def __init__(self,
base,
bases=None,
gfal_options=None,
transfer_config=None,
atomic_contexts=False,
retries=0,
retry_delay=0):
object.__init__(self)
# cache for gfal context objects and transfer parameters per pid for thread safety
self._contexts = {}
self._transfer_parameters = {}
# convert base(s) to list for round-robin
self.base = make_list(base)
self.bases = {k: make_list(v)
for k, v in six.iteritems(bases)} if bases else {}
# prepare gfal options
self.gfal_options = gfal_options or {}
# prepare transfer config
self.transfer_config = transfer_config or {}
self.transfer_config.setdefault("checksum_check", False)
self.transfer_config.setdefault("overwrite", True)
self.transfer_config.setdefault("nbstreams", 1)
# other configs
self.atomic_contexts = atomic_contexts
self.retries = retries
self.retry_delay = retry_delay
def fetch(self, rpaths, lpaths=None, cache=True, **kwargs):
# alias
caches = cache if self.cache else False
multi = isinstance(rpaths, (list, tuple, set))
# check arguments
rpaths = make_list(rpaths)
n = len(rpaths)
if lpaths is None:
lpaths = [None] * n
else:
lpaths = make_list(lpaths)
caches = make_list(caches)
if len(caches) == 1:
caches *= n
if n != len(lpaths):
raise ValueError("rpaths and lpaths count must match")
if n != len(caches):
raise ValueError("rpaths and cache count must match")
if not n:
return [] if multi else None
fetch = lambda tpl: self._fetch(tpl[0], tpl[1], cache=tpl[2], **kwargs)
tpls = zip(rpaths, lpaths, caches)
if not self.pool:
results = map(fetch, tpls)
else:
results = self.pool.map(fetch, tpls)
return results if multi else results[0]
def put(self, lpaths, rpaths, cache=True, **kwargs):
# alias
caches = cache if self.cache else False
# check arguments
rpaths = make_list(rpaths)
lpaths = make_list(lpaths)
n = len(rpaths)
caches = make_list(caches)
if len(caches) == 1:
caches *= n
if n != len(lpaths):
raise ValueError("rpaths and lpaths count must match")
if n != len(caches):
raise ValueError("rpaths and cache count must match")
if not n:
return
put = lambda tpl: self._put(tpl[0], tpl[1], cache=tpl[2], **kwargs)
tpls = zip(lpaths, rpaths, caches)
if not self.pool:
map(put, tpls)
else:
self.pool.map(put, tpls)
def fetch(self,
rpaths=None,
pattern=None,
lpaths=None,
lbase=None,
**kwargs):
if rpaths is None:
rpaths = self.listdir(pattern=pattern)
lpaths = None
else:
rpaths = [rpath.strip("/") for rpath in make_list(rpaths)]
full_rpaths = [os.path.join(self.path, rpath) for rpath in rpaths]
if lpaths is None:
if lbase is not None:
lpaths = [os.path.join(lbase, rpath) for rpath in rpaths]
else:
lpaths = make_list(lpaths)
for i, lpath in enumerate(lpaths):
if isinstance(lpath, FileSystemTarget):
lpaths[i] = lpath.path
lpaths = self.fs.fetch(full_rpaths, lpaths=lpaths, **kwargs)
return dict(zip(rpaths, lpaths))
def __init__(self,
base=None,
bases=None,
retries=0,
retry_delay=0,
random_base=True,
**kwargs):
super(RemoteFileInterface, self).__init__()
# convert base(s) to list for random selection
base = make_list(base or [])
bases = {k: make_list(b)
for k, b in six.iteritems(bases)} if bases else {}
# at least one base in expected
if len(base) == 0:
raise Exception(
"{} expected at least one base path, received none".format(
self.__class__.__name__))
# expand variables in base and bases
self.base = list(map(os.path.expandvars, base))
self.bases = {
k: list(map(os.path.expandvars, b))
for k, b in six.iteritems(bases)
}
# store other attributes
self.retries = retries
self.retry_delay = retry_delay
self.random_base = random_base
def submit(self, job_file, ce=None, delegation_id=None, retries=0, retry_delay=3, silent=False):
# default arguments
if ce is None:
ce = self.ce
if delegation_id is None:
delegation_id = self.delegation_id
# check arguments
if not ce:
raise ValueError("ce must not be empty")
# prepare round robin for ces and delegations
ce = make_list(ce)
if delegation_id:
delegation_id = make_list(delegation_id)
if len(ce) != len(delegation_id):
raise Exception("numbers of CEs ({}) and delegation ids ({}) do not match".format(
len(ce), len(delegation_id)))
