[ARVADOS] updated: cc3857d9fdcd7588af329a9b2452e0ef09eb68a4
Git user
git at public.curoverse.com
Mon Oct 31 13:47:48 EDT 2016
Summary of changes:
COPYING | 14 +-
.../app/assets/javascripts/work_unit_component.js | 18 +
.../app/controllers/work_units_controller.rb | 54 +++
apps/workbench/app/models/container.rb | 2 +-
apps/workbench/app/models/container_request.rb | 2 +-
apps/workbench/app/models/container_work_unit.rb | 6 +-
apps/workbench/app/models/job.rb | 2 +-
apps/workbench/app/models/job_task.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 2 +-
.../app/models/pipeline_instance_work_unit.rb | 4 +-
apps/workbench/app/models/proxy_work_unit.rb | 9 +-
apps/workbench/app/models/work_unit.rb | 4 +
.../pipeline_instances/_show_components.html.erb | 2 +-
.../views/work_units/_component_detail.html.erb | 28 +-
.../app/views/work_units/_show_child.html.erb | 29 +-
.../app/views/work_units/_show_component.html.erb | 47 +-
.../app/views/work_units/_show_status.html.erb | 2 +-
apps/workbench/config/routes.rb | 4 +-
.../test/controllers/work_units_controller_test.rb | 23 -
apps/workbench/test/integration/jobs_test.rb | 2 +-
apps/workbench/test/integration/work_units_test.rb | 25 +
build/run-build-docker-jobs-image.sh | 69 ++-
build/run-build-packages.sh | 2 +-
build/run-library.sh | 12 +-
.../_container_runtime_constraints.liquid | 1 +
docker/jobs/Dockerfile | 12 +-
sdk/cwl/arvados_cwl/__init__.py | 30 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 13 +-
sdk/cwl/arvados_cwl/crunch_script.py | 19 +-
sdk/cwl/gittaggers.py | 38 +-
sdk/cwl/setup.py | 2 +-
sdk/python/arvados/arvfile.py | 78 ++--
sdk/python/arvados/commands/put.py | 516 +++++++++++++++------
sdk/python/tests/test_arv_put.py | 178 +++----
.../arvados/v1/containers_controller.rb | 17 +
services/api/app/models/container.rb | 48 +-
services/api/config/routes.rb | 1 +
.../test/fixtures/api_client_authorizations.yml | 14 +
services/api/test/fixtures/collections.yml | 13 +
services/api/test/fixtures/containers.yml | 4 +-
.../arvados/v1/containers_controller_test.rb | 19 +
services/api/test/unit/container_request_test.rb | 2 +-
services/api/test/unit/container_test.rb | 92 +++-
services/crunch-run/crunchrun.go | 24 +-
services/crunch-run/crunchrun_test.go | 51 +-
services/fuse/arvados_fuse/__init__.py | 14 +
services/fuse/tests/integration_test.py | 1 -
services/fuse/tests/test_mount.py | 34 --
services/fuse/tests/test_token_expiry.py | 68 +++
tools/arvbox/bin/arvbox | 5 +-
50 files changed, 1154 insertions(+), 504 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/work_unit_component.js
mode change 120000 => 100644 sdk/cwl/gittaggers.py
create mode 100644 services/fuse/tests/test_token_expiry.py
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commit cc3857d9fdcd7588af329a9b2452e0ef09eb68a4
Author: radhika <radhika at curoverse.com>
Date: Mon Oct 31 13:47:20 2016 -0400
10231: add keep_cache_ram to doc
diff --git a/doc/_includes/_container_runtime_constraints.liquid b/doc/_includes/_container_runtime_constraints.liquid
index 06bfb4f..849db42 100644
--- a/doc/_includes/_container_runtime_constraints.liquid
+++ b/doc/_includes/_container_runtime_constraints.liquid
@@ -6,5 +6,6 @@ table(table table-bordered table-condensed).
|_. Key|_. Type|_. Description|_. Notes|
|ram|integer|Number of ram bytes to be used to run this process.|Optional. However, a ContainerRequest that is in "Committed" state must provide this.|
|vcpus|integer|Number of cores to be used to run this process.|Optional. However, a ContainerRequest that is in "Committed" state must provide this.|
+|keep_cache_ram|integer|Number of keep cache bytes to be used to run this process.|Optional.|
|API|boolean|When set, ARVADOS_API_HOST and ARVADOS_API_TOKEN will be set, and container will have networking enabled to access the Arvados API server.|Optional.|
|partition|array of strings|Specify the names of one or more compute partitions that may run this container. If not provided, the system chooses where to run the container.|Optional.|
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index c2029b9..ffa9c3e 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -97,7 +97,8 @@ class ArvadosContainer(object):
runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
if runtime_req:
- runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"]
+ if "keep_cache" in runtime_req:
+ runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"]
partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
if partition_req:
diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index 8e5cdb1..ade40c6 100644
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -250,6 +250,11 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
pdhOnly := true
tmpcount := 0
arvMountCmd := []string{"--foreground", "--allow-other", "--read-write"}
+
+ if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
+ arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
+ }
+
collectionPaths := []string{}
runner.Binds = nil
@@ -357,10 +362,6 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
}
arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
- if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
- arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
- }
-
token, err := runner.ContainerToken()
if err != nil {
return fmt.Errorf("could not get container token: %s", err)
diff --git a/services/crunch-run/crunchrun_test.go b/services/crunch-run/crunchrun_test.go
index 2fbbb4d..2c71459 100644
--- a/services/crunch-run/crunchrun_test.go
+++ b/services/crunch-run/crunchrun_test.go
@@ -856,7 +856,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1", "--file-cache", "512"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
sort.StringSlice(cr.Binds).Sort()
c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
realTemp + "/keep1/tmp0:/keepout"})
commit 120a2268606d73317ab2353d79c3046017300f81
Merge: 61b286d 6264565
Author: radhika <radhika at curoverse.com>
Date: Mon Oct 31 12:04:51 2016 -0400
Merge branch 'master' into 10231-keep-cache-runtime-constraints
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