[ARVADOS] updated: 9943f1edaafce7b82c03e4a1926a8c1f5526b03d
git at public.curoverse.com
git at public.curoverse.com
Thu Jun 4 16:49:51 EDT 2015
Summary of changes:
.../app/controllers/collections_controller.rb | 9 ---
apps/workbench/app/models/arvados_api_client.rb | 14 +++-
apps/workbench/app/models/arvados_base.rb | 23 +++++-
apps/workbench/config/application.default.yml | 4 +-
.../controllers/collections_controller_test.rb | 7 ++
apps/workbench/test/helpers/manifest_examples.rb | 1 +
apps/workbench/test/helpers/time_block.rb | 1 +
.../collection_unit_test.rb | 71 ++++++++++++++++++
.../collections_controller_test.rb | 71 ++++++++++++++++++
apps/workbench/test/test_helper.rb | 34 +++++++--
apps/workbench/test/unit/arvados_base_test.rb | 87 ++++++++++++++++++++++
doc/_includes/_arv_run_redirection.liquid | 2 +
doc/_includes/_ssh_addkey.liquid | 17 ++---
doc/_includes/_tutorial_cluster_name.liquid | 3 +
.../_tutorial_expectations_workstation.liquid | 3 +
doc/index.html.liquid | 5 +-
.../getting_started/community.html.textile.liquid | 4 +-
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
doc/user/topics/arv-docker.html.textile.liquid | 4 +-
doc/user/topics/arv-run.html.textile.liquid | 6 ++
doc/user/topics/arv-web.html.textile.liquid | 3 +
doc/user/topics/run-command.html.textile.liquid | 2 +
...nning-pipeline-command-line.html.textile.liquid | 4 +-
.../topics/tutorial-parallel.html.textile.liquid | 2 +-
.../tutorial-firstscript.html.textile.liquid | 8 +-
.../tutorial-keep-get.html.textile.liquid | 2 +-
.../tutorials/tutorial-keep.html.textile.liquid | 11 +--
...tutorial-pipeline-workbench.html.textile.liquid | 8 +-
.../tutorial-submit-job.html.textile.liquid | 6 +-
sdk/cli/bin/crunch-job | 19 +++--
sdk/python/arvados/arvfile.py | 10 ++-
sdk/python/tests/test_arvfile.py | 19 ++++-
.../api/app/controllers/application_controller.rb | 13 +++-
services/api/app/models/blob.rb | 13 ++--
services/api/app/models/collection.rb | 7 +-
services/api/app/models/node.rb | 86 +++++++++++++--------
services/api/config/application.default.yml | 53 ++++++++-----
services/api/db/structure.sql | 2 -
.../arvados/v1/collections_controller_test.rb | 38 ++++++++--
services/api/test/helpers/manifest_examples.rb | 31 ++++++++
services/api/test/helpers/time_block.rb | 11 +++
.../integration/collections_performance_test.rb | 40 ++++++++++
.../api/test/unit/collection_performance_test.rb | 61 +++++++++++++++
services/api/test/unit/node_test.rb | 49 ++++++++++++
44 files changed, 719 insertions(+), 147 deletions(-)
create mode 120000 apps/workbench/test/helpers/manifest_examples.rb
create mode 120000 apps/workbench/test/helpers/time_block.rb
create mode 100644 apps/workbench/test/integration_performance/collection_unit_test.rb
create mode 100644 apps/workbench/test/integration_performance/collections_controller_test.rb
create mode 100644 apps/workbench/test/unit/arvados_base_test.rb
create mode 100644 doc/_includes/_tutorial_cluster_name.liquid
create mode 100644 doc/_includes/_tutorial_expectations_workstation.liquid
create mode 100644 services/api/test/helpers/manifest_examples.rb
create mode 100644 services/api/test/helpers/time_block.rb
create mode 100644 services/api/test/integration/collections_performance_test.rb
create mode 100644 services/api/test/unit/collection_performance_test.rb
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commit 9943f1edaafce7b82c03e4a1926a8c1f5526b03d
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jun 4 16:44:24 2015 -0400
6146: Document how --steps really works. Simplify squeue output format and parsing.
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 786e18f..c86a1b6 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -1299,8 +1299,13 @@ sub check_squeue
return;
}
- # get a list of steps still running
- my @squeue = `squeue --jobs=\Q$ENV{SLURM_JOB_ID}\E --steps --format='%i %j' --noheader`;
+ # Get a list of steps still running. Note: as of slurm 2.3.4,
+ # squeue(1) says --steps selects a format (which we override anyway)
+ # and allows us to specify which steps we're interested in (which we
+ # don't). Although this isn't documented explicitly, --steps also
+ # changes the meaning of %i from "job id" to "step id". Without it,
+ # we'd just get a list of one job, instead of a list of N steps.
+ my @squeue = `squeue --jobs=\Q$ENV{SLURM_JOB_ID}\E --steps --format='%j' --noheader`;
if ($? != 0)
{
Log(undef, "warning: squeue exit status $? ($!)");
@@ -1310,15 +1315,9 @@ sub check_squeue
# which of my jobsteps are running, according to squeue?
my %ok;
- foreach (@squeue)
+ for my $jobstepname (@squeue)
{
- if (/^(\d+)\.(\d+) (\S+)/)
- {
- if ($1 eq $ENV{SLURM_JOB_ID})
- {
- $ok{$3} = 1;
- }
- }
+ $ok{$jobstepname} = 1;
}
# Check for child procs >60s old and not mentioned by squeue.
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