Source code for toil.test.src.promisedRequirementTest

# Copyright (C) 2015-2021 Regents of the University of California
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
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import logging
import os
import time

import toil.test.batchSystems.batchSystemTest as batchSystemTest
from toil.batchSystems.mesos.test import MesosTestSupport
from toil.job import Job, PromisedRequirement
from toil.lib.retry import retry_flaky_test
from toil.test import needs_mesos, slow

log = logging.getLogger(__name__)

[docs] class hidden: """ Hide abstract base class from unittest's test case loader. """
[docs] class AbstractPromisedRequirementsTest(batchSystemTest.hidden.AbstractBatchSystemJobTest): """An abstract base class for testing Toil workflows with promised requirements."""
[docs] @slow def testConcurrencyDynamic(self): """ Asserts that promised core resources are allocated properly using a dynamic Toil workflow """ for coresPerJob in self.allocatedCores: log.debug('Testing %d cores per job with CPU count %d', coresPerJob, self.cpuCount) tempDir = self._createTempDir('testFiles') counterPath = self.getCounterPath(tempDir) root = Job.wrapJobFn(maxConcurrency, self.cpuCount, counterPath, coresPerJob, cores=1, memory='1M', disk='1M') values = Job.Runner.startToil(root, self.getOptions(tempDir)) maxValue = max(values) self.assertLessEqual(maxValue, self.cpuCount // coresPerJob)
[docs] @slow @retry_flaky_test(prepare=[batchSystemTest.hidden.AbstractBatchSystemJobTest.tearDown, batchSystemTest.hidden.AbstractBatchSystemJobTest.setUp]) def testConcurrencyStatic(self): """ Asserts that promised core resources are allocated properly using a static DAG """ for coresPerJob in self.allocatedCores: log.debug('Testing %d cores per job with CPU count %d', coresPerJob, self.cpuCount) tempDir = self._createTempDir('testFiles') counterPath = self.getCounterPath(tempDir) root = Job() one = Job.wrapFn(getOne, cores=0.1, memory='32M', disk='1M') thirtyTwoMb = Job.wrapFn(getThirtyTwoMb, cores=0.1, memory='32M', disk='1M') root.addChild(one) root.addChild(thirtyTwoMb) for _ in range(self.cpuCount): root.addFollowOn(Job.wrapFn(batchSystemTest.measureConcurrency, counterPath, cores=PromisedRequirement(lambda x: x * coresPerJob, one.rv()), memory=PromisedRequirement(thirtyTwoMb.rv()), disk='1M')) Job.Runner.startToil(root, self.getOptions(tempDir)) _, maxValue = batchSystemTest.getCounters(counterPath) self.assertLessEqual(maxValue, self.cpuCount // coresPerJob)
[docs] def getOptions(self, tempDir, caching=True): options = super().getOptions(tempDir) # defaultCores defaults to 1 - this is coincidentally the core requirement relied upon by this # test, so we change defaultCores to 2 to make the test more strict options.defaultCores = 2 options.caching = caching return options
[docs] def getCounterPath(self, tempDir): """ Returns path to a counter file :param str tempDir: path to test directory :return: path to counter file """ counterPath = os.path.join(tempDir, 'counter') batchSystemTest.resetCounters(counterPath) minValue, maxValue = batchSystemTest.getCounters(counterPath) assert (minValue, maxValue) == (0, 0) return counterPath
[docs] def testPromisesWithJobStoreFileObjects(self, caching=True): """ Check whether FileID objects are being pickled properly when used as return values of functions. Then ensure that lambdas of promised FileID objects can be used to describe the requirements of a subsequent job. This type of operation will be used commonly in Toil scripts. :return: None """ file1 = 1024 file2 = 512 F1 = Job.wrapJobFn(_writer, file1) F2 = Job.wrapJobFn(_writer, file2) G = Job.wrapJobFn(_follower, file1 + file2, disk=PromisedRequirement(lambda x, y: x.size + y.size, F1.rv(), F2.rv())) F1.addChild(F2) F2.addChild(G) Job.Runner.startToil(F1, self.getOptions(self._createTempDir('testFiles'), caching=caching))
[docs] def testPromisesWithNonCachingFileStore(self): self.testPromisesWithJobStoreFileObjects(caching=False)
[docs] @slow def testPromiseRequirementRaceStatic(self): """ Checks for a race condition when using promised requirements and child job functions. """ A = Job.wrapJobFn(logDiskUsage, 'A', sleep=5, disk=PromisedRequirement(1024)) B = Job.wrapJobFn(logDiskUsage, 'B', disk=PromisedRequirement(lambda x: x + 1024, A.rv())) A.addChild(B) Job.Runner.startToil(A, self.getOptions(self._createTempDir('testFiles')))
def _writer(job, fileSize): ''' Write a local file and return the FileID obtained from running writeGlobalFile on it. :param job job: job :param int fileSize: Size of the file in bytes :returns: the result of writeGlobalFile on a locally created file :rtype: job.FileID ''' with open(job.fileStore.getLocalTempFileName(), 'wb') as fH: fH.write(os.urandom(fileSize)) return job.fileStore.writeGlobalFile( def _follower(job, expectedDisk): """ This job follows the _writer jobs and ensures the expected disk is used. :param job job: job :param expectedDisk: Expect disk to be used by this job :return: None """ assert job.disk == expectedDisk
[docs] def maxConcurrency(job, cpuCount, filename, coresPerJob): """ Returns the max number of concurrent tasks when using a PromisedRequirement instance to allocate the number of cores per job. :param int cpuCount: number of available cpus :param str filename: path to counter file :param int coresPerJob: number of cores assigned to each job :return int max concurrency value: """ one = job.addChildFn(getOne, cores=0.1, memory='32M', disk='1M') thirtyTwoMb = job.addChildFn(getThirtyTwoMb, cores=0.1, memory='32M', disk='1M') values = [] for _ in range(cpuCount): value = job.addFollowOnFn(batchSystemTest.measureConcurrency, filename, cores=PromisedRequirement(lambda x: x * coresPerJob, one.rv()), memory=PromisedRequirement(thirtyTwoMb.rv()), disk='1M').rv() values.append(value) return values
[docs] def getOne(): return 1
[docs] def getThirtyTwoMb(): return '32M'
[docs] def logDiskUsage(job, funcName, sleep=0): """ Logs the job's disk usage to master and sleeps for specified amount of time. :return: job function's disk usage """ diskUsage = job.disk job.fileStore.logToMaster(f'{funcName}: {diskUsage}') time.sleep(sleep) return diskUsage
[docs] class SingleMachinePromisedRequirementsTest(hidden.AbstractPromisedRequirementsTest): """ Tests against the SingleMachine batch system """
[docs] def getBatchSystemName(self): return "single_machine"
[docs] def tearDown(self): pass
[docs] @needs_mesos class MesosPromisedRequirementsTest(hidden.AbstractPromisedRequirementsTest, MesosTestSupport): """ Tests against the Mesos batch system """
[docs] def getOptions(self, tempDir, caching=True): options = super().getOptions(tempDir, caching=caching) options.mesos_endpoint = 'localhost:5050' return options
[docs] def getBatchSystemName(self): self._startMesos(self.cpuCount) return "mesos"
[docs] def tearDown(self): self._stopMesos()