X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e838828374ceed5ef6da260939251e86f72b6f27..c22d90571a1fcb4b52e5387a791e3aefff5be6af:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index c6bcd04776..4fe82a6fe1 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -11,21 +11,23 @@ import copy import logging from schema_salad.sourceline import SourceLine, cmap +import schema_salad.ref_resolver from cwltool.pack import pack -from cwltool.load_tool import fetch_document +from cwltool.load_tool import fetch_document, resolve_and_validate_document from cwltool.process import shortname from cwltool.workflow import Workflow, WorkflowException, WorkflowStep -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class +from cwltool.utils import adjustFileObjs, adjustDirObjs, visit_class, normalizeFilesDirs from cwltool.context import LoadingContext import ruamel.yaml as yaml from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields, discover_secondary_files, - make_builder) + make_builder, arvados_jobs_image) from .pathmapper import ArvPathMapper, trim_listing from .arvtool import ArvadosCommandTool, set_cluster_target +from ._version import __version__ from .perf import Perf @@ -36,7 +38,8 @@ max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdir sum_res_pars = ("outdirMin", "outdirMax") def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None, - submit_runner_ram=0, name=None, merged_map=None): + submit_runner_ram=0, name=None, merged_map=None, + submit_runner_image=None): packed = packed_workflow(arvRunner, tool, merged_map) @@ -56,18 +59,25 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None, upload_dependencies(arvRunner, name, tool.doc_loader, packed, tool.tool["id"], False) + wf_runner_resources = None + + hints = main.get("hints", []) + found = False + for h in hints: + if h["class"] == "http://arvados.org/cwl#WorkflowRunnerResources": + wf_runner_resources = h + found = True + break + if not found: + wf_runner_resources = {"class": "http://arvados.org/cwl#WorkflowRunnerResources"} + hints.append(wf_runner_resources) + + wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner, submit_runner_image or "arvados/jobs:"+__version__) + if submit_runner_ram: - hints = main.get("hints", []) - found = False - for h in hints: - if h["class"] == "http://arvados.org/cwl#WorkflowRunnerResources": - h["ramMin"] = submit_runner_ram - found = True - break - if not found: - hints.append({"class": "http://arvados.org/cwl#WorkflowRunnerResources", - "ramMin": submit_runner_ram}) - main["hints"] = hints + wf_runner_resources["ramMin"] = submit_runner_ram + + main["hints"] = hints body = { "workflow": { @@ -140,7 +150,8 @@ class ArvadosWorkflowStep(WorkflowStep): runtimeContext = runtimeContext.copy() runtimeContext.toplevel = True # Preserve behavior for #13365 - builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements, runtimeContext) + builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements, + runtimeContext, self.metadata) runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext) return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext) @@ -160,7 +171,7 @@ class ArvadosWorkflow(Workflow): def job(self, joborder, output_callback, runtimeContext): - builder = make_builder(joborder, self.hints, self.requirements, runtimeContext) + builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata) runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext) req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") @@ -172,26 +183,30 @@ class ArvadosWorkflow(Workflow): with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)): if "id" not in self.tool: raise WorkflowException("%s object must have 'id'" % (self.tool["class"])) - document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"]) discover_secondary_files(self.arvrunner.fs_access, builder, self.tool["inputs"], joborder) + normalizeFilesDirs(joborder) with Perf(metrics, "subworkflow upload_deps"): upload_dependencies(self.arvrunner, os.path.basename(joborder.get("id", "#")), - document_loader, + self.doc_loader, joborder, joborder.get("id", "#"), False) if self.wf_pdh is None: - workflowobj["requirements"] = dedup_reqs(self.requirements) - workflowobj["hints"] = dedup_reqs(self.hints) + packed = pack(self.loadingContext, self.tool["id"], loader=self.doc_loader) - packed = pack(document_loader, workflowobj, uri, self.metadata) + for p in packed["$graph"]: + if p["id"] == "#main": + p["requirements"] = dedup_reqs(self.requirements) + p["hints"] = dedup_reqs(self.hints) def visit(item): + if "requirements" in item: + item["requirements"] = [i for i in item["requirements"] if i["class"] != "DockerRequirement"] for t in ("hints", "requirements"): if t not in item: continue @@ -211,9 +226,6 @@ class ArvadosWorkflow(Workflow): raise WorkflowException("Non-top-level ResourceRequirement in single container cannot have expressions") if not dyn: self.static_resource_req.append(req) - if req["class"] == "DockerRequirement": - if "http://arvados.org/cwl#dockerCollectionPDH" in req: - del req["http://arvados.org/cwl#dockerCollectionPDH"] visit_class(packed["$graph"], ("Workflow", "CommandLineTool"), visit) @@ -222,9 +234,9 @@ class ArvadosWorkflow(Workflow): upload_dependencies(self.arvrunner, runtimeContext.name, - document_loader, + self.doc_loader, packed, - uri, + self.tool["id"], False) # Discover files/directories referenced by the @@ -295,6 +307,16 @@ class ArvadosWorkflow(Workflow): self.loadingContext.metadata = self.loadingContext.metadata.copy() self.loadingContext.metadata["http://commonwl.org/cwltool#original_cwlVersion"] = "v1.0" + if len(job_res_reqs) == 1: + # RAM request needs to be at least 128 MiB or the workflow + # runner itself won't run reliably. + if job_res_reqs[0].get("ramMin", 1024) < 128: + job_res_reqs[0]["ramMin"] = 128 + + arguments = ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl", "cwl.input.yml"] + if runtimeContext.debug: + arguments.insert(0, '--debug') + wf_runner = cmap({ "class": "CommandLineTool", "baseCommand": "cwltool", @@ -314,7 +336,7 @@ class ArvadosWorkflow(Workflow): }] }], "hints": self.hints, - "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"], + "arguments": arguments, "id": "#" }) return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)