def _run(self, batch: 'batch.Batch', dry_run: bool, verbose: bool, delete_scratch_on_exit: bool, wait: bool = True, open: bool = False, disable_progress_bar: bool = False, callback: Optional[str] = None, token: Optional[str] = None, **backend_kwargs): # pylint: disable-msg=too-many-statements """Execute a batch. Warning ------- This method should not be called directly. Instead, use :meth:`.batch.Batch.run` and pass :class:`.ServiceBackend` specific arguments as key-word arguments. Parameters ---------- batch: Batch to execute. dry_run: If `True`, don't execute code. verbose: If `True`, print debugging output. delete_scratch_on_exit: If `True`, delete temporary directories with intermediate files. wait: If `True`, wait for the batch to finish executing before returning. open: If `True`, open the UI page for the batch. disable_progress_bar: If `True`, disable the progress bar. callback: If not `None`, a URL that will receive at most one POST request after the entire batch completes. token: If not `None`, a string used for idempotency of batch submission. """ if backend_kwargs: raise ValueError(f'ServiceBackend does not support any of these keywords: {backend_kwargs}') build_dag_start = time.time() uid = uuid.uuid4().hex[:6] remote_tmpdir = f'gs://{self._bucket_name}/batch/{uid}' local_tmpdir = f'/io/batch/{uid}' default_image = 'ubuntu:18.04' attributes = copy.deepcopy(batch.attributes) if batch.name is not None: attributes['name'] = batch.name bc_batch = self._batch_client.create_batch(attributes=attributes, callback=callback, token=token, cancel_after_n_failures=batch._cancel_after_n_failures) n_jobs_submitted = 0 used_remote_tmpdir = False job_to_client_job_mapping: Dict[_job.Job, bc.Job] = {} jobs_to_command = {} commands = [] bash_flags = 'set -e' + ('x' if verbose else '') activate_service_account = 'gcloud -q auth activate-service-account ' \ '--key-file=/gsa-key/key.json' def copy_input(r): if isinstance(r, resource.InputResourceFile): return [(r._input_path, r._get_path(local_tmpdir))] assert isinstance(r, (resource.JobResourceFile, resource.PythonResult)) return [(r._get_path(remote_tmpdir), r._get_path(local_tmpdir))] def copy_internal_output(r): assert isinstance(r, (resource.JobResourceFile, resource.PythonResult)) return [(r._get_path(local_tmpdir), r._get_path(remote_tmpdir))] def copy_external_output(r): if isinstance(r, resource.InputResourceFile): return [(r._input_path, dest) for dest in r._output_paths] assert isinstance(r, (resource.JobResourceFile, resource.PythonResult)) return [(r._get_path(local_tmpdir), dest) for dest in r._output_paths] def symlink_input_resource_group(r): symlinks = [] if isinstance(r, resource.ResourceGroup) and r._source is None: for name, irf in r._resources.items(): src = irf._get_path(local_tmpdir) dest = f'{r._get_path(local_tmpdir)}.{name}' symlinks.append(f'ln -sf {shq(src)} {shq(dest)}') return symlinks write_external_inputs = [x for r in batch._input_resources for x in copy_external_output(r)] if write_external_inputs: def _cp(src, dst): return f'gsutil -m cp -R {shq(src)} {shq(dst)}' write_cmd = f''' {bash_flags} {activate_service_account} {' && '.join([_cp(*files) for files in write_external_inputs])} ''' if dry_run: commands.append(write_cmd) else: j = bc_batch.create_job(image='gcr.io/google.com/cloudsdktool/cloud-sdk:310.0.0-alpine', command=['/bin/bash', '-c', write_cmd], attributes={'name': 'write_external_inputs'}) jobs_to_command[j] = write_cmd n_jobs_submitted += 1 for job in batch._jobs: if isinstance(job, _job.PythonJob): if job._image is None: version = sys.version_info if version.major != 3 or version.minor not in (6, 7, 8): raise BatchException( f"You must specify 'image' for Python jobs if you are using a Python version other than 3.6, 3.7, or 3.8 (you are using {version})") job._image = f'hailgenetics/python-dill:{version.major}.