23:01 -0400)]
8654: Handle error on capturing runner output
Peter Amstutz [Tue, 22 Mar 2016 02:01:35 +0000 (22:01 -0400)]
8654: Support --quiet
Peter Amstutz [Tue, 22 Mar 2016 01:43:25 +0000 (21:43 -0400)]
8654: Support waiting for submitted runner job to complete
Peter Amstutz [Tue, 22 Mar 2016 00:37:39 +0000 (20:37 -0400)]
8654: Upload Docker images
Peter Amstutz [Tue, 22 Mar 2016 00:19:55 +0000 (20:19 -0400)]
8654: Bump arvados-cwl-runner version dependency on arvados python client.
Peter Amstutz [Tue, 22 Mar 2016 00:16:10 +0000 (20:16 -0400)]
8654: When uploading, reuse existing collections with same owner/name/PDH
Peter Amstutz [Mon, 21 Mar 2016 21:09:49 +0000 (17:09 -0400)]
8654: Bump arvados-cwl-runner version dependency on arvados python client.
Peter Amstutz [Mon, 21 Mar 2016 21:05:08 +0000 (17:05 -0400)]
8654: Job has uuid and state fields
Peter Amstutz [Mon, 21 Mar 2016 21:02:51 +0000 (17:02 -0400)]
8654: Add args.debug = True to get backtraces on errors
Peter Amstutz [Mon, 21 Mar 2016 21:01:15 +0000 (17:01 -0400)]
8654: Set args.submit = False
Peter Amstutz [Mon, 21 Mar 2016 20:55:12 +0000 (16:55 -0400)]
8654: Add runner job to pipeline instance.
Peter Amstutz [Mon, 21 Mar 2016 20:46:26 +0000 (16:46 -0400)]
8654: Update cwl:tool entry
Peter Amstutz [Mon, 21 Mar 2016 20:44:31 +0000 (16:44 -0400)]
8654: Fix keeppath and add ensure_unique_name to upload.
Peter Amstutz [Mon, 21 Mar 2016 20:24:06 +0000 (16:24 -0400)]
8654: Scanning for and uploading dependencies for submit works. Add test for
--submit. Fix cwl-runner to handle CWL File objects in script_parameters.
Peter Amstutz [Mon, 21 Mar 2016 16:37:38 +0000 (12:37 -0400)]
Merge branch 'master' into 8654-arv-jobs-cwl-runner
Ward Vandewege [Sun, 20 Mar 2016 18:39:52 +0000 (14:39 -0400)]
More small build script improvements.
No issue #
Ward Vandewege [Sun, 20 Mar 2016 17:16:18 +0000 (13:16 -0400)]
Build script improvements:
* move some more functions into run-library.sh
* add a wrapper script for our single target package build/test/upload step
No issue #
Peter Amstutz [Sat, 19 Mar 2016 20:00:11 +0000 (16:00 -0400)]
Enable BaseComputeNodeDriver.list_nodes to pass through keyword arguments.
closes #8761
Brett Smith [Fri, 18 Mar 2016 18:50:59 +0000 (14:50 -0400)]
Merge branch '8002-no-pyvcf-wip'
Closes #8002, #8759.
Brett Smith [Fri, 18 Mar 2016 18:37:13 +0000 (14:37 -0400)]
8002: Stop backporting PyVCF.
Arvados proper doesn't use it. We only backported it as a convenience
previously.
Brett Smith [Fri, 18 Mar 2016 15:31:00 +0000 (11:31 -0400)]
Merge branch '7852-readline-cache-fix-wip'
Closes #7852, #8755.
Brett Smith [Thu, 17 Mar 2016 22:03:21 +0000 (18:03 -0400)]
7852: Bugfix _filepos tracking in PySDK readline method.
Make sure self._filepos is always in the right position to return
uncached data before another read method could be called, to avoid
inconsistent results when interleaving those calls with readline
calls.
radhika [Wed, 3 Feb 2016 17:19:54 +0000 (12:19 -0500)]
7852: Added one more test "test_readline_then_readall" which does a readline followed by a readall.
This test also fails exactly like the test "test_readline_then_readlines".
radhika [Mon, 25 Jan 2016 21:37:24 +0000 (16:37 -0500)]
7852: add a failing test that does: readline and then readlines. The expectation would be the second call,
readlines, would fetch all the remaining lines after the first line. However, the readlines call is only
fetching the data after the "first block" which was read during the first readline call. It appears that
self._readline_cache and self._filepos are playing a role here, which are set during the first readline.
Peter Amstutz [Fri, 18 Mar 2016 14:21:55 +0000 (10:21 -0400)]
Fix log scanning for "crunchrunner: $(task.outdir)" performed by arvados cwl
runner. no issue #
Ward Vandewege [Fri, 18 Mar 2016 02:19:24 +0000 (22:19 -0400)]
Make the build of the schema_salad packages more quiet.
refs #8671
Tom Clegg [Thu, 17 Mar 2016 22:15:10 +0000 (18:15 -0400)]
gofmt. refs #8754
projects / arvados.git / log