# get the job file location as the submission command is run it the same directory
job_file_dir, job_file_name = os.path.split(os.path.abspath(job_file))
# define the actual submission in a loop to simplify retries
while True:
# build the command
i = random.randint(0, len(ce) - 1)
cmd = ["glite-ce-job-submit", "-r", ce[i]]
if delegation_id:
cmd += ["-D", delegation_id[i]]
cmd += [job_file_name]
cmd = quote_cmd(cmd)
# run the command
# glite prints everything to stdout
logger.debug("submit glite job with command '{}'".format(cmd))
code, out, _ = interruptable_popen(cmd, shell=True, executable="/bin/bash",
stdout=subprocess.PIPE, stderr=sys.stderr, cwd=job_file_dir)
# in some cases, the return code is 0 but the ce did not respond with a valid id
if code == 0:
job_id = out.strip().split("\n")[-1].strip()
if not self.submission_job_id_cre.match(job_id):
code = 1
out = "bad job id '{}' from output:\n{}".format(job_id, out)
# retry or done?
if code == 0:
return job_id
else:
logger.debug("submission of glite job '{}' failed with code {}:\n{}".format(
code, job_file, out))
if retries > 0:
retries -= 1
time.sleep(retry_delay)
continue
elif silent:
return None
else:
raise Exception("submission of glite job '{}' failed:\n{}".format(
job_file, out))
def req_params(cls, inst, _exclude=None, _prefer_cli=None, **kwargs):
# common/intersection params
params = luigi.util.common_params(inst, cls)
# determine parameters to exclude
_exclude = set() if _exclude is None else set(make_list(_exclude))
# also use this class' req and req_get sets
# and the req and req_set sets of the instance's class
_exclude.update(cls.exclude_params_req, cls.exclude_params_req_get)
_exclude.update(inst.exclude_params_req, inst.exclude_params_req_set)
# remove excluded parameters
for name in list(params.keys()):
if multi_match(name, _exclude, any):
del params[name]
# add kwargs
params.update(kwargs)
# remove params that are preferably set via cli class arguments
if _prefer_cli:
cls_args = []
prefix = cls.get_task_family() + "_"
if luigi.cmdline_parser.CmdlineParser.get_instance():
for key in global_cmdline_values().keys():
if key.startswith(prefix):
cls_args.append(key[len(prefix):])
for name in make_list(_prefer_cli):
if name in params and name in cls_args:
del params[name]
return params
def put(self, srcpath, dstpath):
srcpaths = make_list(srcpath)
dstpaths = make_list(dstpath)
if len(srcpaths) != len(dstpaths):
raise ValueError("srcpath(s) and dstpath(s) must have equal lengths")
for srcpath, dstpath in zip(srcpaths, dstpaths):
shutil.copy2(srcpath, dstpath)
def _law_run_inst(cls, inst, _exclude=None, _replace=None, _global=None, _run_kwargs=None):
# get the cli arguments
args = inst.cli_args(exclude=_exclude, replace=_replace)
args = sum((make_list(tpl) for tpl in args.items()), [])
# add global parameters when given
if _global:
args.extend([str(arg) for arg in make_list(_global)])
# build the full command
cmd = [cls.get_task_family()] + args
# run it
return law_run(cmd, **(_run_kwargs or {}))
def cancel(self, job_id, pool=None, scheduler=None, silent=False):
# default arguments
if pool is None:
pool = self.pool
if scheduler is None:
scheduler = self.scheduler
# build the command
cmd = ["condor_rm"]
if pool:
cmd += ["-pool", pool]
if scheduler:
cmd += ["-name", scheduler]
cmd += make_list(job_id)
cmd = quote_cmd(cmd)
# run it
logger.debug("cancel htcondor job(s) with command '{}'".format(cmd))
code, out, err = interruptable_popen(cmd,
shell=True,
executable="/bin/bash",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# check success
if code != 0 and not silent:
raise Exception(
"cancellation of htcondor job(s) '{}' failed with code {}:\n{}"
.format(job_id, code, err))
def submit_batch(self, job_files, threads=None, callback=None, **kwargs):
"""
Submits a batch of jobs given by *job_files* via a thread pool of size *threads* which
defaults to its instance attribute. When *callback* is set, it is invoked after each
successful job submission with the job number (starting from 0) and the result object. All
other *kwargs* are passed the :py:meth:`submit`.
