X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/936ba2824bc791490f7320452c2afa7d68739ac1..83f05664d99a7d80b2d2ae9c0517004cbfb5d00d:/sdk/cwl/tests/test_container.py diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py index 21ae4a7af0..cb57b446da 100644 --- a/sdk/cwl/tests/test_container.py +++ b/sdk/cwl/tests/test_container.py @@ -16,6 +16,7 @@ import mock import unittest import os import functools +import threading import cwltool.process import cwltool.secrets import cwltool.load_tool @@ -62,6 +63,13 @@ class TestContainer(unittest.TestCase): cwltool.process._names = set() arv_docker_clear_cache() + def tearDown(self): + root_logger = logging.getLogger('') + + # Remove existing RuntimeStatusLoggingHandlers if they exist + handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)] + root_logger.handlers = handlers + def helper(self, runner, enable_reuse=True): document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION) @@ -75,7 +83,9 @@ class TestContainer(unittest.TestCase): "basedir": "", "make_fs_access": make_fs_access, "construct_tool_object": runner.arv_make_tool, - "fetcher_constructor": functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=fs_access) + "fetcher_constructor": functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=fs_access), + "loader": Loader({}), + "metadata": cmap({"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}) }) runtimeContext = arvados_cwl.context.ArvRuntimeContext( {"work_api": "containers", @@ -83,9 +93,11 @@ class TestContainer(unittest.TestCase): "name": "test_run_"+str(enable_reuse), "make_fs_access": make_fs_access, "tmpdir": "/tmp", + "outdir": "/tmp", "enable_reuse": enable_reuse, "priority": 500, - "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz" + "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", + "workflow_eval_lock": threading.Condition(threading.RLock()) }) if isinstance(runner, mock.MagicMock): @@ -166,7 +178,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_'+str(enable_reuse), + 'output_name': 'Output from step test_run_'+str(enable_reuse), 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -255,7 +267,7 @@ class TestContainer(unittest.TestCase): "capacity": 5242880000 } }, 'state': 'Committed', - 'output_name': 'Output for step test_resource_requirements', + 'output_name': 'Output from step test_resource_requirements', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 7200, @@ -389,7 +401,7 @@ class TestContainer(unittest.TestCase): } }, 'state': 'Committed', - 'output_name': 'Output for step test_initial_work_dir', + 'output_name': 'Output from step test_initial_work_dir', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -477,7 +489,7 @@ class TestContainer(unittest.TestCase): }, }, 'state': 'Committed', - "output_name": "Output for step test_run_redirect", + "output_name": "Output from step test_run_redirect", 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -713,7 +725,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_mounts', + 'output_name': 'Output from step test_run_mounts', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -807,7 +819,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_secrets', + 'output_name': 'Output from step test_secrets', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -929,7 +941,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_True', + 'output_name': 'Output from step test_run_True', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -1015,7 +1027,7 @@ class TestContainer(unittest.TestCase): "capacity": 1073741824 } }, 'state': 'Committed', - 'output_name': 'Output for step test_run_True', + 'output_name': 'Output from step test_run_True', 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', 'output_path': '/var/spool/cwl', 'output_ttl': 0, @@ -1053,68 +1065,329 @@ class TestContainer(unittest.TestCase): runner.api.collections().get().execute.return_value = { "portable_data_hash": "99999999999999999999999999999993+99"} + test_cwl_req = [{ + "class": "http://commonwl.org/cwltool#CUDARequirement", + "cudaVersionMin": "11.0", + "cudaComputeCapability": "9.0", + }, { + "class": "http://commonwl.org/cwltool#CUDARequirement", + "cudaVersionMin": "11.0", + "cudaComputeCapability": "9.0", + "cudaDeviceCountMin": 2 + }, { + "class": "http://commonwl.org/cwltool#CUDARequirement", + "cudaVersionMin": "11.0", + "cudaComputeCapability": ["4.0", "5.0"], + "cudaDeviceCountMin": 2 + }] + + test_arv_req = [{ + 'device_count': 1, + 'driver_version': "11.0", + 'hardware_capability': "9.0" + }, { + 'device_count': 2, + 'driver_version': "11.0", + 'hardware_capability': "9.0" + }, { + 'device_count': 2, + 'driver_version': "11.0", + 'hardware_capability': "4.0" + }] + + for test_case in range(0, len(test_cwl_req)): + + tool = cmap({ + "inputs": [], + "outputs": [], + "baseCommand": "nvidia-smi", + "arguments": [], + "id": "", + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "requirements": [test_cwl_req[test_case]] + }) + + loadingContext, runtimeContext = self.helper(runner, True) + + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None + + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + runner.