def create_job_file(self, job_num, branches):
task = self.task
config = self.job_file_factory.Config()
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2, 4] -> "_0To5"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
config.postfix = postfix
pf = lambda s: "postfix:{}".format(s)
# get the actual wrapper file that will be executed by the remote job
wrapper_file = get_path(task.arc_wrapper_file())
config.executable = os.path.basename(wrapper_file)
# collect task parameters
task_params = task.as_branch(branches[0]).cli_args(exclude={"branch"})
task_params += global_cmdline_args()
# add and remove some arguments
task_params = remove_cmdline_arg(task_params, "--workers", 2)
if task.arc_use_local_scheduler():
task_params = add_cmdline_arg(task_params, "--local-scheduler")
for arg in task.arc_cmdline_args() or []:
if isinstance(arg, tuple):
task_params = add_cmdline_arg(task_params, *arg)
else:
task_params = add_cmdline_arg(task_params, arg)
# job script arguments
job_args = JobArguments(
task_cls=task.__class__,
task_params=task_params,
branches=branches,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.submission_data.attempts.get(job_num, 0)),
)
config.arguments = job_args.join()
# meta infos
config.job_name = task.task_id
config.output_uri = task.arc_output_uri()
# prepare render variables
config.render_variables = {}
# input files
config.input_files = [wrapper_file, law_src_path("job", "job.sh")]
config.render_variables["job_file"] = pf("job.sh")
# add the bootstrap file
bootstrap_file = task.arc_bootstrap_file()
config.input_files.append(bootstrap_file)
config.render_variables["bootstrap_file"] = pf(
os.path.basename(bootstrap_file))
# add the stageout file
stageout_file = task.arc_stageout_file()
if stageout_file:
config.input_files.append(stageout_file)
config.render_variables["stageout_file"] = pf(
os.path.basename(stageout_file))
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
config.input_files.append(dashboard_file)
config.render_variables["dashboard_file"] = pf(
os.path.basename(dashboard_file))
# output files
config.output_files = []
# custom content
config.custom_content = []
# log files
config.log = None
if task.transfer_logs:
log_file = "stdall.txt"
config.stdout = log_file
config.stderr = log_file
config.output_files.append(log_file)
config.render_variables["log_file"] = pf(log_file)
else:
config.stdout = None
config.stderr = None
# task hook
config = task.arc_job_config(config, job_num, branches)
# determine basenames of input files and add that list to the render data
input_basenames = [
pf(os.path.basename(path)) for path in config.input_files
]
config.render_variables["input_files"] = " ".join(input_basenames)
return self.job_file_factory(**config.__dict__)
def create_job_file(self, job_num, branches):
task = self.task
config = self.job_file_factory.Config()
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2, 4] -> "_0To5"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
config.postfix = postfix
pf = lambda s: "postfix:{}".format(s)
# get the actual wrapper file that will be executed by the remote job
wrapper_file = get_path(task.htcondor_wrapper_file())
config.executable = os.path.basename(wrapper_file)
# collect task parameters
task_params = task.as_branch(branches[0]).cli_args(exclude={"branch"})
task_params += global_cmdline_args(
exclude=[("--workers", 1), ("--local-scheduler", 1)])
if task.htcondor_use_local_scheduler():
task_params = add_cmdline_arg(task_params, "--local-scheduler",
"True")
for arg in task.htcondor_cmdline_args() or []:
if isinstance(arg, tuple):
task_params = add_cmdline_arg(task_params, *arg)
else:
task_params = add_cmdline_arg(task_params, arg)
# job script arguments
job_args = JobArguments(
task_cls=task.__class__,
task_params=task_params,
branches=branches,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.submission_data.attempts.get(job_num, 0)),
)
config.arguments = job_args.join()
# prepare render variables
config.render_variables = {}
# input files
config.input_files = [wrapper_file, law_src_path("job", "job.sh")]
