[ARVADOS] updated: 1.1.4-210-gcfb504f

Git user git at public.curoverse.com
Mon May 7 10:13:52 EDT 2018


Summary of changes:
 .gitignore                                         |    1 +
 .../app/assets/javascripts/models/session_db.js    |   23 +-
 .../app/controllers/work_units_controller.rb       |    7 +-
 .../workbench/test/integration/collections_test.rb |    2 +-
 build/build-dev-docker-jobs-image.sh               |    6 +-
 build/build.list                                   |   72 +-
 build/libcloud-pin.sh                              |    7 +
 build/package-build-dockerfiles/Makefile           |    2 +-
 build/package-build-dockerfiles/centos7/Dockerfile |    2 +-
 build/package-build-dockerfiles/debian8/Dockerfile |    2 +-
 build/package-build-dockerfiles/debian9/Dockerfile |    2 +-
 .../ubuntu1404/Dockerfile                          |    4 +-
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 doc/Rakefile                                       |   56 +-
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 doc/admin/upgrading.html.textile.liquid            |  250 +
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 doc/api/permission-model.html.textile.liquid       |    4 +-
 doc/api/storage.html.textile.liquid                |    8 +-
 doc/architecture/Arvados_arch.odg                  |  Bin 0 -> 14997 bytes
 doc/architecture/index.html.textile.liquid         |   59 +
 doc/css/images.css                                 |    3 +
 doc/images/Arvados_arch.svg                        |  514 ++
 doc/index.html.liquid                              |   31 +-
 doc/install/cheat_sheet.html.textile.liquid        |    4 +-
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 doc/sdk/go/index.html.textile.liquid               |    7 +-
 .../crunch-utility-libraries.html.textile.liquid   |    4 +-
 doc/sdk/python/events.html.textile.liquid          |   18 +-
 doc/user/index.html.textile.liquid                 |    3 -
 .../topics/arvados-sync-groups.html.textile.liquid |    6 +-
 .../tutorial-trait-search.html.textile.liquid      |   12 +-
 sdk/R/NAMESPACE                                    |    3 +-
 sdk/R/R/Arvados.R                                  | 5866 +++++++++++++++++++-
 sdk/R/R/Collection.R                               |   63 +-
 sdk/R/R/HttpRequest.R                              |   75 +-
 sdk/R/R/RESTService.R                              |  137 +-
 sdk/R/R/Subcollection.R                            |    2 +-
 sdk/R/R/autoGenAPI.R                               |  571 ++
 sdk/R/R/util.R                                     |   37 +-
 sdk/R/README.Rmd                                   |  340 +-
 sdk/R/createDoc.R                                  |   20 +
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 sdk/R/man/collections.create.Rd                    |   20 +
 sdk/R/man/collections.delete.Rd                    |   17 +
 sdk/R/man/collections.get.Rd                       |   17 +
 sdk/R/man/collections.list.Rd                      |   36 +
 sdk/R/man/collections.provenance.Rd                |   17 +
 sdk/R/man/collections.trash.Rd                     |   17 +
 sdk/R/man/collections.untrash.Rd                   |   17 +
 sdk/R/man/collections.update.Rd                    |   20 +
 sdk/R/man/collections.used_by.Rd                   |   17 +
 sdk/R/man/container_requests.create.Rd             |   20 +
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 sdk/R/man/container_requests.update.Rd             |   20 +
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 sdk/R/man/groups.contents.Rd                       |   38 +
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 sdk/R/man/groups.update.Rd                         |   19 +
 sdk/R/man/humans.create.Rd                         |   19 +
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 sdk/R/man/job_tasks.create.Rd                      |   19 +
 sdk/R/man/job_tasks.delete.Rd                      |   17 +
 sdk/R/man/job_tasks.get.Rd                         |   17 +
 sdk/R/man/job_tasks.list.Rd                        |   34 +
 sdk/R/man/job_tasks.update.Rd                      |   19 +
 sdk/R/man/jobs.cancel.Rd                           |   17 +
 sdk/R/man/jobs.create.Rd                           |   29 +
 sdk/R/man/jobs.delete.Rd                           |   17 +
 sdk/R/man/jobs.get.Rd                              |   17 +
