[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 +-
.../ubuntu1604/Dockerfile | 2 +-
.../package-test-dockerfiles/ubuntu1404/Dockerfile | 4 +-
build/package-testing/test-packages-ubuntu1204.sh | 1 -
build/run-build-packages-one-target.sh | 9 +-
build/run-build-packages.sh | 52 -
build/run-build-test-packages-one-target.sh | 1 +
build/run-library.sh | 48 +-
build/run-tests.sh | 104 +-
doc/Rakefile | 56 +-
doc/_config.yml | 64 +-
doc/_includes/_events_py.liquid | 18 -
doc/_includes/_example_sdk_go_imports.liquid | 10 -
doc/_includes/_navbar_top.liquid | 2 +
doc/_layouts/default.html.liquid | 1 +
doc/admin/change-account-owner.html.textile.liquid | 41 -
doc/admin/index.html.textile.liquid | 13 +
doc/admin/merge-remote-account.html.textile.liquid | 4 +-
doc/admin/upgrading.html.textile.liquid | 250 +
doc/api/execution.html.textile.liquid | 6 +-
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 +-
...nstall-manual-prerequisites.html.textile.liquid | 4 +
.../install-nodemanager.html.textile.liquid | 8 +-
doc/install/install-postgresql.html.textile.liquid | 12 +-
doc/install/install-sso.html.textile.liquid | 6 +-
doc/install/migrate-docker19.html.textile.liquid | 4 +-
doc/sdk/R/index.html.textile.liquid | 15 -
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 +
sdk/R/install_deps.R | 11 +-
sdk/R/man/Arvados.Rd | 200 +-
sdk/R/man/api_client_authorizations.create.Rd | 20 +
...api_client_authorizations.create_system_auth.Rd | 20 +
sdk/R/man/api_client_authorizations.current.Rd | 14 +
sdk/R/man/api_client_authorizations.delete.Rd | 17 +
sdk/R/man/api_client_authorizations.get.Rd | 17 +
sdk/R/man/api_client_authorizations.list.Rd | 34 +
sdk/R/man/api_client_authorizations.update.Rd | 20 +
sdk/R/man/api_clients.create.Rd | 20 +
sdk/R/man/api_clients.delete.Rd | 17 +
sdk/R/man/api_clients.get.Rd | 17 +
sdk/R/man/api_clients.list.Rd | 34 +
sdk/R/man/api_clients.update.Rd | 20 +
sdk/R/man/authorized_keys.create.Rd | 20 +
sdk/R/man/authorized_keys.delete.Rd | 17 +
sdk/R/man/authorized_keys.get.Rd | 17 +
sdk/R/man/authorized_keys.list.Rd | 34 +
sdk/R/man/authorized_keys.update.Rd | 20 +
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 +
sdk/R/man/container_requests.delete.Rd | 17 +
sdk/R/man/container_requests.get.Rd | 17 +
sdk/R/man/container_requests.list.Rd | 34 +
sdk/R/man/container_requests.update.Rd | 20 +
sdk/R/man/containers.auth.Rd | 17 +
sdk/R/man/containers.create.Rd | 20 +
sdk/R/man/containers.current.Rd | 14 +
sdk/R/man/containers.delete.Rd | 17 +
sdk/R/man/containers.get.Rd | 17 +
sdk/R/man/containers.list.Rd | 34 +
sdk/R/man/containers.lock.Rd | 17 +
sdk/R/man/containers.secret_mounts.Rd | 17 +
sdk/R/man/containers.unlock.Rd | 17 +
sdk/R/man/containers.update.Rd | 20 +
sdk/R/man/groups.contents.Rd | 38 +
sdk/R/man/groups.create.Rd | 19 +
sdk/R/man/groups.delete.Rd | 17 +
sdk/R/man/groups.get.Rd | 17 +
sdk/R/man/groups.list.Rd | 36 +
sdk/R/man/groups.trash.Rd | 17 +
sdk/R/man/groups.untrash.Rd | 17 +
sdk/R/man/groups.update.Rd | 19 +
sdk/R/man/humans.create.Rd | 19 +
sdk/R/man/humans.delete.Rd | 17 +
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sdk/R/man/job_tasks.create.Rd | 19 +
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sdk/R/man/jobs.lock.Rd | 17 +
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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 +
sdk/R/man/keep_services.delete.Rd | 17 +
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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 +
sdk/R/man/logs.delete.Rd | 17 +
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 +
sdk/R/man/pipeline_instances.update.Rd | 20 +
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 +
sdk/R/man/projects.delete.Rd | 17 +
sdk/R/man/projects.get.Rd | 17 +
sdk/R/man/projects.list.Rd | 38 +
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sdk/R/man/repositories.create.Rd | 20 +
sdk/R/man/repositories.delete.Rd | 17 +
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sdk/R/man/repositories.get_all_permissions.Rd | 14 +
