[ARVADOS] updated: 742bbf8e00b104786a151d18bb300f955e2933eb
git at public.curoverse.com
git at public.curoverse.com
Fri May 2 17:57:55 EDT 2014
Summary of changes:
.gitignore | 12 +-
apps/workbench/.gitignore | 19 +-
apps/workbench/Gemfile | 3 +-
apps/workbench/Gemfile.lock | 2 +
apps/workbench/README.textile | 6 +-
.../app/assets/javascripts/application.js | 11 +-
.../app/assets/javascripts/collections.js | 59 ++
.../app/assets/javascripts/collections.js.coffee | 3 -
apps/workbench/app/assets/javascripts/selection.js | 10 +-
.../app/assets/stylesheets/collections.css.scss | 21 +-
.../app/controllers/actions_controller.rb | 2 -
.../app/controllers/application_controller.rb | 13 +-
.../app/controllers/collections_controller.rb | 49 ++-
.../controllers/pipeline_instances_controller.rb | 41 --
apps/workbench/app/controllers/users_controller.rb | 161 +++++-
.../app/controllers/websocket_controller.rb | 10 +
apps/workbench/app/helpers/application_helper.rb | 171 ++++---
apps/workbench/app/helpers/collections_helper.rb | 33 ++
.../app/helpers/pipeline_instances_helper.rb | 18 +-
.../app/helpers/pipeline_templates_helper.rb | 24 -
apps/workbench/app/models/arvados_api_client.rb | 4 +-
apps/workbench/app/models/arvados_base.rb | 14 +-
apps/workbench/app/models/group.rb | 4 +
apps/workbench/app/models/link.rb | 2 +-
apps/workbench/app/models/user.rb | 9 +
.../views/application/_arvados_attr_value.html.erb | 2 +-
.../views/application/_selection_checkbox.html.erb | 19 +-
.../workbench/app/views/application/index.html.erb | 19 +-
.../app/views/collections/_index_tbody.html.erb | 18 +-
.../app/views/collections/_show_files.html.erb | 42 ++-
.../app/views/collections/_show_recent.html.erb | 8 +-
.../app/views/collections/_toggle_persist.html.erb | 3 +
.../app/views/layouts/application.html.erb | 4 +-
.../pipeline_instances/_show_components.html.erb | 14 +-
.../_show_components_editable.html.erb | 48 ++
.../app/views/pipeline_instances/show.js.erb | 15 +-
.../pipeline_templates/_show_components.html.erb | 2 +-
.../_show_components_template.html.erb | 54 --
.../app/views/users/_setup_popup.html.erb | 69 +++
.../app/views/users/_show_activity.html.erb | 2 +-
.../workbench/app/views/users/_show_admin.html.erb | 10 +
apps/workbench/app/views/users/_tables.html.erb | 120 +++--
apps/workbench/app/views/users/activity.html.erb | 16 +-
apps/workbench/app/views/users/setup.js.erb | 2 +
apps/workbench/app/views/users/setup_popup.js.erb | 44 ++
apps/workbench/app/views/users/storage.html.erb | 66 +++
apps/workbench/app/views/websocket/index.html.erb | 34 ++
apps/workbench/config/application.default.yml | 2 +
apps/workbench/config/environments/test.rb | 1 +
apps/workbench/config/routes.rb | 9 +-
.../pipeline_instances_controller_test.rb | 70 +++
.../test/functional/users_controller_test.rb | 21 +
.../workbench/test/integration/collections_test.rb | 42 ++
apps/workbench/test/integration/logins_test.rb | 8 +
apps/workbench/test/integration/users_test.rb | 219 ++++++++
apps/workbench/test/integration_helper.rb | 57 +--
apps/workbench/test/test_helper.rb | 94 +++-
apps/workbench/test/unit/user_test.rb | 15 +-
doc/_config.yml | 5 +-
doc/_includes/_tutorial_hash_script_py.liquid | 8 +-
doc/admin/cheat_sheet.html.textile.liquid | 4 -
doc/api/methods.html.textile.liquid | 17 +-
.../api_client_authorizations.html.textile.liquid | 37 +--
doc/api/methods/api_clients.html.textile.liquid | 38 +--
.../methods/authorized_keys.html.textile.liquid | 37 +--
doc/api/methods/collections.html.textile.liquid | 38 +--
doc/api/methods/groups.html.textile.liquid | 34 +-
doc/api/methods/humans.html.textile.liquid | 37 +--
doc/api/methods/job_tasks.html.textile.liquid | 37 +--