 sdk/R/man/jobs.list.Rd                             |   33 +
 sdk/R/man/jobs.lock.Rd                             |   17 +
 sdk/R/man/jobs.queue.Rd                            |   34 +
 sdk/R/man/jobs.queue_size.Rd                       |   14 +
 sdk/R/man/jobs.update.Rd                           |   19 +
 sdk/R/man/keep_disks.create.Rd                     |   20 +
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 sdk/R/man/keep_disks.get.Rd                        |   17 +
 sdk/R/man/keep_disks.list.Rd                       |   34 +
 sdk/R/man/keep_disks.ping.Rd                       |   31 +
 sdk/R/man/keep_disks.update.Rd                     |   20 +
 sdk/R/man/keep_services.accessible.Rd              |   14 +
 sdk/R/man/keep_services.create.Rd                  |   20 +
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 sdk/R/man/keep_services.list.Rd                    |   34 +
 sdk/R/man/keep_services.update.Rd                  |   20 +
 sdk/R/man/links.create.Rd                          |   19 +
 sdk/R/man/links.delete.Rd                          |   17 +
 sdk/R/man/links.get.Rd                             |   17 +
 sdk/R/man/links.get_permissions.Rd                 |   17 +
 sdk/R/man/links.list.Rd                            |   34 +
 sdk/R/man/links.update.Rd                          |   19 +
 sdk/R/man/listAll.Rd                               |   22 +
 sdk/R/man/logs.create.Rd                           |   19 +
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 sdk/R/man/logs.get.Rd                              |   17 +
 sdk/R/man/logs.list.Rd                             |   33 +
 sdk/R/man/logs.update.Rd                           |   19 +
 sdk/R/man/nodes.create.Rd                          |   22 +
 sdk/R/man/nodes.delete.Rd                          |   17 +
 sdk/R/man/nodes.get.Rd                             |   17 +
 sdk/R/man/nodes.list.Rd                            |   34 +
 sdk/R/man/nodes.ping.Rd                            |   19 +
 sdk/R/man/nodes.update.Rd                          |   21 +
 sdk/R/man/pipeline_instances.cancel.Rd             |   17 +
 sdk/R/man/pipeline_instances.create.Rd             |   20 +
 sdk/R/man/pipeline_instances.delete.Rd             |   17 +
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 sdk/R/man/pipeline_instances.list.Rd               |   34 +
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 sdk/R/man/pipeline_templates.create.Rd             |   20 +
 sdk/R/man/pipeline_templates.delete.Rd             |   17 +
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 sdk/R/man/pipeline_templates.list.Rd               |   34 +
 sdk/R/man/pipeline_templates.update.Rd             |   20 +
 sdk/R/man/print.Arvados.Rd                         |   16 -
 sdk/R/man/projects.create.Rd                       |   19 +
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 sdk/R/man/traits.create.Rd                         |   19 +
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 sdk/R/man/traits.get.Rd                            |   17 +
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 sdk/R/man/user_agreements.create.Rd                |   20 +
 sdk/R/man/user_agreements.delete.Rd                |   17 +
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 sdk/R/tests/testthat/test-Arvados.R                |  306 -
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 sdk/R/tests/testthat/test-RESTService.R            |  258 -
 sdk/R/tests/testthat/test-Subcollection.R          |    2 +-
 sdk/R/tests/testthat/test-util.R                   |   24 +
 sdk/cli/arvados-cli.gemspec                        |    4 +-
 sdk/cwl/MANIFEST.in                                |    1 +
 sdk/cwl/arvados_cwl/__init__.py                    |  187 +-
 sdk/cwl/arvados_cwl/_version.py                    |    7 -
 sdk/cwl/arvados_cwl/arvcontainer.py                |   40 +-
 sdk/cwl/arvados_cwl/arvdocker.py                   |    3 +-
 sdk/cwl/arvados_cwl/arvjob.py                      |   54 +-
 sdk/cwl/arvados_cwl/arvworkflow.py                 |   76 +-
 sdk/cwl/arvados_cwl/crunch_script.py               |    5 +-
 sdk/cwl/arvados_cwl/runner.py                      |    3 +-
 sdk/cwl/arvados_cwl/task_queue.py                  |   60 +
 sdk/cwl/arvados_version.py                         |   40 +
 sdk/cwl/gittaggers.py                              |    6 +-
 sdk/cwl/setup.py                                   |   21 +-