The return value is a list containing the return values of the particular :py:meth:`submit`
calls, in an order that corresponds to *job_files*. When an exception was raised during a
submission, this exception is added to the returned list.
"""
# default arguments
threads = threads or self.threads
def _callback(i):
return (lambda r: callback(i, r)) if callable(callback) else None
# threaded processing
pool = ThreadPool(max(threads, 1))
results = [pool.apply_async(self.submit, (job_file,), kwargs, callback=_callback(i))
for i, job_file in enumerate(job_files)]
pool.close()
pool.join()
# store return values or errors
outputs = []
for res in results:
try:
outputs += make_list(res.get())
except Exception as e:
outputs.append(e)
return outputs
def cleanup(self, job_id, job_list=None, silent=False):
# default arguments
if job_list is None:
job_list = self.job_list
# build the command
cmd = ["arcclean"]
if job_list:
cmd += ["-j", job_list]
cmd += make_list(job_id)
cmd = quote_cmd(cmd)
# run it
logger.debug("cleanup arc job(s) with command '{}'".format(cmd))
code, out, _ = interruptable_popen(cmd,
shell=True,
executable="/bin/bash",
stdout=subprocess.PIPE,
stderr=sys.stderr)
# check success
if code != 0 and not silent:
# glite prints everything to stdout
raise Exception(
"cleanup of arc job(s) '{}' failed with code {}:\n{}".format(
job_id, code, out))
def cancel(self, job_id, queue=None, silent=False):
# default arguments
if queue is None:
queue = self.queue
# build the command
cmd = ["bkill"]
if queue:
cmd += ["-q", queue]
cmd += make_list(job_id)
cmd = quote_cmd(cmd)
# run it
logger.debug("cancel lsf job(s) with command '{}'".format(cmd))
code, out, err = interruptable_popen(cmd,
shell=True,
executable="/bin/bash",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# check success
if code != 0 and not silent:
raise Exception(
"cancellation of lsf job(s) '{}' failed with code {}:\n{}".
format(code, job_id, err))
def submit_batch(self, job_files, threads=None, callback=None, **kwargs):
# default arguments
threads = threads or self.threads
def _callback(i):
return (lambda r: callback(r, i)) if callable(callback) else None
# threaded processing
pool = ThreadPool(max(threads, 1))
results = [
pool.apply_async(self.submit, (job_file, ),
kwargs,
callback=_callback(i))
for i, job_file in enumerate(job_files)
]
pool.close()
pool.join()
# store return values or errors
outputs = []
for res in results:
try:
outputs += make_list(res.get())
except Exception as e:
outputs.append(e)
return outputs
def cli_args(self, exclude=None, replace=None):
exclude = set() if exclude is None else set(make_list(exclude))
# always exclude interactive parameters
exclude |= set(self.interactive_params)
return super(Task, self).cli_args(exclude=exclude, replace=replace)
def query(self, job_id, silent=False):
multi = isinstance(job_id, (list, tuple))
job_ids = make_list(job_id)
# build the command and run it
cmd = ["glite-ce-job-status", "-n", "-L", "0"] + job_ids
logger.debug("query glite job(s) with command '{}'".format(cmd))
code, out, _ = interruptable_popen(cmd, stdout=subprocess.PIPE, stderr=sys.stderr)
# handle errors
if code != 0:
if silent:
return None
else:
# glite prints everything to stdout
raise Exception("status query of glite job(s) '{}' failed:\n{}".format(job_id, out))
# parse the output and extract the status per job
query_data = self.parse_query_output(out)
# compare to the requested job ids and perform some checks
for _job_id in job_ids:
if _job_id not in query_data:
if not multi:
if silent:
return None
else:
raise Exception("glite job(s) '{}' not found in query response".format(
job_id))
else:
query_data[_job_id] = self.job_status_dict(job_id=_job_id, status=self.FAILED,
error="job not found in query response")
return query_data if multi else query_data[job_id]
def _docker_run_cmd(self):
"""
Part of the "docker run" command that is common to env requests and run.