{version.minor}-slim' job._compile(local_tmpdir, remote_tmpdir) inputs = [x for r in job._inputs for x in copy_input(r)] outputs = [x for r in job._internal_outputs for x in copy_internal_output(r)] if outputs: used_remote_tmpdir = True outputs += [x for r in job._external_outputs for x in copy_external_output(r)] symlinks = [x for r in job._mentioned for x in symlink_input_resource_group(r)] env_vars = { **job._env, **{r._uid: r._get_path(local_tmpdir) for r in job._mentioned}} if job._image is None: if verbose: print(f"Using image '{default_image}' since no image was specified.") make_local_tmpdir = f'mkdir -p {local_tmpdir}/{job._job_id}' job_command = [cmd.strip() for cmd in job._command] prepared_job_command = (f'{{\n{x}\n}}' for x in job_command) cmd = f''' {bash_flags} {make_local_tmpdir} {"; ".join(symlinks)} {" && ".join(prepared_job_command)} ''' if dry_run: commands.append(cmd) continue parents = [job_to_client_job_mapping[j] for j in job._dependencies] attributes = copy.deepcopy(job.attributes) if job.attributes else dict() if job.name: attributes['name'] = job.name resources: Dict[str, Any] = {} if job._cpu: resources['cpu'] = job._cpu if job._memory: resources['memory'] = job._memory if job._storage: resources['storage'] = job._storage if job._machine_type: resources['machine_type'] = job._machine_type if job._preemptible is not None: resources['preemptible'] = job._preemptible image = job._image if job._image else default_image image_ref = parse_docker_image_reference(image) if not is_google_registry_domain(image_ref.domain) and image_ref.name() not in HAIL_GENETICS_IMAGES: warnings.warn(f'Using an image {image} not in GCR. ' f'Jobs may fail due to Docker Hub rate limits.') j = bc_batch.create_job(image=image, command=[job._shell if job._shell else self._DEFAULT_SHELL, '-c', cmd], parents=parents, attributes=attributes, resources=resources, input_files=inputs if len(inputs) > 0 else None, output_files=outputs if len(outputs) > 0 else None, always_run=job._always_run, timeout=job._timeout, gcsfuse=job._gcsfuse if len(job._gcsfuse) > 0 else None, env=env_vars, requester_pays_project=batch.requester_pays_project, mount_tokens=True) n_jobs_submitted += 1 job_to_client_job_mapping[job] = j jobs_to_command[j] = cmd if dry_run: print("\n\n".join(commands)) return None if delete_scratch_on_exit and used_remote_tmpdir: parents = list(jobs_to_command.keys()) rm_cmd = f'gsutil -m rm -r {remote_tmpdir}' cmd = f''' {bash_flags} {activate_service_account} {rm_cmd} ''' j = bc_batch.create_job( image='gcr.io/google.com/cloudsdktool/cloud-sdk:310.0.0-alpine', command=['/bin/bash', '-c', cmd], parents=parents, attributes={'name': 'remove_tmpdir'}, always_run=True) jobs_to_command[j] = cmd n_jobs_submitted += 1 if verbose: print(f'Built DAG with {n_jobs_submitted} jobs in {round(time.time() - build_dag_start, 3)} seconds.') submit_batch_start = time.time() bc_batch = bc_batch.submit(disable_progress_bar=disable_progress_bar) jobs_to_command = {j.id: cmd for j, cmd in jobs_to_command.items()} if verbose: print(f'Submitted batch {bc_batch.id} with {n_jobs_submitted} jobs in {round(time.time() - submit_batch_start, 3)} seconds:') for jid, cmd in jobs_to_command.items(): print(f'{jid}: {cmd}') print('') deploy_config = get_deploy_config() url = deploy_config.url('batch', f'/batches/{bc_batch.id}') print(f'Submitted batch {bc_batch.id}, see {url}') if open: webbrowser.open(url) if wait: print(f'Waiting for batch {bc_batch.id}...') status = bc_batch.wait() print(f'batch {bc_batch.id} complete: {status["state"]}') return bc_batch