config.render_variables["job_file"] = pf("job.sh")
# add the bootstrap file
bootstrap_file = task.htcondor_bootstrap_file()
if bootstrap_file:
config.input_files.append(bootstrap_file)
config.render_variables["bootstrap_file"] = pf(
os.path.basename(bootstrap_file))
# add the stageout file
stageout_file = task.htcondor_stageout_file()
if stageout_file:
config.input_files.append(stageout_file)
config.render_variables["stageout_file"] = pf(
os.path.basename(stageout_file))
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
config.input_files.append(dashboard_file)
config.render_variables["dashboard_file"] = pf(
os.path.basename(dashboard_file))
# output files
config.output_files = []
# custom content
config.custom_content = []
# logging
# we do not use condor's logging mechanism since it requires that the submission directory
# is present when it retrieves logs, and therefore we rely on the job.sh script
config.log = None
config.stdout = None
config.stderr = None
if task.transfer_logs:
log_file = "stdall.txt"
config.output_files.append(log_file)
config.render_variables["log_file"] = pf(log_file)
# we can use condor's file stageout only when the output directory is local
# otherwise, one should use the stageout_file and stageout manually
output_dir = task.htcondor_output_directory()
if isinstance(output_dir, LocalDirectoryTarget):
config.absolute_paths = True
config.custom_content.append(("initialdir", output_dir.path))
else:
del config.output_files[:]
# task hook
config = task.htcondor_job_config(config, job_num, branches)
# determine basenames of input files and add that list to the render data
input_basenames = [
pf(os.path.basename(path)) for path in config.input_files[1:]
]
config.render_variables["input_files"] = " ".join(input_basenames)
return self.job_file_factory(**config.__dict__)
def create_job_file(self, job_num, branches):
task = self.task
config = self.job_file_factory.Config()
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2, 4] -> "_0To5"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
config.postfix = postfix
_postfix = lambda path: self.job_file_factory.postfix_file(
path, postfix)
pf = lambda s: "__law_job_postfix__:{}".format(s)
# collect task parameters
proxy_cmd = ProxyCommand(
task.as_branch(branches[0]),
exclude_task_args={"branch"},
exclude_global_args=["workers", "local-scheduler"])
if task.lsf_use_local_scheduler():
proxy_cmd.add_arg("--local-scheduler", "True", overwrite=True)
for key, value in OrderedDict(task.lsf_cmdline_args()).items():
proxy_cmd.add_arg(key, value, overwrite=True)
# job script arguments
job_args = JobArguments(
task_cls=task.__class__,
task_params=proxy_cmd.build(skip_run=True),
branches=branches,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.submission_data.attempts.get(job_num, 0)),
)
# get the actual wrapper file that will be executed by the remote job
wrapper_file = get_path(task.lsf_wrapper_file())
config.command = "bash {} {}".format(
_postfix(os.path.basename(wrapper_file)), job_args.join())
# meta infos
config.job_name = task.task_id
config.emails = True
# prepare render variables
config.render_variables = {}
# input files
config.input_files = [wrapper_file, law_src_path("job", "job.sh")]
# add the bootstrap file
bootstrap_file = task.lsf_bootstrap_file()
if bootstrap_file:
config.input_files.append(bootstrap_file)
config.render_variables["bootstrap_file"] = pf(
os.path.basename(bootstrap_file))
# add the stageout file
stageout_file = task.lsf_stageout_file()
if stageout_file:
config.input_files.append(stageout_file)
config.render_variables["stageout_file"] = pf(
os.path.basename(stageout_file))
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
config.input_files.append(dashboard_file)
config.render_variables["dashboard_file"] = pf(
os.path.basename(dashboard_file))
# output files
config.output_files = []
# custom content
config.custom_content = []
# logging
# we do not use lsf's logging mechanism since it requires that the submission directory
# is present when it retrieves logs, and therefore we rely on the job.sh script
config.stdout = None