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher({ + 'environment': { + 'HOME': '/var/spool/cwl', + 'TMPDIR': '/tmp' + }, + 'name': 'test_run_True' + ("" if test_case == 0 else "_"+str(test_case+1)), + 'runtime_constraints': { + 'vcpus': 1, + 'ram': 268435456, + 'cuda': test_arv_req[test_case] + }, + 'use_existing': True, + 'priority': 500, + 'mounts': { + '/tmp': {'kind': 'tmp', + "capacity": 1073741824 + }, + '/var/spool/cwl': {'kind': 'tmp', + "capacity": 1073741824 } + }, + 'state': 'Committed', + 'output_name': 'Output from step test_run_True' + ("" if test_case == 0 else "_"+str(test_case+1)), + 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', + 'output_path': '/var/spool/cwl', + 'output_ttl': 0, + 'container_image': '99999999999999999999999999999993+99', + 'command': ['nvidia-smi'], + 'cwd': '/var/spool/cwl', + 'scheduling_parameters': {}, + 'properties': {}, + 'secret_mounts': {}, + 'output_storage_classes': ["default"] + })) + + + # The test passes no builder.resources + # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} + @mock.patch("arvados_cwl.arvdocker.determine_image_id") + @mock.patch("arvados.commands.keepdocker.list_images_in_arv") + def test_match_local_docker(self, keepdocker, determine_image_id): + arvados_cwl.add_arv_hints() + arv_docker_clear_cache() + + runner = mock.MagicMock() + runner.ignore_docker_for_reuse = False + runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": "20210628"} + + keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz4", {"dockerhash": "456"}), + ("zzzzz-4zz18-zzzzzzzzzzzzzz3", {"dockerhash": "123"})] + determine_image_id.side_effect = lambda x: "123" + def execute(uuid): + ex = mock.MagicMock() + lookup = {"zzzzz-4zz18-zzzzzzzzzzzzzz4": {"portable_data_hash": "99999999999999999999999999999994+99"}, + "zzzzz-4zz18-zzzzzzzzzzzzzz3": {"portable_data_hash": "99999999999999999999999999999993+99"}} + ex.execute.return_value = lookup[uuid] + return ex + runner.api.collections().get.side_effect = execute + tool = cmap({ "inputs": [], "outputs": [], - "baseCommand": "nvidia-smi", + "baseCommand": "echo", "arguments": [], "id": "", - "cwlVersion": "v1.2", - "class": "CommandLineTool", - "requirements": [ - { - "class": "http://commonwl.org/cwltool#CUDARequirement", - "cudaVersionMin": "11.0", - "cudaComputeCapabilityMin": "9.0", - } - ] + "cwlVersion": "v1.0", + "class": "org.w3id.cwl.cwl.CommandLineTool" }) loadingContext, runtimeContext = self.helper(runner, True) - arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) arvtool.formatgraph = None + container_request = { + 'environment': { + 'HOME': '/var/spool/cwl', + 'TMPDIR': '/tmp' + }, + 'name': 'test_run_True', + 'runtime_constraints': { + 'vcpus': 1, + 'ram': 1073741824, + }, + 'use_existing': True, + 'priority': 500, + 'mounts': { + '/tmp': {'kind': 'tmp', + "capacity": 1073741824 + }, + '/var/spool/cwl': {'kind': 'tmp', + "capacity": 1073741824 } + }, + 'state': 'Committed', + 'output_name': 'Output from step test_run_True', + 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', + 'output_path': '/var/spool/cwl', + 'output_ttl': 0, + 'container_image': '99999999999999999999999999999994+99', + 'command': ['echo'], + 'cwd': '/var/spool/cwl', + 'scheduling_parameters': {}, + 'properties': {}, + 'secret_mounts': {}, + 'output_storage_classes': ["default"] + } + + runtimeContext.match_local_docker = False for j in arvtool.job({}, mock.MagicMock(), runtimeContext): j.run(runtimeContext) runner.api.container_requests().create.assert_called_with( - body=JsonDiffMatcher({ - 'environment': { - 'HOME': '/var/spool/cwl', - 'TMPDIR': '/tmp' - }, - 'name': 'test_run_True', - 'runtime_constraints': { - 'vcpus': 1, - 'ram': 268435456, - 'cuda': { - 'device_count': 1, - 'driver_version': "11.0", - 'hardware_capability': "9.0" + body=JsonDiffMatcher(container_request)) + + arv_docker_clear_cache() + runtimeContext.match_local_docker = True + container_request['container_image'] = '99999999999999999999999999999993+99' + container_request['name'] = 'test_run_True_2' + container_request['output_name'] = 'Output from step test_run_True_2' + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + runner.