doc/api/methods/jobs.html.textile.liquid | 143 ++++--
doc/api/methods/keep_disks.html.textile.liquid | 38 +--
doc/api/methods/links.html.textile.liquid | 39 +--
doc/api/methods/logs.html.textile.liquid | 37 +--
doc/api/methods/nodes.html.textile.liquid | 37 +--
.../methods/pipeline_instances.html.textile.liquid | 37 +--
.../methods/pipeline_templates.html.textile.liquid | 37 +--
doc/api/methods/repositories.html.textile.liquid | 37 +--
doc/api/methods/specimens.html.textile.liquid | 37 +--
doc/api/methods/traits.html.textile.liquid | 37 +--
doc/api/methods/users.html.textile.liquid | 33 +-
.../methods/virtual_machines.html.textile.liquid | 63 +--
doc/api/resources.html.textile.liquid | 4 +-
doc/api/schema/ApiClient.html.textile.liquid | 22 +-
.../ApiClientAuthorization.html.textile.liquid | 23 +-
doc/api/schema/AuthorizedKey.html.textile.liquid | 21 +-
doc/api/schema/Collection.html.textile.liquid | 11 +-
doc/api/schema/Commit.html.textile.liquid | 38 --
doc/api/schema/CommitAncestor.html.textile.liquid | 39 --
doc/api/schema/Group.html.textile.liquid | 23 +-
doc/api/schema/Human.html.textile.liquid | 23 +-
doc/api/schema/Job.html.textile.liquid | 60 +--
doc/api/schema/JobTask.html.textile.liquid | 10 +-
doc/api/schema/KeepDisk.html.textile.liquid | 21 +-
doc/api/schema/Link.html.textile.liquid | 18 +-
doc/api/schema/Log.html.textile.liquid | 14 +-
doc/api/schema/Node.html.textile.liquid | 23 +-
.../schema/PipelineInstance.html.textile.liquid | 23 +-
.../schema/PipelineTemplate.html.textile.liquid | 134 +++++-
doc/api/schema/Repository.html.textile.liquid | 21 +-
doc/api/schema/Specimen.html.textile.liquid | 23 +-
doc/api/schema/Trait.html.textile.liquid | 23 +-
doc/api/schema/User.html.textile.liquid | 23 +-
doc/api/schema/VirtualMachine.html.textile.liquid | 21 +-
.../create-standard-objects.html.textile.liquid | 12 +-
doc/install/install-api-server.html.textile.liquid | 87 +++-
.../install-crunch-dispatch.html.textile.liquid | 2 +-
.../install-workbench-app.html.textile.liquid | 42 ++-
.../getting_started/ssh-access.html.textile.liquid | 42 +-
doc/user/index.html.textile.liquid | 10 +-
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
.../job-and-pipeline-reference.html.textile.liquid | 223 --------
doc/user/topics/keep.html.textile.liquid | 4 +-
...nning-pipeline-command-line.html.textile.liquid | 4 +-
.../topics/tutorial-job-debug.html.textile.liquid | 6 +-
doc/user/topics/tutorial-job1.html.textile.liquid | 10 +-
.../topics/tutorial-parallel.html.textile.liquid | 8 +-
.../tutorial-trait-search.html.textile.liquid | 46 +-
.../tutorials/intro-crunch.html.textile.liquid | 2 +-
.../running-external-program.html.textile.liquid | 6 +-
.../tutorial-firstscript.html.textile.liquid | 26 +-
.../tutorials/tutorial-keep.html.textile.liquid | 4 +-
.../tutorial-new-pipeline.html.textile.liquid | 8 +-
sdk/cli/bin/arv-run-pipeline-instance | 38 +-
sdk/cli/bin/crunch-job | 98 +++--
sdk/python/bin/arv-mount | 11 +-
sdk/ruby/lib/arvados.rb | 62 ++-
services/api/.gitignore | 20 +-
services/api/Gemfile | 6 +-
services/api/Gemfile.lock | 123 +++--
.../api/app/controllers/api_clients_controller.rb | 2 -
.../api/app/controllers/application_controller.rb | 377 ++++++-------
.../v1/api_client_authorizations_controller.rb | 32 +-
.../arvados/v1/collections_controller.rb | 7 -
.../app/controllers/arvados/v1/jobs_controller.rb | 60 ++-
.../arvados/v1/keep_disks_controller.rb | 17 +-
.../app/controllers/arvados/v1/links_controller.rb | 61 ++-
.../app/controllers/arvados/v1/logs_controller.rb | 32 ++
.../app/controllers/arvados/v1/nodes_controller.rb | 29 +-
.../arvados/v1/repositories_controller.rb | 2 +-
.../controllers/arvados/v1/schema_controller.rb | 12 +-
.../arvados/v1/user_agreements_controller.rb | 26 +-