def test_parse_docker_image_reference(): x = parse_docker_image_reference('animage') assert x.domain is None assert x.path == 'animage' assert x.tag is None assert x.digest is None assert x.name() == 'animage' assert str(x) == 'animage' x = parse_docker_image_reference('hailgenetics/animage') assert x.domain == 'hailgenetics' assert x.path == 'animage' assert x.tag is None assert x.digest is None assert x.name() == 'hailgenetics/animage' assert str(x) == 'hailgenetics/animage' x = parse_docker_image_reference('localhost:5000/animage') assert x.domain == 'localhost:5000' assert x.path == 'animage' assert x.tag is None assert x.digest is None assert x.name() == 'localhost:5000/animage' assert str(x) == 'localhost:5000/animage' x = parse_docker_image_reference('localhost:5000/a/b/name') assert x.domain == 'localhost:5000' assert x.path == 'a/b/name' assert x.tag is None assert x.digest is None assert x.name() == 'localhost:5000/a/b/name' assert str(x) == 'localhost:5000/a/b/name' x = parse_docker_image_reference('localhost:5000/a/b/name:tag') assert x.domain == 'localhost:5000' assert x.path == 'a/b/name' assert x.tag == 'tag' assert x.digest is None assert x.name() == 'localhost:5000/a/b/name' assert str(x) == 'localhost:5000/a/b/name:tag' x = parse_docker_image_reference( 'localhost:5000/a/b/name:tag@sha256:abc123') assert x.domain == 'localhost:5000' assert x.path == 'a/b/name' assert x.tag == 'tag' assert x.digest == 'sha256:abc123' assert x.name() == 'localhost:5000/a/b/name' assert str(x) == 'localhost:5000/a/b/name:tag@sha256:abc123' x = parse_docker_image_reference('localhost:5000/a/b/name@sha256:abc123') assert x.domain == 'localhost:5000' assert x.path == 'a/b/name' assert x.tag is None assert x.digest == 'sha256:abc123' assert x.name() == 'localhost:5000/a/b/name' assert str(x) == 'localhost:5000/a/b/name@sha256:abc123' x = parse_docker_image_reference('name@sha256:abc123') assert x.domain is None assert x.path == 'name' assert x.tag is None assert x.digest == 'sha256:abc123' assert x.name() == 'name' assert str(x) == 'name@sha256:abc123' x = parse_docker_image_reference('gcr.io/hail-vdc/batch-worker:123fds312') assert x.domain == 'gcr.io' assert x.path == 'hail-vdc/batch-worker' assert x.tag == '123fds312' assert x.digest is None assert x.name() == 'gcr.io/hail-vdc/batch-worker' assert str(x) == 'gcr.io/hail-vdc/batch-worker:123fds312' x = parse_docker_image_reference( 'us-docker.pkg.dev/my-project/my-repo/test-image') assert x.domain == 'us-docker.pkg.dev' assert x.path == 'my-project/my-repo/test-image' assert x.tag is None assert x.digest is None assert x.name() == 'us-docker.pkg.dev/my-project/my-repo/test-image' assert str(x) == 'us-docker.pkg.dev/my-project/my-repo/test-image'
async def _async_run( self, batch: 'batch.Batch', dry_run: bool, verbose: bool, delete_scratch_on_exit: bool, wait: bool = True, open: bool = False, disable_progress_bar: bool = False, callback: Optional[str] = None, token: Optional[str] = None, **backend_kwargs): # pylint: disable-msg=too-many-statements if backend_kwargs: raise ValueError( f'ServiceBackend does not support any of these keywords: {backend_kwargs}' ) build_dag_start = time.time() uid = uuid.uuid4().hex[:6] batch_remote_tmpdir = f'{self.remote_tmpdir}{uid}' local_tmpdir = f'/io/batch/{uid}' default_image = 'ubuntu:20.04' attributes = copy.deepcopy(batch.attributes) if batch.name is not None: attributes['name'] = batch.name bc_batch = self._batch_client.create_batch( attributes=attributes, callback=callback, token=token, cancel_after_n_failures=batch._cancel_after_n_failures) n_jobs_submitted = 0 used_remote_tmpdir = False job_to_client_job_mapping: Dict[_job.Job, bc.Job] = {} jobs_to_command = {} commands = [] bash_flags = 'set -e' + ('x' if verbose else '') def copy_input(r): if isinstance(r, resource.InputResourceFile): return [(r._input_path, r._get_path(local_tmpdir))] assert isinstance( r, (resource.JobResourceFile, resource.PythonResult)) return [(r._get_path(batch_remote_tmpdir), r._get_path(local_tmpdir))] def copy_internal_output(r): assert isinstance( r, (resource.JobResourceFile, resource.PythonResult)) return [(r._get_path(local_tmpdir), r._get_path(batch_remote_tmpdir))] def copy_external_output(r): if isinstance(r, resource.InputResourceFile): return [(r._input_path, dest) for dest in r._output_paths] assert isinstance( r, (resource.JobResourceFile, resource.PythonResult)) return [(r._get_path(local_tmpdir), dest) for dest in r._output_paths] def symlink_input_resource_group(r): symlinks = [] if isinstance(r, resource.ResourceGroup) and r._source is None: for name, irf in r._resources.items(): src = irf._get_path(local_tmpdir) dest = f'{r._get_path(local_tmpdir)}.{name}' symlinks.append(f'ln -sf {shq(src)} {shq(dest)}') return symlinks write_external_inputs = [ x for r in batch._input_resources for x in copy_external_output(r) ] if write_external_inputs: transfers_bytes = orjson.dumps([{ "from": src, "to": dest } for src, dest in write_external_inputs]) transfers = transfers_bytes.decode('utf-8') write_cmd = [ 'python3', '-m', 'hailtop.aiotools.copy', 'null', transfers ] if dry_run: commands.append(' '.join(shq(x) for x in write_cmd)) else: j = bc_batch.create_job( image=HAIL_GENETICS_HAIL_IMAGE, command=write_cmd, attributes={'name': 'write_external_inputs'}) jobs_to_command[j] = ' '.join(shq(x) for x in write_cmd) n_jobs_submitted += 1 pyjobs = [j for j in batch._jobs if isinstance(j, _job.PythonJob)] for job in pyjobs: if job._image is None: version = sys.version_info if version.major != 3 or version.minor not in (6, 7, 8): raise BatchException( f"You must specify 'image' for Python jobs if you are using a Python version other than 3.6, 3.7, or 3.8 (you are using {version})" ) job._image = f'hailgenetics/python-dill:{version.major}.{version.minor}-slim' with tqdm(total=len(batch._jobs), desc='upload code', disable=disable_progress_bar) as pbar: async def compile_job(job): used_remote_tmpdir = await job._compile(local_tmpdir, batch_remote_tmpdir, dry_run=dry_run) pbar.update(1) return used_remote_tmpdir used_remote_tmpdir_results = await bounded_gather( *[functools.partial(compile_job, j) for j in batch._jobs], parallelism=150) used_remote_tmpdir |= any(used_remote_tmpdir_results) for job in tqdm(batch._jobs, desc='create job objects', disable=disable_progress_bar): inputs = [x for r in job._inputs for x in copy_input(r)] outputs = [ x for r in job._internal_outputs for x in copy_internal_output(r) ] if outputs: used_remote_tmpdir = True outputs += [ x for r in job._external_outputs for x in copy_external_output(r) ] symlinks = [ x for r in job._mentioned for x in symlink_input_resource_group(r) ] if job._image is None: if verbose: print( f"Using image '{default_image}' since no image was specified." ) make_local_tmpdir = f'mkdir -p {local_tmpdir}/{job._dirname}' job_command = [cmd.strip() for cmd in