"""
cmd = ["docker", "run"]
# rm flag
cmd.extend(["--rm"])
# use the pid namespace of the host so killing the outer process will stop the container
cmd.extend(["--pid", "host"])
# task-specific arguments
if self.task:
# user flag
sandbox_user = self.task.sandbox_user()
if sandbox_user:
if not isinstance(sandbox_user,
(tuple, list)) or len(sandbox_user) != 2:
raise Exception("sandbox_user() must return 2-tuple")
cmd.extend(["-u", "{}:{}".format(*sandbox_user)])
# add args configured on the task
args_getter = getattr(self.task, "docker_args", None)
if callable(args_getter):
cmd.extend(make_list(args_getter()))
return cmd
def cancel(self, job_id, partition=None, silent=False):
# default arguments
if partition is None:
partition = self.partition
# build the command
cmd = ["scancel"]
if partition:
cmd += ["--partition", partition]
cmd += make_list(job_id)
cmd = quote_cmd(cmd)
# run it
logger.debug("cancel slurm job(s) with command '{}'".format(cmd))
code, out, err = interruptable_popen(cmd,
shell=True,
executable="/bin/bash",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# check success
if code != 0 and not silent:
raise Exception(
"cancellation of slurm job(s) '{}' failed with code {}:\n{}".
format(job_id, code, err))
def submit(self,
job_file,
ce=None,
job_list=None,
retries=0,
retry_delay=3,
silent=False):
# default arguments
ce = ce or self.ce
job_list = job_list or self.job_list
# check arguments
if not ce:
raise ValueError("ce must not be empty")
ce = make_list(ce)
# get the job file location as the submission command is run it the same directory
job_file_dir, job_file_name = os.path.split(os.path.abspath(job_file))
# define the actual submission in a loop to simplify retries
while True:
# build the command
cmd = ["arcsub", "-c", random.choice(ce)]
if job_list:
cmd += ["-j", job_list]
cmd += [job_file_name]
# run the command
logger.debug("submit arc job with command '{}'".format(cmd))
code, out, _ = interruptable_popen(cmd,
stdout=subprocess.PIPE,
stderr=sys.stderr,
cwd=job_file_dir)
# in some cases, the return code is 0 but the ce did not respond with a valid id
if code == 0:
m = self.submission_job_id_cre.match(out.strip())
if m:
job_id = m.group(1)
else:
code = 1
out = "cannot find job id output:\n{}".format(out)
# retry or done?
if code == 0:
return job_id
else:
logger.debug("submission of arc job '{}' failed:\n{}".format(
job_file, out))
if retries > 0:
retries -= 1
time.sleep(retry_delay)
continue
elif silent:
return None
else:
raise Exception(
"submission of arc job '{}' failed:\n{}".format(
job_file, out))
def hadd_cmd(input_paths, output_path):
cmd = ["hadd", "-n", "0"]
cmd.extend(["-d", cwd.path])
if hadd_args:
cmd.extend(make_list(hadd_args))
cmd.append(output_path)
cmd.extend(input_paths)
return quote_cmd(cmd)
def split_remote_kwargs(cls, kwargs, include=None, skip=None):
"""
Takes keyword arguments *kwargs*, splits them into two separate dictionaries depending on
their content, and returns them in a tuple. The first one will contain arguments related to
potential remote file operations (e.g. ``"cache"`` or ``"retries"``), while the second one
will contain all remaining arguments. This function is used internally to decide which
arguments to pass to target formatters. *include* (*skip*) can be a list of argument keys
that are considered as well (ignored).
