runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
+ filters = [["repository", "=", "arvados"],
+ ["script", "=", "crunchrunner"],
+ ["script_version", "in git", "9e5b98e8f5f4727856b53447191f9c06e3da2ba6"]]
+ if not self.arvrunner.ignore_docker_for_reuse:
+ filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
+
try:
- response = self.arvrunner.api.jobs().create(body={
- "owner_uuid": self.arvrunner.project_uuid,
- "script": "crunchrunner",
- "repository": "arvados",
- "script_version": "master",
- "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
- "script_parameters": {"tasks": [script_parameters]},
- "runtime_constraints": runtime_constraints
- }, find_or_create=kwargs.get("enable_reuse", True)).execute(num_retries=self.arvrunner.num_retries)
+ response = self.arvrunner.api.jobs().create(
+ body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "script": "crunchrunner",
+ "repository": "arvados",
+ "script_version": "master",
+ "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
+ "script_parameters": {"tasks": [script_parameters]},
+ "runtime_constraints": runtime_constraints
+ },
+ filters=filters,
+ find_or_create=kwargs.get("enable_reuse", True)
+ ).execute(num_retries=self.arvrunner.num_retries)
self.arvrunner.jobs[response["uuid"]] = self
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
+ self.debug = args.debug
+ self.ignore_docker_for_reuse = args.ignore_docker_for_reuse
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["fs_access"] = self.fs_access
help="")
parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
+ parser.add_argument("--ignore-docker-for-reuse", action="store_true",
+ help="Ignore Docker image version when deciding whether to reuse past jobs.",
+ default=False)
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
def test_run(self):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+
tool = {
"inputs": [],
"outputs": [],
arvtool.formatgraph = None
for j in arvtool.job({}, "", mock.MagicMock()):
j.run()
- runner.api.jobs().create.assert_called_with(body={
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
- 'runtime_constraints': {},
- 'script_parameters': {
- 'tasks': [{
- 'task.env': {'TMPDIR': '$(task.tmpdir)'},
- 'command': ['ls']
- }]
+ runner.api.jobs().create.assert_called_with(
+ body={
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'runtime_constraints': {},
+ 'script_parameters': {
+ 'tasks': [{
+ 'task.env': {'TMPDIR': '$(task.tmpdir)'},
+ 'command': ['ls']
+ }]
},
'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script': 'crunchrunner',
- 'runtime_constraints': {
- 'docker_image': 'arvados/jobs',
- 'min_cores_per_node': 1,
- 'min_ram_mb_per_node': 1024,
- 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
- }
- }, find_or_create=True)
+ 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'repository': 'arvados',
+ 'script': 'crunchrunner',
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ 'min_cores_per_node': 1,
+ 'min_ram_mb_per_node': 1024,
+ 'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
+ }
+ },
+ find_or_create=True,
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']]
+ )
# The test passes some fields in builder.resources
# For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
def test_resource_requirements(self):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+
tool = {
"inputs": [],
"outputs": [],
arvtool.formatgraph = None
for j in arvtool.job({}, "", mock.MagicMock()):
j.run()
- runner.api.jobs().create.assert_called_with(body={
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
- 'runtime_constraints': {},
- 'script_parameters': {
- 'tasks': [{
- 'task.env': {'TMPDIR': '$(task.tmpdir)'},
- 'command': ['ls']
- }]
+ runner.api.jobs().create.assert_called_with(
+ body={
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'runtime_constraints': {},
+ 'script_parameters': {
+ 'tasks': [{
+ 'task.env': {'TMPDIR': '$(task.tmpdir)'},
+ 'command': ['ls']
+ }]
},
'script_version': 'master',
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script': 'crunchrunner',
- 'runtime_constraints': {
- 'docker_image': 'arvados/jobs',
- 'min_cores_per_node': 3,
- 'min_ram_mb_per_node': 3000,
- 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
- }
- }, find_or_create=True)
+ 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'repository': 'arvados',
+ 'script': 'crunchrunner',
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs',
+ 'min_cores_per_node': 3,
+ 'min_ram_mb_per_node': 3000,
+ 'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
+ }
+ },
+ find_or_create=True,
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']])
@mock.patch("arvados.collection.Collection")
def test_done(self, col):
runner.api = api
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
+ runner.ignore_docker_for_reuse = False
col().open.return_value = []
api.collections().list().execute.side_effect = ({"items": []},