def cpu_spec_to_float(spec: Union[int, str]) -> float:
if isinstance(spec, str):
mcpu = parse_cpu_in_mcpu(spec)
assert mcpu is not None
return mcpu / 1000
return float(spec)
def __init__(self, batch_id, user, gsa_key, job_spec, format_version):
self.batch_id = batch_id
self.user = user
self.gsa_key = gsa_key
self.job_spec = job_spec
self.format_version = format_version
self.deleted = False
self.token = uuid.uuid4().hex
self.scratch = f'/batch/{self.token}'
self.state = 'pending'
self.error = None
self.start_time = None
self.end_time = None
pvc_size = job_spec.get('pvc_size')
input_files = job_spec.get('input_files')
output_files = job_spec.get('output_files')
copy_volume_mounts = []
main_volume_mounts = []
requester_pays_project = job_spec.get('requester_pays_project')
if job_spec.get('mount_docker_socket'):
main_volume_mounts.append(
'/var/run/docker.sock:/var/run/docker.sock')
self.mount_io = (pvc_size or input_files or output_files)
if self.mount_io:
volume_mount = f'{self.io_host_path()}:/io'
main_volume_mounts.append(volume_mount)
copy_volume_mounts.append(volume_mount)
gcsfuse = job_spec.get('gcsfuse')
self.gcsfuse = gcsfuse
if gcsfuse:
for b in gcsfuse:
main_volume_mounts.append(
f'{self.gcsfuse_path(b["bucket"])}:{b["mount_path"]}:shared'
)
secrets = job_spec.get('secrets')
self.secrets = secrets
if secrets:
for secret in secrets:
volume_mount = f'{self.secret_host_path(secret)}:{secret["mount_path"]}'
main_volume_mounts.append(volume_mount)
# this will be the user gsa-key
if secret.get('mount_in_copy', False):
copy_volume_mounts.append(volume_mount)
env = []
for item in job_spec.get('env', []):
env.append(f'{item["name"]}={item["value"]}')
req_cpu_in_mcpu = parse_cpu_in_mcpu(job_spec['resources']['cpu'])
req_memory_in_bytes = parse_memory_in_bytes(
job_spec['resources']['memory'])
cpu_in_mcpu = adjust_cores_for_memory_request(
req_cpu_in_mcpu, req_memory_in_bytes, worker_config.instance_type)
cpu_in_mcpu = adjust_cores_for_packability(cpu_in_mcpu)
self.cpu_in_mcpu = cpu_in_mcpu
self.memory_in_bytes = cores_mcpu_to_memory_bytes(
self.cpu_in_mcpu, worker_config.instance_type)
self.resources = worker_config.resources(self.cpu_in_mcpu,
self.memory_in_bytes)
# create containers
containers = {}
if input_files:
containers['input'] = copy_container(self, 'input', input_files,
copy_volume_mounts,
self.cpu_in_mcpu,
self.memory_in_bytes,
requester_pays_project)
# main container
main_spec = {
'command': job_spec['command'],
'image': job_spec['image'],
'name': 'main',
'env': env,
'cpu': self.cpu_in_mcpu,
'memory': self.memory_in_bytes,
'volume_mounts': main_volume_mounts
}
port = job_spec.get('port')
if port:
main_spec['port'] = port
timeout = job_spec.get('timeout')
if timeout:
main_spec['timeout'] = timeout
containers['main'] = Container(self, 'main', main_spec)
if output_files:
containers['output'] = copy_container(self, 'output', output_files,
copy_volume_mounts,
self.cpu_in_mcpu,
self.memory_in_bytes,
requester_pays_project)
self.containers = containers
def _run(self,
batch: 'batch.Batch',
dry_run: bool,
verbose: bool,
delete_scratch_on_exit: bool,
**backend_kwargs): # pylint: disable=R0915
"""
Execute a batch.
Warning
-------
This method should not be called directly. Instead, use :meth:`.batch.Batch.run`.
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.
