X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f170c5a75f22a6db11ca93eed5b0dfc9c65c4270..926c011fb4f7a4d7722b88a19afed51c5d4bd1c4:/sdk/cwl/tests/test_container.py diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py index 2b46b89c60..bfffe6eacb 100644 --- a/sdk/cwl/tests/test_container.py +++ b/sdk/cwl/tests/test_container.py @@ -18,6 +18,7 @@ import os import functools import cwltool.process import cwltool.secrets +import cwltool.load_tool from cwltool.update import INTERNAL_VERSION from schema_salad.ref_resolver import Loader from schema_salad.sourceline import cmap @@ -66,12 +67,16 @@ class TestContainer(unittest.TestCase): make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0)) + fs_access = mock.MagicMock() + fs_access.exists.return_value = True + loadingContext = arvados_cwl.context.ArvLoadingContext( {"avsc_names": avsc_names, "basedir": "", "make_fs_access": make_fs_access, - "loader": Loader({}), - "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}}) + "construct_tool_object": runner.arv_make_tool, + "fetcher_constructor": functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=fs_access) + }) runtimeContext = arvados_cwl.context.ArvRuntimeContext( {"work_api": "containers", "basedir": "", @@ -83,6 +88,11 @@ class TestContainer(unittest.TestCase): "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz" }) + if isinstance(runner, mock.MagicMock): + def make_tool(toolpath_object, loadingContext): + return arvados_cwl.ArvadosCommandTool(runner, toolpath_object, loadingContext) + runner.arv_make_tool.side_effect = make_tool + return loadingContext, runtimeContext # Helper function to set up the ArvCwlExecutor to use the containers api @@ -112,6 +122,7 @@ class TestContainer(unittest.TestCase): 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 = { @@ -122,13 +133,14 @@ class TestContainer(unittest.TestCase): "outputs": [], "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], - "id": "#", - "class": "CommandLineTool" + "id": "", + "class": "CommandLineTool", + "cwlVersion": "v1.2" }) loadingContext, runtimeContext = self.helper(runner, enable_reuse) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), runtimeContext): @@ -142,7 +154,7 @@ class TestContainer(unittest.TestCase): 'name': 'test_run_'+str(enable_reuse), 'runtime_constraints': { 'vcpus': 1, - 'ram': 1073741824 + 'ram': 268435456 }, 'use_existing': enable_reuse, 'priority': 500, @@ -171,10 +183,12 @@ class TestContainer(unittest.TestCase): # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} @mock.patch("arvados.commands.keepdocker.list_images_in_arv") def test_resource_requirements(self, keepdocker): + arvados_cwl.add_arv_hints() runner = mock.MagicMock() runner.ignore_docker_for_reuse = False runner.intermediate_output_ttl = 3600 runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": "20210628"} keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] runner.api.collections().get().execute.return_value = { @@ -201,18 +215,19 @@ class TestContainer(unittest.TestCase): "class": "http://arvados.org/cwl#IntermediateOutput", "outputTTL": 7200 }, { - "class": "http://arvados.org/cwl#ReuseRequirement", + "class": "WorkReuse", "enableReuse": False }], "baseCommand": "ls", - "id": "#", - "class": "CommandLineTool" + "id": "", + "class": "CommandLineTool", + "cwlVersion": "v1.2" }) loadingContext, runtimeContext = self.helper(runner) runtimeContext.name = "test_resource_requirements" - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), runtimeContext): j.run(runtimeContext) @@ -270,6 +285,7 @@ class TestContainer(unittest.TestCase): 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 = { @@ -313,14 +329,16 @@ class TestContainer(unittest.TestCase): } ] }], "baseCommand": "ls", - "id": "#", - "class": "CommandLineTool" + "class": "CommandLineTool", + "cwlVersion": "v1.2", + "id": "" }) loadingContext, runtimeContext = self.helper(runner) runtimeContext.name = "test_initial_work_dir" - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), runtimeContext): j.run(runtimeContext) @@ -340,7 +358,7 @@ class TestContainer(unittest.TestCase): 'name': 'test_initial_work_dir', 'runtime_constraints': { 'vcpus': 1, - 'ram': 1073741824 + 'ram': 268435456 }, 'use_existing': True, 'priority': 500, @@ -398,6 +416,7 @@ class TestContainer(unittest.TestCase): 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 = { @@ -413,14 +432,15 @@ class TestContainer(unittest.TestCase): "stderr": "stderr.txt", "stdin": "/keep/99999999999999999999999999999996+99/file.txt", "arguments": [{"valueFrom": "$(runtime.outdir)"}], - "id": "#", - "class": "CommandLineTool" + "id": "", + "class": "CommandLineTool", + "cwlVersion": "v1.2" }) loadingContext, runtimeContext = self.helper(runner) runtimeContext.name = "test_run_redirect" - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), runtimeContext): j.run(runtimeContext) @@ -433,7 +453,7 @@ class TestContainer(unittest.TestCase): 'name': 'test_run_redirect', 'runtime_constraints': { 'vcpus': 1, - 'ram': 1073741824 + 'ram': 268435456 }, 'use_existing': True, 'priority': 500, @@ -622,6 +642,7 @@ class TestContainer(unittest.TestCase): 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 = { @@ -638,14 +659,15 @@ class TestContainer(unittest.TestCase): "outputs": [], "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], - "id": "#", - "class": "CommandLineTool" + "id": "", + "class": "CommandLineTool", + "cwlVersion": "v1.2" }) loadingContext, runtimeContext = self.helper(runner) runtimeContext.name = "test_run_mounts" - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) arvtool.formatgraph = None job_order = { "p1": { @@ -675,7 +697,7 @@ class TestContainer(unittest.TestCase): 'name': 'test_run_mounts', 'runtime_constraints': { 'vcpus': 1, - 'ram': 1073741824 + 'ram': 268435456 }, 'use_existing': True, 'priority': 500, @@ -708,10 +730,12 @@ class TestContainer(unittest.TestCase): # 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_secrets(self, keepdocker): + arvados_cwl.add_arv_hints() 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 = { @@ -721,6 +745,7 @@ class TestContainer(unittest.TestCase): tool = cmap({"arguments": ["md5sum", "example.conf"], "class": "CommandLineTool", + "cwlVersion": "v1.2", "hints": [ { "class": "http://commonwl.org/cwltool#Secrets", @@ -729,7 +754,7 @@ class TestContainer(unittest.TestCase): ] } ], - "id": "#secret_job.cwl", + "id": "", "inputs": [ { "id": "#secret_job.cwl/pw", @@ -753,7 +778,7 @@ class TestContainer(unittest.TestCase): loadingContext, runtimeContext = self.helper(runner) runtimeContext.name = "test_secrets" - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) arvtool.formatgraph = None job_order = {"pw": "blorp"} @@ -770,7 +795,7 @@ class TestContainer(unittest.TestCase): 'name': 'test_secrets', 'runtime_constraints': { 'vcpus': 1, - 'ram': 1073741824 + 'ram': 268435456 }, 'use_existing': True, 'priority': 500, @@ -808,6 +833,7 @@ class TestContainer(unittest.TestCase): 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 = { @@ -818,7 +844,8 @@ class TestContainer(unittest.TestCase): "outputs": [], "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], - "id": "#", + "id": "", + "cwlVersion": "v1.2", "class": "CommandLineTool", "hints": [ { @@ -831,7 +858,7 @@ class TestContainer(unittest.TestCase): loadingContext, runtimeContext = self.helper(runner) runtimeContext.name = "test_timelimit" - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), runtimeContext): @@ -851,6 +878,7 @@ class TestContainer(unittest.TestCase): 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 = { @@ -861,7 +889,8 @@ class TestContainer(unittest.TestCase): "outputs": [], "baseCommand": "ls", "arguments": [{"valueFrom": "$(runtime.outdir)"}], - "id": "#", + "id": "", + "cwlVersion": "v1.2", "class": "CommandLineTool", "hints": [ { @@ -874,7 +903,7 @@ class TestContainer(unittest.TestCase): loadingContext, runtimeContext = self.helper(runner, True) - arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext) + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) arvtool.formatgraph = None for j in arvtool.job({}, mock.MagicMock(), runtimeContext): @@ -888,7 +917,7 @@ class TestContainer(unittest.TestCase): 'name': 'test_run_True', 'runtime_constraints': { 'vcpus': 1, - 'ram': 1073741824 + 'ram': 268435456 }, 'use_existing': True, 'priority': 500, @@ -914,6 +943,293 @@ class TestContainer(unittest.TestCase): })) + # The test passes no builder.resources + # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024} + @mock.patch("arvados.commands.keepdocker.list_images_in_arv") + def test_setting_process_properties(self, keepdocker): + arv_docker_clear_cache() + + runner = mock.MagicMock() + runner.ignore_docker_for_reuse = False + runner.intermediate_output_ttl = 0 + runner.secret_store = cwltool.secrets.SecretStore() + runner.api._rootDesc = {"revision": "20210628"} + + keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + runner.api.collections().get().execute.return_value = { + "portable_data_hash": "99999999999999999999999999999993+99"} + + tool = cmap({ + "inputs": [ + {"id": "x", "type": "string"}], + "outputs": [], + "baseCommand": "ls", + "arguments": [{"valueFrom": "$(runtime.outdir)"}], + "id": "", + "class": "CommandLineTool", + "cwlVersion": "v1.2", + "hints": [ + { + "class": "http://arvados.org/cwl#ProcessProperties", + "processProperties": [ + {"propertyName": "foo", + "propertyValue": "bar"}, + {"propertyName": "baz", + "propertyValue": "$(inputs.x)"}, + {"propertyName": "quux", + "propertyValue": { + "q1": 1, + "q2": 2 + } + } + ], + } + ] + }) + + loadingContext, runtimeContext = self.helper(runner, True) + + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None + + for j in arvtool.job({"x": "blorp"}, 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 + }, + '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': ['ls', '/var/spool/cwl'], + 'cwd': '/var/spool/cwl', + 'scheduling_parameters': {}, + 'properties': { + "baz": "blorp", + "foo": "bar", + "quux": { + "q1": 1, + "q2": 2 + } + }, + '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.commands.keepdocker.list_images_in_arv") + def test_cuda_requirement(self, keepdocker): + 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-zzzzzzzzzzzzzz3", "")] + 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 for 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": "echo", + "arguments": [], + "id": "", + "cwlVersion": "v1.2", + "class": "CommandLineTool" + }) + + loadingContext, runtimeContext = self.helper(runner, True) + + arvtool = cwltool.load_tool.load_tool(tool, loadingContext) + arvtool.formatgraph = None + + container_request = { + 'environment': { + 'HOME': '/var/spool/cwl', + 'TMPDIR': '/tmp' + }, + 'name': 'test_run_True', + '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 for 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(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 for 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)) + + + class TestWorkflow(unittest.TestCase): def setUp(self): cwltool.process._names = set()