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How to use wait_for_all_workers method in lisa

Best Python code snippet using lisa_python

test_wsgi_latest.py

Source:test_wsgi_latest.py

...57        self.podf = os.path.join(self.revdir, "1491", "_pod.json")58        self.hdlr = None59        self.resp = []60    def tearDown(self):61        self.svc.wait_for_all_workers(300)62        self.tf.clean()63    def gethandler(self, path, env):64        return wsgi.LatestHandler(path, self.svc, env, self.start, "secret")65    def test_do_POST(self):66        req = {67            'REQUEST_METHOD': "POST",68            'CONTENT_TYPE': 'application/json',69            'PATH_INFO': '/pdr/latest',70            'HTTP_AUTHORIZATION': 'Bearer secret'71        }72        self.hdlr = self.gethandler('', req)73        with open(self.podf) as fd:74            req['wsgi.input'] = fd75            body = self.hdlr.handle()76        self.assertIn("201", self.resp[0])77        self.assertEquals(body, [])78        self.assertTrue(os.path.isdir(os.path.join(self.bagparent,"mdbags",self.midasid)))79        self.svc.wait_for_all_workers(300)80        self.assertTrue(os.path.isfile(os.path.join(self.bagparent,"nrdserv",81                                                    self.midasid+".json")))82    def test_do_private_POST(self):83        req = {84            'REQUEST_METHOD': "POST",85            'CONTENT_TYPE': 'application/json',86            'PATH_INFO': '/pdr/latest',87            'HTTP_AUTHORIZATION': 'Bearer secret'88        }89        self.hdlr = self.gethandler('', req)90        pod = None91        with open(self.podf) as fd:92            pod = json.load(fd)93        req['wsgi.input'] = StringIO(json.dumps(pod))94        body = self.hdlr.handle()95        self.assertIn("201", self.resp[0])96        self.assertEquals(body, [])97        bagdir = os.path.join(self.bagparent,"mdbags",self.midasid)98        self.assertTrue(os.path.isdir(bagdir))99        self.svc.wait_for_all_workers(300)100        self.assertTrue(os.path.isfile(os.path.join(self.bagparent,"nrdserv",101                                                    self.midasid+".json")))102        # now turn it private103        pod['accessLevel'] = "non-public"104        self.resp = []105        req['wsgi.input'] = StringIO(json.dumps(pod))106        body = self.hdlr.handle()107        self.assertTrue(not os.path.isdir(bagdir))108        self.svc.wait_for_all_workers(300)109        self.assertTrue(not os.path.isfile(os.path.join(self.bagparent,"nrdserv",110                                                        self.midasid+".json")))111    def test_block_private_clobber(self):112        # first do a normal POST to create a submission113        req = {114            'REQUEST_METHOD': "POST",115            'CONTENT_TYPE': 'application/json',116            'PATH_INFO': '/pdr/latest',117            'HTTP_AUTHORIZATION': 'Bearer secret'118        }119        self.hdlr = self.gethandler('', req)120        pod = None121        with open(self.podf) as fd:122            pod = json.load(fd)123        req['wsgi.input'] = StringIO(json.dumps(pod))124        body = self.hdlr.handle()125        self.assertIn("201", self.resp[0])126        self.assertEquals(body, [])127        bagdir = os.path.join(self.bagparent,"mdbags",self.midasid)128        self.assertTrue(os.path.isdir(bagdir))129        self.svc.wait_for_all_workers(300)130        # now try to clobber it131        self.resp = []132        req = {133            'REQUEST_METHOD': "POST",134            'CONTENT_TYPE': 'application/json',135            'PATH_INFO': '/pdr/latest',136            'HTTP_AUTHORIZATION': 'Bearer secret'137        }138        self.hdlr = self.gethandler('', req)139        pod['identifier'] = ""140        pod['accessLevel'] = "non-public"141        req['wsgi.input'] = StringIO(json.dumps(pod))142        body = self.hdlr.handle()143        self.assertIn("400", self.resp[0])...

