X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/af17604c5a93830380fb50db93ce543926c116cf..cb97316068f201ffd03f54d67074a83601c2bb45:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index f0f9c77f40..5939b0413e 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -14,6 +14,8 @@ from cwltool.load_tool import fetch_document from cwltool.process import shortname from cwltool.workflow import Workflow, WorkflowException from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class +from cwltool.builder import Builder +from cwltool.context import LoadingContext import ruamel.yaml as yaml @@ -26,6 +28,9 @@ from .perf import Perf logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') +max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax") +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): @@ -71,17 +76,50 @@ def dedup_reqs(reqs): dedup[r["class"]] = r return [dedup[r] for r in sorted(dedup.keys())] +def get_overall_res_req(res_reqs): + """Take the overall of a list of ResourceRequirement, + i.e., the max of coresMin, coresMax, ramMin, ramMax, tmpdirMin, tmpdirMax + and the sum of outdirMin, outdirMax.""" + + all_res_req = {} + exception_msgs = [] + for a in max_res_pars + sum_res_pars: + all_res_req[a] = [] + for res_req in res_reqs: + if a in res_req: + if isinstance(res_req[a], int): # integer check + all_res_req[a].append(res_req[a]) + else: + msg = SourceLine(res_req, a).makeError( + "Non-top-level ResourceRequirement in single container cannot have expressions") + exception_msgs.append(msg) + if exception_msgs: + raise WorkflowException("\n".join(exception_msgs)) + else: + overall_res_req = {} + for a in all_res_req: + if all_res_req[a]: + if a in max_res_pars: + overall_res_req[a] = max(all_res_req[a]) + elif a in sum_res_pars: + overall_res_req[a] = sum(all_res_req[a]) + if overall_res_req: + overall_res_req["class"] = "ResourceRequirement" + return cmap(overall_res_req) + class ArvadosWorkflow(Workflow): """Wrap cwltool Workflow to override selected methods.""" - def __init__(self, arvrunner, toolpath_object, **kwargs): - super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs) + def __init__(self, arvrunner, toolpath_object, loadingContext): + super(ArvadosWorkflow, self).__init__(toolpath_object, loadingContext) self.arvrunner = arvrunner - self.work_api = kwargs["work_api"] self.wf_pdh = None + self.dynamic_resource_req = [] + self.static_resource_req = [] + self.wf_reffiles = [] + self.loadingContext = loadingContext - def job(self, joborder, output_callback, **kwargs): - kwargs["work_api"] = self.work_api + def job(self, joborder, output_callback, runtimeContext): req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") if req: with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)): @@ -105,24 +143,85 @@ class ArvadosWorkflow(Workflow): packed = pack(document_loader, workflowobj, uri, self.metadata) + builder = Builder(joborder, + requirements=workflowobj["requirements"], + hints=workflowobj["hints"], + resources={}) + + def visit(item): + for t in ("hints", "requirements"): + if t not in item: + continue + for req in item[t]: + if req["class"] == "ResourceRequirement": + dyn = False + for k in max_res_pars + sum_res_pars: + if k in req: + if isinstance(req[k], basestring): + if item["id"] == "#main": + # only the top-level requirements/hints may contain expressions + self.dynamic_resource_req.append(req) + dyn = True + break + else: + with SourceLine(req, k, WorkflowException): + raise WorkflowException("Non-top-level ResourceRequirement in single container cannot have expressions") + if not dyn: + self.static_resource_req.append(req) + + visit_class(packed["$graph"], ("Workflow", "CommandLineTool"), visit) + + if self.static_resource_req: + self.static_resource_req = [get_overall_res_req(self.static_resource_req)] + upload_dependencies(self.arvrunner, - kwargs.get("name", ""), + runtimeContext.name, document_loader, packed, uri, False) + # Discover files/directories referenced by the + # workflow (mainly "default" values) + visit_class(packed, ("File", "Directory"), self.wf_reffiles.append) + + + if self.dynamic_resource_req: + builder = Builder() + builder.job = joborder + builder.requirements = self.requirements + builder.hints = self.hints + builder.resources = {} + + # Evaluate dynamic resource requirements using current builder + rs = copy.copy(self.static_resource_req) + for dyn_rs in self.dynamic_resource_req: + eval_req = {"class": "ResourceRequirement"} + for a in max_res_pars + sum_res_pars: + if a in dyn_rs: + eval_req[a] = builder.do_eval(dyn_rs[a]) + rs.append(eval_req) + job_res_reqs = [get_overall_res_req(rs)] + else: + job_res_reqs = self.static_resource_req + with Perf(metrics, "subworkflow adjust"): joborder_resolved = copy.deepcopy(joborder) joborder_keepmount = copy.deepcopy(joborder) reffiles = [] - visit_class(joborder_keepmount, ("File", "Directory"), lambda x: reffiles.append(x)) + visit_class(joborder_keepmount, ("File", "Directory"), reffiles.append) + + mapper = ArvPathMapper(self.arvrunner, reffiles+self.wf_reffiles, runtimeContext.basedir, + "/keep/%s", + "/keep/%s/%s") - mapper = ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"], - "/keep/%s", - "/keep/%s/%s", - **kwargs) + # For containers API, we need to make sure any extra + # referenced files (ie referenced by the workflow but + # not in the inputs) are included in the mounts. + if self.wf_reffiles: + runtimeContext = runtimeContext.copy() + runtimeContext.extra_reffiles = copy.deepcopy(self.wf_reffiles) def keepmount(obj): remove_redundant_fields(obj) @@ -158,15 +257,13 @@ class ArvadosWorkflow(Workflow): "inputs": self.tool["inputs"], "outputs": self.tool["outputs"], "stdout": "cwl.output.json", - "requirements": self.requirements+[ + "requirements": self.requirements+job_res_reqs+[ + {"class": "InlineJavascriptRequirement"}, { "class": "InitialWorkDirRequirement", "listing": [{ "entryname": "workflow.cwl", - "entry": { - "class": "File", - "location": "keep:%s/workflow.cwl" % self.wf_pdh - } + "entry": '$({"class": "File", "location": "keep:%s/workflow.cwl"})' % self.wf_pdh }, { "entryname": "cwl.input.yml", "entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${') @@ -176,8 +273,6 @@ class ArvadosWorkflow(Workflow): "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"], "id": "#" }) - kwargs["loader"] = self.doc_loader - kwargs["avsc_names"] = self.doc_schema - return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder_resolved, output_callback, **kwargs) + return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext) else: - return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs) + return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)