config.stderr = None
if task.transfer_logs:
log_file = "stdall.txt"
config.custom_log_file = log_file
config.render_variables["log_file"] = pf(log_file)
# we can use lsf's file stageout only when the output directory is local
# otherwise, one should use the stageout_file and stageout manually
output_dir = task.lsf_output_directory()
if isinstance(output_dir, LocalDirectoryTarget):
config.absolute_paths = True
config.cwd = output_dir.path
else:
del config.output_files[:]
# task hook
config = task.lsf_job_config(config, job_num, branches)
# determine basenames of input files and add that list to the render data
input_basenames = [
pf(os.path.basename(path)) for path in config.input_files
]
config.render_variables["input_files"] = " ".join(input_basenames)
# build the job file and get the sanitized config
job_file, config = self.job_file_factory(**config.__dict__)
# determine the absolute custom log file if set
abs_log_file = None
if config.custom_log_file and isinstance(output_dir,
LocalDirectoryTarget):
abs_log_file = output_dir.child(config.custom_log_file,
type="f").path
# return job and log files
return {"job": job_file, "log": abs_log_file}
def create_job_file(self, job_num, branches):
task = self.task
config = self.job_file_factory.Config()
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2, 4] -> "_0To5"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
config.postfix = postfix
pf = lambda s: "postfix:{}".format(s)
# executable
config.executable = "bash_wrapper.sh"
# collect task parameters
task_params = task.as_branch(branches[0]).cli_args(exclude={"branch"})
task_params += global_cmdline_args()
# force the local scheduler?
ls_flag = "--local-scheduler"
if ls_flag not in task_params and task.glite_use_local_scheduler():
task_params.append(ls_flag)
# job script arguments
job_args = JobArguments(
task_module=task.__class__.__module__,
task_family=task.task_family,
task_params=task_params,
branches=branches,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.attempts.get(job_num, 0)),
)
config.arguments = job_args.join()
# meta infos
config.output_uri = task.glite_output_uri()
# prepare render variables
config.render_variables = {}
# input files
config.input_files = [
law_src_path("job", "bash_wrapper.sh"),
law_src_path("job", "job.sh")
]
config.render_variables["job_file"] = pf("job.sh")
# add the bootstrap file
bootstrap_file = task.glite_bootstrap_file()
config.input_files.append(bootstrap_file)
config.render_variables["bootstrap_file"] = pf(
os.path.basename(bootstrap_file))
# add the stageout file
stageout_file = task.glite_stageout_file()
if stageout_file:
config.input_files.append(stageout_file)
config.render_variables["stageout_file"] = pf(
os.path.basename(stageout_file))
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
config.input_files.append(dashboard_file)
config.render_variables["dashboard_file"] = pf(
os.path.basename(dashboard_file))
# determine basenames of input files and add that list to the render data
input_basenames = [
pf(os.path.basename(path)) for path in config.input_files
]
config.render_variables["input_files"] = " ".join(input_basenames)
# output files
config.output_files = []
# custom content
config.custom_content = []
# log file
if task.transfer_logs:
log_file = "stdall.txt"
config.stdout = log_file
config.stderr = log_file
config.output_files.append(log_file)
config.render_variables["log_file"] = pf(log_file)
else:
config.stdout = None
config.stderr = None
# task hook
config = task.glite_job_config(config, job_num, branches)
return self.job_file_factory(**config.__dict__)
def create_job_file(self, job_num, branches):
task = self.task
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2, 4] -> "_0To5"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
# create the config
c = self.job_file_factory.Config()
c.input_files = DeprecatedInputFiles()
c.output_files = []
c.render_variables = {}
c.custom_content = []
# get the actual wrapper file that will be executed by the remote job
c.executable = get_path(task.glite_wrapper_file())