.../app/controllers/arvados/v1/users_controller.rb | 33 +-
.../arvados/v1/virtual_machines_controller.rb | 16 -
.../api/app/controllers/collections_controller.rb | 2 -
.../app/controllers/commit_ancestors_controller.rb | 2 -
services/api/app/controllers/commits_controller.rb | 2 -
services/api/app/controllers/nodes_controller.rb | 30 -
.../controllers/pipeline_instances_controller.rb | 2 -
services/api/app/controllers/static_controller.rb | 2 +-
.../app/controllers/user_sessions_controller.rb | 12 +-
services/api/app/controllers/users_controller.rb | 2 -
services/api/app/mailers/user_notifier.rb | 8 +
services/api/app/middlewares/arvados_api_token.rb | 61 +++
services/api/app/middlewares/rack_socket.rb | 86 +++
.../api/app/models/api_client_authorization.rb | 24 +
services/api/app/models/arvados_model.rb | 218 +++++++--
services/api/app/models/blob.rb | 19 +-
services/api/app/models/collection.rb | 4 +
services/api/app/models/group.rb | 1 +
services/api/app/models/job.rb | 10 +-
services/api/app/models/keep_disk.rb | 6 +-
services/api/app/models/link.rb | 24 +-
services/api/app/models/log.rb | 64 ++-
services/api/app/models/node.rb | 2 +-
services/api/app/models/pipeline_instance.rb | 104 ++++-
services/api/app/models/user.rb | 115 +++--
.../views/user_notifier/account_is_setup.text.erb | 13 +
services/api/config/application.default.yml | 3 +
services/api/config/application.rb | 2 +
services/api/config/application.yml.example | 7 +
services/api/config/database.yml.sample | 12 +-
services/api/config/environments/test.rb.example | 3 +
services/api/config/initializers/authorization.rb | 5 +
services/api/config/initializers/eventbus.rb | 18 +
services/api/config/routes.rb | 163 ++----
.../migrate/20140325175653_remove_kind_columns.rb | 27 +
...20140407184311_rename_log_info_to_properties.rb | 5 +
.../20140421140924_add_group_class_to_groups.rb | 6 +
.../20140421151939_rename_auth_keys_user_index.rb | 11 +
.../migrate/20140421151940_timestamps_not_null.rb | 13 +
.../20140422011506_pipeline_instance_state.rb | 87 +++
.../20140423132913_add_object_owner_to_logs.rb | 27 +
.../db/migrate/20140423133559_new_scope_format.rb | 48 ++
services/api/db/schema.rb | 37 +-
services/api/lib/assign_uuid.rb | 11 +-
services/api/lib/common_api_template.rb | 1 -
services/api/lib/current_api_client.rb | 18 +-
services/api/lib/eventbus.rb | 226 ++++++++
services/api/lib/kind_and_etag.rb | 5 +-
services/api/lib/load_param.rb | 88 +++
services/api/lib/record_filters.rb | 75 +++
services/api/script/crunch-dispatch.rb | 2 +-
services/api/script/setup-new-user.rb | 9 +-
.../test/fixtures/api_client_authorizations.yml | 58 ++
services/api/test/fixtures/groups.yml | 30 +
services/api/test/fixtures/jobs.yml | 36 ++-
services/api/test/fixtures/links.yml | 80 ++--
services/api/test/fixtures/logs.yml | 32 ++
services/api/test/fixtures/pipeline_instances.yml | 20 +
services/api/test/fixtures/pipeline_templates.yml | 36 ++
services/api/test/fixtures/repositories.yml | 7 +-
services/api/test/fixtures/specimens.yml | 12 +
services/api/test/fixtures/virtual_machines.yml | 5 +
.../api/test/functional/admin_notifier_test.rb | 7 -
.../api_client_authorizations_controller_test.rb | 30 +-
.../arvados/v1/collections_controller_test.rb | 6 +-
.../arvados/v1/groups_controller_test.rb | 112 ++++
.../arvados/v1/job_reuse_controller_test.rb | 148 +++++-
.../functional/arvados/v1/jobs_controller_test.rb | 15 +
.../arvados/v1/keep_disks_controller_test.rb | 2 +-
.../functional/arvados/v1/links_controller_test.rb | 254 +++++++++-
.../functional/arvados/v1/logs_controller_test.rb | 38 ++
.../functional/arvados/v1/nodes_controller_test.rb | 13 +-
.../v1/pipeline_instances_controller_test.rb | 24 +