"""
if backend_kwargs:
raise ValueError(f'LocalBackend does not support any of these keywords: {backend_kwargs}')
tmpdir = self._get_scratch_dir()
lines = ['set -e' + ('x' if verbose else ''),
'\n',
'# change cd to tmp directory',
f"cd {tmpdir}",
'\n']
copied_input_resource_files = set()
os.makedirs(tmpdir + '/inputs/', exist_ok=True)
if batch.requester_pays_project:
requester_pays_project = f'-u {batch.requester_pays_project}'
else:
requester_pays_project = ''
def copy_input(job, r):
if isinstance(r, resource.InputResourceFile):
if r not in copied_input_resource_files:
copied_input_resource_files.add(r)
if r._input_path.startswith('gs://'):
return [f'gsutil {requester_pays_project} cp {shq(r._input_path)} {shq(r._get_path(tmpdir))}']
absolute_input_path = os.path.realpath(r._input_path)
dest = r._get_path(tmpdir)
dir = os.path.dirname(dest)
os.makedirs(dir, exist_ok=True)
if job._image is not None: # pylint: disable-msg=W0640
return [f'cp {shq(absolute_input_path)} {shq(dest)}']
return [f'ln -sf {shq(absolute_input_path)} {shq(dest)}']
return []
assert isinstance(r, (resource.JobResourceFile, resource.PythonResult))
return []
def copy_external_output(r):
def _cp(dest):
if not dest.startswith('gs://'):
dest = os.path.abspath(dest)
directory = os.path.dirname(dest)
os.makedirs(directory, exist_ok=True)
return 'cp'
return f'gsutil {requester_pays_project} cp'
if isinstance(r, resource.InputResourceFile):
return [f'{_cp(dest)} {shq(r._input_path)} {shq(dest)}'
for dest in r._output_paths]
assert isinstance(r, (resource.JobResourceFile, resource.PythonResult))
return [f'{_cp(dest)} {r._get_path(tmpdir)} {shq(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(tmpdir)
dest = f'{r._get_path(tmpdir)}.{name}'
symlinks.append(f'ln -sf {shq(src)} {shq(dest)}')
return symlinks
write_inputs = [x for r in batch._input_resources for x in copy_external_output(r)]
if write_inputs:
lines += ["# Write input resources to output destinations"]
lines += write_inputs
lines += ['\n']
for job in batch._jobs:
if isinstance(job, _job.PythonJob):
job._compile(tmpdir, tmpdir)
os.makedirs(f'{tmpdir}/{job._job_id}/', exist_ok=True)
lines.append(f"# {job._job_id}: {job.name if job.name else ''}")
lines += [x for r in job._inputs for x in copy_input(job, r)]
lines += [x for r in job._mentioned for x in symlink_input_resource_group(r)]
resource_defs = [r._declare(tmpdir) for r in job._mentioned]
env = [f'export {k}={v}' for k, v in job._env.items()]
job_shell = job._shell if job._shell else self._DEFAULT_SHELL
defs = '; '.join(resource_defs) + '; ' if resource_defs else ''
joined_env = '; '.join(env) + '; ' if env else ''
cmd = " && ".join(f'{{\n{x}\n}}' for x in job._command)
quoted_job_script = shq(joined_env + defs + cmd)
if job._image:
cpu = f'--cpus={job._cpu}' if job._cpu else ''
memory = job._memory
if memory is not None:
memory_ratios = {'lowmem': 1024**3, 'standard': 4 * 1024**3, 'highmem': 7 * 1024**3}
if memory in memory_ratios:
if job._cpu is not None:
mcpu = parse_cpu_in_mcpu(job._cpu)
if mcpu is not None:
memory = str(int(memory_ratios[memory] * (mcpu / 1000)))
else:
raise BatchException(f'invalid value for cpu: {job._cpu}')
else:
raise BatchException(f'must specify cpu when using {memory} to specify the memory')
memory = f'-m {memory}' if memory else ''
lines.append(f"docker run "
"--entrypoint=''"
f"{self._extra_docker_run_flags} "
f"-v {tmpdir}:{tmpdir} "
f"-w {tmpdir} "
f"{memory} "
f"{cpu} "
f"{job._image} "
f"{job_shell} -c {quoted_job_script}")
else:
lines.append(f"{job_shell} -c {quoted_job_script}")
lines += [x for r in job._external_outputs for x in copy_external_output(r)]
lines += ['\n']
script = "\n".join(lines)
if dry_run:
print(lines)
else:
try:
sp.check_call(script, shell=True)
except sp.CalledProcessError as e:
print(e)
print(e.output)
raise
finally:
if delete_scratch_on_exit:
sp.run(f'rm -rf {tmpdir}', shell=True, check=False)
print('Batch completed successfully!')
def _run(self, batch: 'batch.Batch', dry_run: bool, verbose: bool,
delete_scratch_on_exit: bool, **backend_kwargs) -> None: # pylint: disable=R0915
"""
Execute a batch.
Warning
-------
This method should not be called directly. Instead, use :meth:`.batch.Batch.run`.
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.