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sdk/R/man/traits.create.Rd | 19 +
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sdk/R/man/user_agreements.create.Rd | 20 +
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sdk/R/man/users.activate.Rd | 17 +
sdk/R/man/users.create.Rd | 19 +
sdk/R/man/users.current.Rd | 14 +
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sdk/R/man/users.get.Rd | 17 +
sdk/R/man/users.list.Rd | 34 +
sdk/R/man/users.setup.Rd | 26 +
sdk/R/man/users.system.Rd | 14 +
sdk/R/man/users.unsetup.Rd | 17 +
sdk/R/man/users.update.Rd | 19 +
sdk/R/man/users.update_uuid.Rd | 19 +
sdk/R/man/virtual_machines.create.Rd | 20 +
sdk/R/man/virtual_machines.delete.Rd | 17 +
sdk/R/man/virtual_machines.get.Rd | 17 +
sdk/R/man/virtual_machines.get_all_logins.Rd | 14 +
sdk/R/man/virtual_machines.list.Rd | 34 +
sdk/R/man/virtual_machines.logins.Rd | 17 +
sdk/R/man/virtual_machines.update.Rd | 20 +
sdk/R/man/workflows.create.Rd | 20 +
sdk/R/man/workflows.delete.Rd | 17 +
sdk/R/man/workflows.get.Rd | 17 +
sdk/R/man/workflows.list.Rd | 34 +
sdk/R/man/workflows.update.Rd | 20 +
sdk/R/tests/testthat/test-Arvados.R | 306 -
sdk/R/tests/testthat/test-ArvadosFile.R | 2 +-
sdk/R/tests/testthat/test-HttpRequest.R | 19 +-
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 +-
sdk/go/keepclient/keepclient_test.go | 44 +-
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 +
services/fuse/arvados_fuse/_version.py | 7 -
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 +-
services/keep-balance/balance_run_test.go | 12 +-
services/keep-balance/balance_test.go | 202 +-
services/keep-balance/block_state.go | 38 +-
services/keep-balance/change_set.go | 20 +-
services/keep-balance/change_set_test.go | 11 +-
services/keep-web/cadaver_test.go | 145 +-
services/keep-web/doc.go | 25 +-
services/keep-web/handler.go | 177 +-
services/keep-web/handler_test.go | 145 +-
services/keep-web/main.go | 6 +-
services/keep-web/server.go | 2 +-
services/keep-web/server_test.go | 2 -
services/keep-web/webdav.go | 23 +-
services/keepproxy/keepproxy.go | 13 +-
services/keepproxy/keepproxy_test.go | 13 +-
services/keepproxy/proxy_client.go | 6 +-
services/keepstore/azure_blob_volume.go | 77 +-
services/keepstore/config.go | 3 +
services/keepstore/handlers.go | 2 +-
services/keepstore/keepstore.go | 14 +-
services/keepstore/s3_volume.go | 80 +-
services/keepstore/s3_volume_test.go | 6 +-
services/keepstore/usage.go | 15 +
services/keepstore/volume_generic_test.go | 2 +-
services/keepstore/volume_unix.go | 56 +-
services/login-sync/arvados-login-sync.gemspec | 4 +-
services/login-sync/bin/arvados-login-sync | 25 +-
services/login-sync/test/test_add_user.rb | 7 +-
services/nodemanager/MANIFEST.in | 1 +
services/nodemanager/arvados_version.py | 40 +
services/nodemanager/arvnodeman/_version.py | 7 -
services/nodemanager/arvnodeman/baseactor.py | 3 +
.../nodemanager/arvnodeman/computenode/__init__.py | 8 +-
.../arvnodeman/computenode/dispatch/__init__.py | 10 +
.../arvnodeman/computenode/driver/__init__.py | 11 +-
services/nodemanager/arvnodeman/daemon.py | 13 +-
services/nodemanager/arvnodeman/jobqueue.py | 13 +-
services/nodemanager/arvnodeman/status.py | 39 +-
services/nodemanager/setup.py | 24 +-
services/nodemanager/tests/integration_test.py | 98 +-
.../nodemanager/tests/test_computenode_dispatch.py | 26 +-
.../tests/test_computenode_dispatch_slurm.py | 12 +
.../nodemanager/tests/test_computenode_driver.py | 49 +
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 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 2 +-
.../lib/arvbox/docker/service/sdk/run-service | 2 +-
tools/crunchstat-summary/MANIFEST.in | 1 +
tools/crunchstat-summary/arvados_version.py | 40 +
.../crunchstat_summary/reader.py | 5 +-
tools/crunchstat-summary/setup.py | 23 +-
386 files changed, 17120 insertions(+), 4311 deletions(-)
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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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