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(container_request)) + + + # The test passes no builder.resources + # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} + @mock.patch("arvados.commands.keepdocker.list_images_in_arv") + def test_run_preemptible_hint(self, keepdocker): + arvados_cwl.add_arv_hints() + for enable_preemptible in (None, True, False): + for preemptible_hint in (None, True, False): + arv_docker_clear_cache() + + runner = mock.MagicMock() + runner.ignore_docker_for_reuse = False + runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": "20210628"} + + keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + runner.api.collections().get().execute.return_value = { + "portable_data_hash": "99999999999999999999999999999993+99"} + + if preemptible_hint is not None: + hints = [{ + "class": "http://arvados.org/cwl#UsePreemptible", + "usePreemptible": preemptible_hint + }] + else: + hints = [] + + tool = cmap({ + "inputs": [], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "", + "class": "CommandLineTool", + "cwlVersion": "v1.2", + "hints": hints + }) + + loadingContext, runtimeContext = self.helper(runner) + + runtimeContext.name = 'test_run_enable_preemptible_'+str(enable_preemptible)+str(preemptible_hint) + runtimeContext.enable_preemptible = enable_preemptible + + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None + + # Test the interactions between --enable/disable-preemptible + # and UsePreemptible hint + + if enable_preemptible is None: + if preemptible_hint is None: + sched = {} + else: + sched = {'preemptible': preemptible_hint} + else: + if preemptible_hint is None: + sched = {'preemptible': enable_preemptible} + else: + sched = {'preemptible': enable_preemptible and preemptible_hint} + + for j in arvtool.job({}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + runner.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher({ + 'environment': { + 'HOME': '/var/spool/cwl', + 'TMPDIR': '/tmp' + }, + 'name': runtimeContext.name, + 'runtime_constraints': { + 'vcpus': 1, + 'ram': 268435456 + }, + 'use_existing': True, + 'priority': 500, + 'mounts': { + '/tmp': {'kind': 'tmp', + "capacity": 1073741824 + }, + '/var/spool/cwl': {'kind': 'tmp', + "capacity": 1073741824 } + }, + 'state': 'Committed', + 'output_name': 'Output from step '+runtimeContext.name, + 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', + 'output_path': '/var/spool/cwl', + 'output_ttl': 0, + 'container_image': '99999999999999999999999999999993+99', + 'command': ['ls', '/var/spool/cwl'], + 'cwd': '/var/spool/cwl', + 'scheduling_parameters': sched, + 'properties': {}, + 'secret_mounts': {}, + 'output_storage_classes': ["default"] + })) + + + @mock.patch("arvados.commands.keepdocker.list_images_in_arv") + def test_output_properties(self, keepdocker): + arvados_cwl.add_arv_hints() + for rev in ["20210628", "20220510"]: + runner = mock.MagicMock() + runner.ignore_docker_for_reuse = False + runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": rev} + + keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + runner.api.collections().get().execute.return_value = { + "portable_data_hash": "99999999999999999999999999999993+99"} + + tool = cmap({ + "inputs": [{ + "id": "inp", + "type": "string" + }], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "", + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "hints": [ + { + "class": "http://arvados.org/cwl#OutputCollectionProperties", + "outputProperties": { + "foo": "bar", + "baz": "$(inputs.inp)" } - }, - 'use_existing': True, - 'priority': 500, - 'mounts': { - '/tmp': {'kind': 'tmp', - "capacity": 1073741824 - }, - '/var/spool/cwl': {'kind': 'tmp', - "capacity": 1073741824 } - }, - 'state': 'Committed', - 'output_name': 'Output for step test_run_True', - 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz', - 'output_path': '/var/spool/cwl', - 'output_ttl': 0, - 'container_image': '99999999999999999999999999999993+99', - 'command': ['nvidia-smi'], - 'cwd': '/var/spool/cwl', - 'scheduling_parameters': {}, - 'properties': {}, - 'secret_mounts': {}, - 'output_storage_classes': ["default"] - })) + } + ] + }) + + loadingContext, runtimeContext = self.helper(runner) + runtimeContext.name = "test_timelimit" + + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None + + for j in arvtool.job({"inp": "quux"}, mock.MagicMock(), runtimeContext): + j.run(runtimeContext) + + _, kwargs = runner.api.container_requests().create.call_args + if rev == "20220510": + self.assertEqual({"foo": "bar", "baz": "quux"}, kwargs['body'].get('output_properties')) + else: + self.assertEqual(None, kwargs['body'].get('output_properties')) class TestWorkflow(unittest.TestCase): @@ -1170,6 +1443,8 @@ class TestWorkflow(unittest.TestCase): runner.api.collections().list().execute.return_value = {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999993+99"}]} + runner.api.containers().current().execute.return_value = {} + runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" runner.ignore_docker_for_reuse = False runner.num_retries = 0 @@ -1242,7 +1517,7 @@ class TestWorkflow(unittest.TestCase): } }, "name": "scatterstep", - "output_name": "Output for step scatterstep", + "output_name": "Output from step scatterstep", "output_path": "/var/spool/cwl", "output_ttl": 0, "priority": 500, @@ -1356,7 +1631,7 @@ class TestWorkflow(unittest.TestCase): u'cwl.input.yml' ], 'use_existing': True, - 'output_name': u'Output for step echo-subwf', + 'output_name': u'Output from step echo-subwf', 'cwd': '/var/spool/cwl', 'output_storage_classes': ["default"] }))