.../functional/arvados/v1/users_controller_test.rb | 234 +++++++-
.../functional/commit_ancestors_controller_test.rb | 7 -
.../api/test/functional/commits_controller_test.rb | 7 -
.../api_client_authorizations_api_test.rb | 6 +-
.../api_client_authorizations_scopes_test.rb | 85 +++
.../api/test/integration/collections_api_test.rb | 68 ++-
services/api/test/integration/errors_test.rb | 27 +
services/api/test/integration/jobs_api_test.rb | 4 +-
.../api/test/integration/login_workflow_test.rb | 25 +
services/api/test/integration/permissions_test.rb | 34 +-
.../api/test/integration/reader_tokens_test.rb | 85 +++
services/api/test/integration/valid_links_test.rb | 39 ++
services/api/test/integration/websocket_test.rb | 570 ++++++++++++++++++++
services/api/test/test_helper.rb | 36 ++-
services/api/test/unit/application_test.rb | 32 ++
services/api/test/unit/blob_test.rb | 27 +
services/api/test/unit/log_test.rb | 247 +++++++++-
services/api/test/unit/pipeline_instance_test.rb | 141 +++++-
services/api/test/unit/user_notifier_test.rb | 24 +
services/api/test/unit/user_test.rb | 115 +++-
services/api/test/websocket_runner.rb | 42 ++
services/keep/build.sh | 36 ++
services/keep/keep.go | 139 -----
services/keep/keep_test.go | 187 -------
services/keep/src/keep/keep.go | 461 ++++++++++++++++
services/keep/src/keep/keep_test.go | 416 ++++++++++++++
services/keep/src/keep/volume.go | 129 +++++
services/keep/src/keep/volume_unix.go | 295 ++++++++++
services/keep/src/keep/volume_unix_test.go | 245 +++++++++
243 files changed, 8217 insertions(+), 3176 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/collections.js
delete mode 100644 apps/workbench/app/assets/javascripts/collections.js.coffee
create mode 100644 apps/workbench/app/controllers/websocket_controller.rb
delete mode 100644 apps/workbench/app/helpers/pipeline_templates_helper.rb
create mode 100644 apps/workbench/app/views/collections/_toggle_persist.html.erb
create mode 100644 apps/workbench/app/views/pipeline_instances/_show_components_editable.html.erb
delete mode 100644 apps/workbench/app/views/pipeline_templates/_show_components_template.html.erb
create mode 100644 apps/workbench/app/views/users/_setup_popup.html.erb
create mode 100644 apps/workbench/app/views/users/setup.js.erb
create mode 100644 apps/workbench/app/views/users/setup_popup.js.erb
create mode 100644 apps/workbench/app/views/users/storage.html.erb
create mode 100644 apps/workbench/app/views/websocket/index.html.erb
create mode 120000 apps/workbench/config/environments/test.rb
create mode 100644 apps/workbench/test/integration/collections_test.rb
create mode 100644 apps/workbench/test/integration/users_test.rb
delete mode 100644 doc/api/schema/Commit.html.textile.liquid
delete mode 100644 doc/api/schema/CommitAncestor.html.textile.liquid
delete mode 100644 doc/user/reference/job-and-pipeline-reference.html.textile.liquid
delete mode 100644 services/api/app/controllers/api_clients_controller.rb
delete mode 100644 services/api/app/controllers/collections_controller.rb
delete mode 100644 services/api/app/controllers/commit_ancestors_controller.rb
delete mode 100644 services/api/app/controllers/commits_controller.rb
delete mode 100644 services/api/app/controllers/nodes_controller.rb
delete mode 100644 services/api/app/controllers/pipeline_instances_controller.rb
delete mode 100644 services/api/app/controllers/users_controller.rb
create mode 100644 services/api/app/mailers/user_notifier.rb
create mode 100644 services/api/app/middlewares/arvados_api_token.rb
create mode 100644 services/api/app/middlewares/rack_socket.rb
create mode 100644 services/api/app/views/user_notifier/account_is_setup.text.erb