"""
include = make_list(include) if include else []
skip = make_list(skip) if skip else []
transfer_kwargs = {
name: kwargs.pop(name)
for name in ["cache", "prefer_cache", "retries", "retry_delay"] +
include if name in kwargs and name not in skip
}
return transfer_kwargs, kwargs
def req_params(cls, inst, _exclude=None, _prefer_cli=None, **kwargs):
_exclude = set() if _exclude is None else set(make_list(_exclude))
# always exclude interactive parameters
_exclude |= set(inst.interactive_params)
return super(Task, cls).req_params(inst, _exclude=_exclude, _prefer_cli=_prefer_cli,
**kwargs)
def cli_args(self, exclude=None, replace=None):
exclude = set() if exclude is None else set(make_list(exclude))
if self.is_branch():
exclude |= self.exclude_params_branch
else:
exclude |= self.exclude_params_workflow
return super(BaseWorkflow, self).cli_args(exclude=exclude, replace=replace)
def cancel(self, job_id, silent=False):
# build the command and run it
cmd = ["glite-ce-job-cancel", "-N"] + make_list(job_id)
logger.debug("cancel glite job(s) with command '{}'".format(cmd))
code, out, _ = interruptable_popen(cmd, stdout=subprocess.PIPE, stderr=sys.stderr)
# check success
if code != 0 and not silent:
# glite prints everything to stdout
raise Exception("cancellation of glite job(s) '{}' failed:\n{}".format(job_id, out))
def cmd(self, task, task_cmd):
# get args for the docker command as configured in the task
docker_args = make_list(
getattr(task, "docker_args", self.default_docker_args))
# destination of all forwarded paths
forward_dst = "/law_forward"
def dst(*args):
return os.path.join(forward_dst, *(str(arg) for arg in args))
# path variables to adjust
pathvars = defaultdict(list)
# forward the law executable
pathvars["PATH"].append(dst("bin"))
docker_args.extend(["-v", which("law") + ":" + dst("bin", "law")])
# forward python directories of law and dependencies
pathvars["PYTHONPATH"].append(dst("py"))
for mod in (six, luigi, law):
path = mod.__file__
dirname = os.path.dirname(path)
name, ext = os.path.splitext(os.path.basename(path))
if name == "__init__":
vsrc = dirname
vdst = dst("py", os.path.basename(dirname))
else:
vsrc = os.path.join(dirname, name) + ".py"
vdst = dst("py", name) + ".py"
docker_args.extend(["-v", "%s:%s" % (vsrc, vdst)])
# update paths in task_cmd
for name, paths in pathvars.items():
task_cmd = "export %s=$%s:%s; " % (name, name,
":".join(paths)) + task_cmd
# forward the luigi config file
for p in luigi.configuration.LuigiConfigParser._config_paths[::-1]:
if os.path.exists(p):
docker_args.extend(["-v", "%s:%s" % (p, dst("luigi.cfg"))])
task_cmd = "export LUIGI_CONFIG_PATH=%s; " % dst(
"luigi.cfg") + task_cmd
break
# prevent python from writing byte code files
task_cmd = "export PYTHONDONTWRITEBYTECODE=1; " + task_cmd
cmd = "docker run {docker_args} {image} bash -c '{task_cmd}'"
cmd = cmd.format(docker_args=" ".join(docker_args),
image=self.image,
task_cmd=task_cmd)
return cmd
def _singularity_exec_cmd(self):
cmd = ["singularity", "exec"]
# task-specific argiments
if self.task:
# add args configured on the task
args_getter = getattr(self.task, "singularity_args", None)
if callable(args_getter):
cmd.extend(make_list(args_getter()))
return cmd
def query(self, job_id, queue=None, silent=False):
# default arguments
if queue is None:
queue = self.queue
chunking = isinstance(job_id, (list, tuple))
job_ids = make_list(job_id)
# build the command
cmd = ["bjobs"]
if self.lsf_v912:
cmd.append("-noheader")
if queue:
cmd += ["-q", queue]
cmd += job_ids
cmd = quote_cmd(cmd)
# run it
logger.debug("query lsf job(s) with command '{}'".format(cmd))
code, out, err = interruptable_popen(cmd,
shell=True,
executable="/bin/bash",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# handle errors
if code != 0:
if silent:
return None
else:
raise Exception(
"status query of lsf job(s) '{}' failed with code {}:\n{}".