"""
if backend_kwargs:
raise ValueError(
f'LocalBackend does not support any of these keywords: {backend_kwargs}'
)
tmpdir = self._get_scratch_dir()
def new_code_block():
return [
'set -e' + ('x' if verbose else ''), '\n',
'# change cd to tmp directory', f"cd {tmpdir}", '\n'
]
def run_code(code):
code = '\n'.join(code)
if dry_run:
print(code)
else:
try:
sp.check_call(code, shell=True)
except sp.CalledProcessError as e:
print(e)
print(e.output)
raise
copied_input_resource_files = set()
os.makedirs(tmpdir + '/inputs/', exist_ok=True)
requester_pays_project_json = orjson.dumps(
batch.requester_pays_project).decode('utf-8')
def copy_input(job, r):
if isinstance(r, resource.InputResourceFile):
if r not in copied_input_resource_files:
copied_input_resource_files.add(r)
input_scheme = url_scheme(r._input_path)
if input_scheme != '':
transfers_bytes = orjson.dumps([{
"from":
r._input_path,
"to":
r._get_path(tmpdir)
}])
transfers = transfers_bytes.decode('utf-8')
return [
f'python3 -m hailtop.aiotools.copy {shq(requester_pays_project_json)} {shq(transfers)}'
]
absolute_input_path = os.path.realpath(
os.path.expanduser(r._input_path))
dest = r._get_path(os.path.expanduser(tmpdir))
dir = os.path.dirname(dest)
os.makedirs(dir, exist_ok=True)
if job._image is not None: # pylint: disable-msg=W0640
return [f'cp {shq(absolute_input_path)} {shq(dest)}']
return [f'ln -sf {shq(absolute_input_path)} {shq(dest)}']
return []
assert isinstance(
r, (resource.JobResourceFile, resource.PythonResult))
return []
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(tmpdir)
dest = f'{r._get_path(tmpdir)}.{name}'
symlinks.append(f'ln -sf {shq(src)} {shq(dest)}')
return symlinks
def transfer_dicts_for_resource_file(
res_file: Union[resource.ResourceFile, resource.PythonResult]
) -> List[dict]:
if isinstance(res_file, resource.InputResourceFile):
source = res_file._input_path
else:
assert isinstance(
res_file,
(resource.JobResourceFile, resource.PythonResult))
source = res_file._get_path(tmpdir)
return [{
"from": source,
"to": dest
} for dest in res_file._output_paths]
try:
input_transfer_dicts = [
transfer_dict for input_resource in batch._input_resources
for transfer_dict in transfer_dicts_for_resource_file(
input_resource)
]
if input_transfer_dicts:
input_transfers = orjson.dumps(input_transfer_dicts).decode(
'utf-8')
code = new_code_block()
code += ["# Write input resources to output destinations"]
code += [
f'python3 -m hailtop.aiotools.copy {shq(requester_pays_project_json)} {shq(input_transfers)}'
]
code += ['\n']
run_code(code)
for job in batch._jobs:
async_to_blocking(job._compile(tmpdir, tmpdir))
os.makedirs(f'{tmpdir}/{job._dirname}/', exist_ok=True)
code = new_code_block()
code.append(f"# {job._job_id}: {job.name if job.name else ''}")
if job._user_code:
code.append('# USER CODE')
user_code = [
f'# {line}' for cmd in job._user_code
for line in cmd.split('\n')
]
code.append('\n'.join(user_code))
code += [x for r in job._inputs for x in copy_input(job, r)]
code += [
x for r in job._mentioned
for x in symlink_input_resource_group(r)
]
env = {**job._env, 'BATCH_TMPDIR': tmpdir}
env_declarations = [f'export {k}={v}' for k, v in env.items()]
joined_env = '; '.join(env_declarations) + '; ' if env else ''
job_shell = job._shell if job._shell else DEFAULT_SHELL
cmd = " && ".join(f'{{\n{x}\n}}' for x in job._wrapper_code)
quoted_job_script = shq(joined_env + cmd)
if job._image:
cpu = f'--cpus={job._cpu}' if job._cpu else ''
memory = job._memory
if memory is not None:
memory_ratios = {
'lowmem': 1024**3,
'standard': 4 * 1024**3,
'highmem': 7 * 1024**3
}
if memory in memory_ratios:
if job._cpu is not None:
mcpu = parse_cpu_in_mcpu(job._cpu)
if mcpu is not None:
memory = str(
int(memory_ratios[memory] *
(mcpu / 1000)))
else:
raise BatchException(
f'invalid value for cpu: {job._cpu}')
else:
raise BatchException(
f'must specify cpu when using {memory} to specify the memory'
)
memory = f'-m {memory}' if memory else ''
else:
memory = ''
code.append(f"docker run "
"--entrypoint=''"
f"{self._extra_docker_run_flags} "
f"-v {tmpdir}:{tmpdir} "
f"-w {tmpdir} "
f"{memory} "
f"{cpu} "
f"{job._image} "
f"{job_shell} -c {quoted_job_script}")
else:
code.append(f"{job_shell} -c {quoted_job_script}")
output_transfer_dicts = [
transfer_dict for output_resource in job._external_outputs
for transfer_dict in transfer_dicts_for_resource_file(
output_resource)
]
output_transfers = orjson.dumps(output_transfer_dicts).decode(
'utf-8')
code += [
f'python3 -m hailtop.aiotools.copy {shq(requester_pays_project_json)} {shq(output_transfers)}'
]
code += ['\n']
run_code(code)
finally:
if delete_scratch_on_exit:
sp.run(f'rm -rf {tmpdir}', shell=True, check=False)
print('Batch completed successfully!')