 sdk/cwl/tests/arvados-tests.yml                    |   26 +
 sdk/cwl/tests/test_submit.py                       |  119 +-
 sdk/cwl/tests/test_tq.py                           |   50 +
 sdk/cwl/tests/wf/check_mem.py                      |   12 +
 sdk/cwl/tests/wf/runin-reqs-wf.cwl                 |   58 +
 sdk/cwl/tests/wf/runin-reqs-wf2.cwl                |   59 +
 sdk/cwl/tests/wf/runin-reqs-wf3.cwl                |   59 +
 sdk/cwl/tests/wf/runin-reqs-wf4.cwl                |   59 +
 sdk/go/arvados/client.go                           |   39 +-
 sdk/go/arvados/collection.go                       |   30 +-
 sdk/go/arvados/fs_backend.go                       |   29 +
 sdk/go/arvados/fs_base.go                          |  595 ++
 .../arvados/{collection_fs.go => fs_collection.go} |  790 +--
 ...collection_fs_test.go => fs_collection_test.go} |   34 +-
 sdk/go/arvados/fs_deferred.go                      |  103 +
 sdk/go/arvados/fs_filehandle.go                    |  108 +
 sdk/go/arvados/fs_getternode.go                    |   66 +
 sdk/go/arvados/fs_lookup.go                        |   73 +
 sdk/go/arvados/fs_project.go                       |  117 +
 sdk/go/arvados/fs_project_test.go                  |  201 +
 sdk/go/arvados/fs_site.go                          |  200 +
 sdk/go/arvados/fs_site_test.go                     |   98 +
 sdk/go/arvados/fs_users.go                         |   48 +
 sdk/go/arvados/group.go                            |   11 +-
 sdk/go/arvadosclient/arvadosclient.go              |    6 +
 sdk/go/arvadostest/fixtures.go                     |    4 +
 sdk/go/arvadostest/run_servers.go                  |   17 +-
 sdk/go/httpserver/id_generator.go                  |    3 +
 sdk/go/httpserver/logger.go                        |    2 +
 sdk/go/httpserver/responsewriter.go                |    3 +
 sdk/go/keepclient/collectionreader_test.go         |    1 +
 sdk/go/keepclient/discover_test.go                 |    5 +-
 sdk/go/keepclient/keepclient.go                    |   68 +-
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 sdk/go/keepclient/support.go                       |   28 +-
 sdk/pam/MANIFEST.in                                |    1 +
 sdk/pam/arvados_version.py                         |   40 +
 sdk/pam/setup.py                                   |   22 +-
 sdk/python/MANIFEST.in                             |    1 +
 sdk/python/README.rst                              |    2 +-
 sdk/python/arvados/_version.py                     |    7 -
 sdk/python/arvados/commands/_util.py               |   19 +
 sdk/python/arvados/commands/keepdocker.py          |  239 +-
 sdk/python/arvados/commands/put.py                 |   18 +-
 sdk/python/arvados/safeapi.py                      |    6 +-
 sdk/python/arvados_version.py                      |   40 +
 sdk/python/gittaggers.py                           |    7 +-
 sdk/python/setup.py                                |   17 +-
 sdk/ruby/arvados.gemspec                           |    4 +-
 .../arvados/v1/collections_controller.rb           |   14 +-
 .../app/controllers/arvados/v1/users_controller.rb |    2 +-
 services/api/app/models/arvados_model.rb           |    6 +-
 services/api/app/models/collection.rb              |    4 +-
 services/api/app/models/container.rb               |   34 +-
 services/api/app/models/container_request.rb       |    5 +-
 services/api/lib/arvados_model_updates.rb          |   21 +
 services/api/lib/current_api_client.rb             |    6 -
 services/api/lib/sweep_trashed_collections.rb      |   41 -
 services/api/lib/sweep_trashed_objects.rb          |   74 +
 services/api/script/get_anonymous_user_token.rb    |   23 +-
 services/api/test/fixtures/collections.yml         |    2 +-
 services/api/test/fixtures/groups.yml              |   12 +-
 services/api/test/fixtures/jobs.yml                |   11 +
 .../functional/arvados/v1/users_controller_test.rb |    2 +-
 services/api/test/unit/collection_test.rb          |   14 +-
 services/api/test/unit/container_request_test.rb   |    6 +
 services/api/test/unit/group_test.rb               |   55 +-
 .../crunch-dispatch-slurm.service                  |    1 +
 .../crunch-dispatch-slurm_test.go                  |    1 +
 services/crunch-dispatch-slurm/squeue.go           |    3 +
 services/crunch-run/copier.go                      |  357 ++