create mode 100644 services/api/config/initializers/authorization.rb
create mode 100644 services/api/config/initializers/eventbus.rb
create mode 100644 services/api/db/migrate/20140325175653_remove_kind_columns.rb
create mode 100644 services/api/db/migrate/20140407184311_rename_log_info_to_properties.rb
create mode 100644 services/api/db/migrate/20140421140924_add_group_class_to_groups.rb
create mode 100644 services/api/db/migrate/20140421151939_rename_auth_keys_user_index.rb
create mode 100644 services/api/db/migrate/20140421151940_timestamps_not_null.rb
create mode 100644 services/api/db/migrate/20140422011506_pipeline_instance_state.rb
create mode 100644 services/api/db/migrate/20140423132913_add_object_owner_to_logs.rb
create mode 100644 services/api/db/migrate/20140423133559_new_scope_format.rb
create mode 100644 services/api/lib/eventbus.rb
create mode 100644 services/api/lib/load_param.rb
create mode 100644 services/api/lib/record_filters.rb
create mode 100644 services/api/test/fixtures/logs.yml
create mode 100644 services/api/test/fixtures/pipeline_instances.yml
create mode 100644 services/api/test/fixtures/pipeline_templates.yml
delete mode 100644 services/api/test/functional/admin_notifier_test.rb
delete mode 100644 services/api/test/functional/commit_ancestors_controller_test.rb
delete mode 100644 services/api/test/functional/commits_controller_test.rb
create mode 100644 services/api/test/integration/api_client_authorizations_scopes_test.rb
create mode 100644 services/api/test/integration/errors_test.rb
create mode 100644 services/api/test/integration/login_workflow_test.rb
create mode 100644 services/api/test/integration/reader_tokens_test.rb
create mode 100644 services/api/test/integration/valid_links_test.rb
create mode 100644 services/api/test/integration/websocket_test.rb
create mode 100644 services/api/test/unit/application_test.rb
create mode 100644 services/api/test/unit/user_notifier_test.rb
create mode 100644 services/api/test/websocket_runner.rb
create mode 100755 services/keep/build.sh
delete mode 100644 services/keep/keep.go
delete mode 100644 services/keep/keep_test.go
create mode 100644 services/keep/src/keep/keep.go
create mode 100644 services/keep/src/keep/keep_test.go
create mode 100644 services/keep/src/keep/volume.go
create mode 100644 services/keep/src/keep/volume_unix.go
create mode 100644 services/keep/src/keep/volume_unix_test.go
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commit 742bbf8e00b104786a151d18bb300f955e2933eb
Author: Brett Smith <brett at curoverse.com>
Date: Fri May 2 17:46:19 2014 -0400
arv-mount: Add --allow-other option.
We need this to support running job tasks in Docker containers. We
rely on the allow_other mount option to make the Keep mount available
to the container.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 722705e..681349b 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -635,7 +635,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
$command .=
"&& perl -";
}
- $command .= "&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec ";
+ $command .= "&& exec arv-mount --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
if (defined($docker_image))
{
$command .= "$docker_bin run -i -a stdin -a stdout -a stderr ";
diff --git a/sdk/python/bin/arv-mount b/sdk/python/bin/arv-mount
index 5e773df..cc7e288 100755
--- a/sdk/python/bin/arv-mount
+++ b/sdk/python/bin/arv-mount
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-from arvados.fuse import *
+from arvados.fuse import *
import arvados
import subprocess
import argparse
@@ -15,6 +15,8 @@ mountpoint before --exec, or mark the end of your --exec arguments
with "--".
""")
parser.add_argument('mountpoint', type=str, help="""Mount point.""")