format(job_id, code, err))
# parse the output and extract the status per job
query_data = self.parse_query_output(out)
# compare to the requested job ids and perform some checks
for _job_id in job_ids:
if _job_id not in query_data:
if not chunking:
if silent:
return None
else:
raise Exception(
"lsf job(s) '{}' not found in query response".
format(job_id))
else:
query_data[_job_id] = self.job_status_dict(
job_id=_job_id,
status=self.FAILED,
error="job not found in query response")
return query_data if chunking else query_data[job_id]
def __init__(self,
base,
bases=None,
gfal_options=None,
transfer_config=None,
atomic_contexts=False,
retries=0,
retry_delay=0,
random_base=True):
object.__init__(self)
# cache for gfal context objects and transfer parameters per pid for thread safety
self._contexts = {}
self._transfer_parameters = {}
# convert base(s) to list for random selection
self.base = make_list(base)
self.bases = {k: make_list(b)
for k, b in six.iteritems(bases)} if bases else {}
# expand variables in base and bases
self.base = list(map(os.path.expandvars, self.base))
self.bases = {
k: list(map(os.path.expandvars, b))
for k, b in six.iteritems(self.bases)
}
# prepare gfal options
self.gfal_options = gfal_options or {}
# prepare transfer config
self.transfer_config = transfer_config or {}
self.transfer_config.setdefault("checksum_check", False)
self.transfer_config.setdefault("overwrite", True)
self.transfer_config.setdefault("nbstreams", 1)
# other configs
self.atomic_contexts = atomic_contexts
self.retries = retries
self.retry_delay = retry_delay
self.random_base = random_base
def query(self, job_id, job_list=None, silent=False):
# default arguments
if job_list is None:
job_list = self.job_list
chunking = isinstance(job_id, (list, tuple))
job_ids = make_list(job_id)
# build the command
cmd = ["arcstat"]
if job_list:
cmd += ["-j", job_list]
cmd += job_ids
cmd = quote_cmd(cmd)
# run it
logger.debug("query arc job(s) with command '{}'".format(cmd))
code, out, _ = interruptable_popen(cmd,
shell=True,
executable="/bin/bash",
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
# handle errors
if code != 0:
if silent:
return None
else:
# glite prints everything to stdout
raise Exception(
"status query of arc job(s) '{}' failed with code {}:\n{}".
format(job_id, code, out))
# parse the output and extract the status per job
query_data = self.parse_query_output(out)
# compare to the requested job ids and perform some checks
for _job_id in job_ids:
if _job_id not in query_data:
if not chunking:
if silent:
return None
else:
raise Exception(
"arc job(s) '{}' not found in query response".
format(job_id))
else:
query_data[_job_id] = self.job_status_dict(
job_id=_job_id,
status=self.FAILED,
error="job not found in query response")
return query_data if chunking else query_data[job_id]
def put(self, lpaths, rpaths=None, **kwargs):
lpaths = make_list(lpaths)
for i, lpath in enumerate(lpaths):
if isinstance(lpath, FileSystemTarget):
lpaths[i] = lpath.path
if rpaths is None:
full_rpaths = [os.path.join(self.path, os.path.basename(lpath.rstrip("/"))) \
for lpath in lpaths]
else:
rpaths = make_list(rpaths)
full_rpaths = []
for i, rpath in enumerate(rpaths):
if isinstance(rpath, RemoteTarget):
full_rpaths.append(rpath.path)
else:
full_rpaths.append(
os.path.join(self.path, rpath.strip("/")))
self.fs.put(lpaths, full_rpaths, **kwargs)