 services/crunch-run/copier_test.go                 |  222 +
 services/crunch-run/crunchrun.go                   |  470 +-
 services/crunch-run/crunchrun_test.go              |  273 +-
 services/crunch-run/logging_test.go                |   45 +-
 services/crunch-run/upload.go                      |  342 --
 services/crunch-run/upload_test.go                 |  189 -
 services/dockercleaner/MANIFEST.in                 |    1 +
 services/dockercleaner/arvados_version.py          |   40 +
 services/dockercleaner/setup.py                    |   25 +-
 services/fuse/MANIFEST.in                          |    1 +
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 services/fuse/arvados_fuse/fusedir.py              |   25 +-
 services/fuse/arvados_version.py                   |   40 +
 services/fuse/setup.py                             |   20 +-
 services/fuse/tests/test_mount.py                  |   17 +-
 services/keep-balance/balance.go                   |  422 +-
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 services/keep-web/cadaver_test.go                  |  145 +-
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 services/keep-web/main.go                          |    6 +-
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 services/keep-web/server_test.go                   |    2 -
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 services/keepstore/azure_blob_volume.go            |   77 +-
 services/keepstore/config.go                       |    3 +
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 services/keepstore/s3_volume.go                    |   80 +-
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 services/login-sync/arvados-login-sync.gemspec     |    4 +-
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 services/login-sync/test/test_add_user.rb          |    7 +-
 services/nodemanager/MANIFEST.in                   |    1 +
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 services/nodemanager/arvnodeman/baseactor.py       |    3 +
 .../nodemanager/arvnodeman/computenode/__init__.py |    8 +-
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 services/nodemanager/arvnodeman/daemon.py          |   13 +-
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 services/nodemanager/arvnodeman/status.py          |   39 +-
 services/nodemanager/setup.py                      |   24 +-
 services/nodemanager/tests/integration_test.py     |   98 +-
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 .../tests/test_computenode_dispatch_slurm.py       |   12 +
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 services/nodemanager/tests/test_daemon.py          |   45 +-
 services/nodemanager/tests/test_failure.py         |    3 +
 services/nodemanager/tests/test_jobqueue.py        |   12 +-
 services/nodemanager/tests/test_status.py          |   40 +
 tools/arvbox/bin/arvbox                            |    2 +-
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commit cfb504fe34ed3006f36f00d9ced641be200c97dd
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date:   Tue Mar 27 13:01:38 2018 -0400

    13278: Release jobs that are pending because "launch failed".
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>

diff --git a/services/crunch-dispatch-slurm/squeue.go b/services/crunch-dispatch-slurm/squeue.go
index 9514da8..742943f 100644
--- a/services/crunch-dispatch-slurm/squeue.go
+++ b/services/crunch-dispatch-slurm/squeue.go
@@ -157,7 +157,7 @@ func (sqc *SqueueChecker) check() {
 		replacing.nice = n
 		newq[uuid] = replacing
 
-		if state == "PENDING" && reason == "BadConstraints" && p == 0 && replacing.wantPriority > 0 {
+		if state == "PENDING" && ((reason == "BadConstraints" && p == 0) || reason == "launch failed requeued held") && replacing.wantPriority > 0 {
 			// When using SLURM 14.x or 15.x, our queued
 			// jobs land in this state when "scontrol
 			// reconfigure" invalidates their feature
@@ -171,6 +171,10 @@ func (sqc *SqueueChecker) check() {
 			// reappeared, so rather than second-guessing
 			// whether SLURM is ready, we just keep trying
 			// this until it works.
+			//
+			// "launch failed requeued held" seems to be
+			// another manifestation of this problem,
+			// resolved the same way.
 			log.Printf("releasing held job %q", uuid)
 			sqc.Slurm.Release(uuid)
 		} else if p < 1<<20 && replacing.wantPriority > 0 {

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