+ parser.add_argument('--allow-other', action='store_true',
+ help="""Let other users read the mount""")
parser.add_argument('--collection', type=str, help="""Collection locator""")
parser.add_argument('--debug', action='store_true', help="""Debug mode""")
parser.add_argument('--exec', type=str, nargs=argparse.REMAINDER,
@@ -35,12 +37,9 @@ with "--".
operations.inodes.add_entry(MagicDirectory(llfuse.ROOT_INODE, operations.inodes))
# FUSE options, see mount.fuse(8)
- opts = []
+ opts = [optname for optname in ['allow_other', 'debug']
+ if getattr(args, optname)]
- # Enable FUSE debugging (logs each FUSE request)
- if args.debug:
- opts += ['debug']
-
# Initialize the fuse connection
llfuse.init(operations, args.mountpoint, opts)
commit 5454d6ad30e87ce6782e80682cb00cc8263db2d5
Author: Brett Smith <brett at curoverse.com>
Date: Fri May 2 17:27:51 2014 -0400
crunch-job: Manually configure containers' DNS.
All the compute nodes run dnsmasq to enable friendly names for
different hosts on the private Arvados network. Crunch jobs will need
to talk to that DNS server to reach, e.g., the local Keep servers.
This makes that happen.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index fa4550d..722705e 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -639,6 +639,12 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
if (defined($docker_image))
{
$command .= "$docker_bin run -i -a stdin -a stdout -a stderr ";
+ # Dynamically configure the container to use the host system as its
+ # DNS server. Get the host's global addresses from the ip command,
+ # and turn them into docker --dns options using gawk.
+ $command .=
+ q{$(ip -o address show scope global |
+ gawk 'match($4, /^([0-9\.:]+)\//, x){print "--dns", x[1]}') };
foreach my $env_key (qw(CRUNCH_SRC CRUNCH_TMP TASK_KEEPMOUNT))
{
$command .= "-v \Q$ENV{$env_key}:$ENV{$env_key}:rw\E ";
commit d5d577f3467fba4e3de43fb47da8369b4be0691e
Merge: 860042e 7ce745d
Author: Brett Smith <brett at curoverse.com>
Date: Fri May 2 11:18:19 2014 -0400
Merge branch 'master' into 2492-docker-crunch-jobs
commit 860042e2941a179b8ab2b985d83ba2e30d20dd4e
Author: Brett Smith <brett at curoverse.com>
Date: Fri May 2 11:18:02 2014 -0400
crunch-job: Install Docker images on demand.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 284a916..927f534 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -488,7 +488,28 @@ if (!$have_slurm)
must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
}
-
+# If this job requires a Docker image, install that.
+my $docker_bin = "/usr/bin/docker.io";
+my $docker_image = $Job->{runtime_constraints}->{docker_image};
+if (defined($docker_image)) {
+ my $docker_pid = fork();
+ if ($docker_pid == 0)
+ {
+ srun (["srun", "--nodelist=" . join(' ', @node)],
+ [$docker_bin, 'pull', $docker_image]);
+ exit ($?);
+ }
+ while (1)
+ {
+ last if $docker_pid == waitpid (-1, WNOHANG);
+ freeze_if_want_freeze ($docker_pid);
+ select (undef, undef, undef, 0.1);
+ }
+ if ($? != 0)
+ {
+ croak("Installing Docker image $docker_image returned exit code $?");
+ }
+}
foreach (qw (script script_version script_parameters runtime_constraints))
{
@@ -593,7 +614,6 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
qw(-n1 -c1 -N1 -D), $ENV{'TMPDIR'},
"--job-name=$job_id.$id.$$",
);
- my @execargs = qw(sh);
my $build_script_to_send = "";
my $command =
"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
@@ -606,10 +626,9 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
"&& perl -";
}
$command .= "&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec ";
- my $docker_image = $Job->{runtime_constraints}->{docker_image};
if (defined($docker_image))
{
- $command .= "docker run -i -a stdin -a stdout -a stderr ";
+ $command .= "$docker_bin run -i -a stdin -a stdout -a stderr ";
foreach my $env_key (qw(CRUNCH_SRC CRUNCH_TMP TASK_KEEPMOUNT))
{
$command .= "-v \Q$ENV{$env_key}:$ENV{$env_key}:rw\E ";
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