job._wrapper_code] prepared_job_command = (f'{{\n{x}\n}}' for x in job_command) cmd = f''' {bash_flags} {make_local_tmpdir} {"; ".join(symlinks)} {" && ".join(prepared_job_command)} ''' user_code = '\n\n'.join(job._user_code) if job._user_code else None if dry_run: formatted_command = f''' ================================================================================ # Job {job._job_id} {f": {job.name}" if job.name else ''} -------------------------------------------------------------------------------- ## USER CODE -------------------------------------------------------------------------------- {user_code} -------------------------------------------------------------------------------- ## COMMAND -------------------------------------------------------------------------------- {cmd} ================================================================================ ''' commands.append(formatted_command) continue parents = [job_to_client_job_mapping[j] for j in job._dependencies] attributes = copy.deepcopy( job.attributes) if job.attributes else {} if job.name: attributes['name'] = job.name resources: Dict[str, Any] = {} if job._cpu: resources['cpu'] = job._cpu if job._memory: resources['memory'] = job._memory if job._storage: resources['storage'] = job._storage if job._machine_type: resources['machine_type'] = job._machine_type if job._preemptible is not None: resources['preemptible'] = job._preemptible image = job._image if job._image else default_image image_ref = parse_docker_image_reference(image) if image_ref.hosted_in('dockerhub') and image_ref.name( ) not in HAIL_GENETICS_IMAGES: warnings.warn(f'Using an image {image} from Docker Hub. ' f'Jobs may fail due to Docker Hub rate limits.') env = {**job._env, 'BATCH_TMPDIR': local_tmpdir} j = bc_batch.create_job( image=image, command=[ job._shell if job._shell else DEFAULT_SHELL, '-c', cmd ], parents=parents, attributes=attributes, resources=resources, input_files=inputs if len(inputs) > 0 else None, output_files=outputs if len(outputs) > 0 else None, always_run=job._always_run, timeout=job._timeout, cloudfuse=job._cloudfuse if len(job._cloudfuse) > 0 else None, env=env, requester_pays_project=batch.requester_pays_project, mount_tokens=True, user_code=user_code) n_jobs_submitted += 1 job_to_client_job_mapping[job] = j jobs_to_command[j] = cmd if dry_run: print("\n\n".join(commands)) return None if delete_scratch_on_exit and used_remote_tmpdir: parents = list(jobs_to_command.keys()) j = bc_batch.create_job(image=HAIL_GENETICS_HAIL_IMAGE, command=[ 'python3', '-m', 'hailtop.aiotools.delete', batch_remote_tmpdir ], parents=parents, attributes={'name': 'remove_tmpdir'}, always_run=True) jobs_to_command[j] = cmd n_jobs_submitted += 1 if verbose: print( f'Built DAG with {n_jobs_submitted} jobs in {round(time.time() - build_dag_start, 3)} seconds.' ) submit_batch_start = time.time() batch_handle = bc_batch.submit( disable_progress_bar=disable_progress_bar) jobs_to_command = {j.id: cmd for j, cmd in jobs_to_command.items()} if verbose: print( f'Submitted batch {batch_handle.id} with {n_jobs_submitted} jobs in {round(time.time() - submit_batch_start, 3)} seconds:' ) for jid, cmd in jobs_to_command.items(): print(f'{jid}: {cmd}') print('') deploy_config = get_deploy_config() url = deploy_config.url('batch', f'/batches/{batch_handle.id}') print(f'Submitted batch {batch_handle.id}, see {url}') if open: webbrowser.open(url) if wait: print(f'Waiting for batch {batch_handle.id}...') status = batch_handle.wait() print(f'batch {batch_handle.id} complete: {status["state"]}') return batch_handle