test_wsgi_compdelbug.py

Source:test_wsgi_compdelbug.py

...77        self.sipdir = os.path.join(self.upldir, "7213")78        self.hdlr = None79        self.resp = []80    def tearDown(self):81        self.svc.wait_for_all_workers(300)82        self.tf.clean()83    def gethandler(self, path, env):84        return wsgi.LatestHandler(path, self.svc, env, self.start, "secret")85    def test_comp_delete_bug(self):86        req = {87            'REQUEST_METHOD': "POST",88            'CONTENT_TYPE': 'application/json',89            'PATH_INFO': '/pdr/latest',90            'HTTP_AUTHORIZATION': 'Bearer secret'91        }92        self.hdlr = self.gethandler('', req)93        94        podf = os.path.join(self.sipdir, "pod1.json")95        with open(podf) as fd:96            req['wsgi.input'] = fd97            body = self.hdlr.handle()98        self.assertIn("201", self.resp[0])99        self.assertEquals(body, [])100        self.assertTrue(os.path.isdir(self.bagdir))101        self.assertTrue(os.path.isdir(self.mddir))102        self.svc.wait_for_all_workers(300)103        self.assertTrue(os.path.isfile(os.path.join(self.workdir,"nrdserv",104                                                    self.midasid+".json")))105        self.assertTrue(os.path.isdir(os.path.join(self.mddir,106                                                   "RegistryFederationFigure.pptx.sha256")))107        self.assertTrue(os.path.isdir(os.path.join(self.mddir,108                                                   "RegistryFederationFigure.pptx")))109        self.assertTrue(not os.path.exists(os.path.join(self.mddir, "res-md.xsd.sha256")))110        self.assertTrue(not os.path.exists(os.path.join(self.mddir, "res-md.xsd")))111        self.assertTrue(not os.path.exists(os.path.join(self.mddir, "k+_data.txt.sha256")))112        self.assertTrue(not os.path.exists(os.path.join(self.mddir, "k+_data.txt")))113        podf = os.path.join(self.sipdir, "pod2.json")114        with open(podf) as fd:115            req['wsgi.input'] = fd116            body = self.hdlr.handle()117        self.assertIn("201", self.resp[0])118        self.assertEquals(body, [])119        self.svc.wait_for_all_workers(300)120        # new file added but old file was not deleted121        self.assertTrue(os.path.isdir(os.path.join(self.mddir, "res-md.xsd.sha256")))122        self.assertTrue(os.path.isdir(os.path.join(self.mddir, "res-md.xsd")))123        self.assertTrue(os.path.isdir(os.path.join(self.mddir,124                                                   "RegistryFederationFigure.pptx.sha256")))125        self.assertTrue(os.path.isdir(os.path.join(self.mddir,126                                                   "RegistryFederationFigure.pptx")))127        self.assertTrue(not os.path.exists(os.path.join(self.mddir, "k+_data.txt.sha256")))128        self.assertTrue(not os.path.exists(os.path.join(self.mddir, "k+_data.txt")))129        podf = os.path.join(self.sipdir, "pod3.json")130        with open(podf) as fd:131            req['wsgi.input'] = fd132            body = self.hdlr.handle()133        self.assertIn("201", self.resp[0])134        self.assertEquals(body, [])135        self.svc.wait_for_all_workers(300)136        # new file added but old files were not deleted137        self.assertTrue(os.path.isdir(os.path.join(self.mddir, "k+_data.txt.sha256")))138        self.assertTrue(os.path.isdir(os.path.join(self.mddir, "k+_data.txt")))139        self.assertTrue(os.path.isdir(os.path.join(self.mddir, "res-md.xsd.sha256")))140        self.assertTrue(os.path.isdir(os.path.join(self.mddir, "res-md.xsd")))141        self.assertTrue(os.path.isdir(os.path.join(self.mddir,142                                                   "RegistryFederationFigure.pptx.sha256")))143        self.assertTrue(os.path.isdir(os.path.join(self.mddir,144                                                   "RegistryFederationFigure.pptx")))145        146        147        148if __name__ == '__main__':149    test.main()

lsf_cluster_example.py

Source:lsf_cluster_example.py

1"""2Example code to launch a dask cluster, when you aren't using flyemflows.3This example is not related to flyemflows per se.4It's just a simple example for new dask users, showing how to spin5up a dask distributed cluster on LSF, using LSFCluster() from dask_jobqueue.6(Normally when you run a Workflow using flyemflows,7the cluster is automatically started for you, so there is8no need to use this code in that case.)9For an example dask configuration to use with LSFCluster,10see example-dask-config.yaml11To run this example, start ipython like this:12    $ export DASK_CONFIG=example-dask-config.yaml13    $ ipython14And then paste this code into the terminal.15"""16import time17import getpass18import dask19import dask.config20import dask.bag as db21from distributed import Client22def init_cluster(num_workers, wait_for_all_workers=True):23    """24    Start up a dask cluster, optionally wait until all workers have been launched,25    and then return the resulting distributed.Client object.26    27    Args:28        num_workers:29            How many workers to launch.30        wait_for_all_workers:31            If True, pause until all workers have been launched before returning.32            Otherwise, just wait for a single worker to launch.33    34    Returns:35        distributed.Client36    """37    # Local import: LSFCluster probably isn't importable on your local machine,38    # so it's nice to avoid importing it when you're just running local tests without a cluster.39    from dask_jobqueue import LSFCluster40    cluster = LSFCluster(ip='0.0.0.0')41    cluster.scale(num_workers)42    43    required_workers = 144    if wait_for_all_workers:45        required_workers = num_workers46        47    client = Client(cluster)48    while (wait_for_all_workers and49           client.status == "running" and50           len(cluster.scheduler.workers) < required_workers):51        print(f"Waiting for {required_workers - len(cluster.scheduler.workers)} workers...")52        time.sleep(1.0)53    54    print(f'Dashboard running at {client.cluster.dashboard_link}')55    return client56def main():57    USER = getpass.getuser()58    # See example-dask-config.yaml for explanations.59    dask.config.update(dask.config.config,60                       {'jobqueue':61                          {'lsf':62                            {'cores': 1,63                             'memory': '15GB',64                             'walltime': '01:00',65                             'log-directory': 'dask-logs',66                             'local-directory': f'/scratch/{USER}',67                             'use-stdin': True    # Implementation detail regarding how bsub is called by dask-jobqueue.68                                                  # Under Janelia's LSF configuration, this must be set to 'True'.69                       }}})70    71    client = init_cluster(2)72    73    try:74        def double(x):75            return 2*x76    77        bag = db.from_sequence(range(100))78        doubled = bag.map(double).compute()79        print(doubled)80    81    finally:82        client.close()83        client.cluster.close()84if __name__ == "__main__":...

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