c.input_files["executable_file"] = c.executable
law_job_file = law_src_path("job", "law_job.sh")
if c.executable != law_job_file:
c.input_files["job_file"] = law_job_file
# collect task parameters
proxy_cmd = ProxyCommand(
task.as_branch(branches[0]),
exclude_task_args={"branch"},
exclude_global_args=["workers", "local-scheduler"])
if task.glite_use_local_scheduler():
proxy_cmd.add_arg("--local-scheduler", "True", overwrite=True)
for key, value in OrderedDict(task.glite_cmdline_args()).items():
proxy_cmd.add_arg(key, value, overwrite=True)
# job script arguments
job_args = JobArguments(
task_cls=task.__class__,
task_params=proxy_cmd.build(skip_run=True),
branches=branches,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.submission_data.attempts.get(job_num, 0)),
)
c.arguments = job_args.join()
# add the bootstrap file
bootstrap_file = task.glite_bootstrap_file()
if bootstrap_file:
c.input_files["bootstrap_file"] = bootstrap_file
# add the stageout file
stageout_file = task.glite_stageout_file()
if stageout_file:
c.input_files["stageout_file"] = stageout_file
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
c.input_files["dashboard_file"] = dashboard_file
# log file
c.stdout = None
c.stderr = None
if task.transfer_logs:
log_file = "stdall.txt"
c.stdout = log_file
c.stderr = log_file
c.custom_log_file = log_file
# meta infos
c.output_uri = task.glite_output_uri()
# task hook
c = task.glite_job_config(c, job_num, branches)
# build the job file and get the sanitized config
job_file, c = self.job_file_factory(postfix=postfix, **c.__dict__)
# determine the custom log file uri if set
abs_log_file = None
if c.custom_log_file:
abs_log_file = os.path.join(c.output_uri, c.custom_log_file)
# return job and log files
return {"job": job_file, "log": abs_log_file}
def create_job_file(self, job_num, branches):
task = self.task
config = self.job_file_factory.Config()
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2, 4] -> "_0To5"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
config.postfix = postfix
pf = lambda s: "__law_job_postfix__:{}".format(s)
# get the actual wrapper file that will be executed by the remote job
wrapper_file = get_path(task.glite_wrapper_file())
config.executable = os.path.basename(wrapper_file)
# collect task parameters
proxy_cmd = ProxyCommand(task.as_branch(branches[0]), exclude_task_args={"branch"},
exclude_global_args=["workers", "local-scheduler"])
if task.glite_use_local_scheduler():
proxy_cmd.add_arg("--local-scheduler", "True", overwrite=True)
for key, value in OrderedDict(task.glite_cmdline_args()).items():
proxy_cmd.add_arg(key, value, overwrite=True)
# job script arguments
job_args = JobArguments(
task_cls=task.__class__,
task_params=proxy_cmd.build(skip_run=True),
branches=branches,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.submission_data.attempts.get(job_num, 0)),
)
config.arguments = job_args.join()
# meta infos
config.output_uri = task.glite_output_uri()
# prepare render variables
config.render_variables = {}
# input files
config.input_files = [wrapper_file, law_src_path("job", "job.sh")]
config.render_variables["job_file"] = pf("job.sh")
# add the bootstrap file
bootstrap_file = task.glite_bootstrap_file()
config.input_files.append(bootstrap_file)
config.render_variables["bootstrap_file"] = pf(os.path.basename(bootstrap_file))
# add the stageout file
stageout_file = task.glite_stageout_file()
if stageout_file:
config.input_files.append(stageout_file)
config.render_variables["stageout_file"] = pf(os.path.basename(stageout_file))
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
config.input_files.append(dashboard_file)
config.render_variables["dashboard_file"] = pf(os.path.basename(dashboard_file))
# output files
config.output_files = []
# custom content
config.custom_content = []
# log file
if task.transfer_logs:
log_file = "stdall.txt"
config.stdout = log_file
config.stderr = log_file
config.custom_log_file = log_file
config.render_variables["log_file"] = pf(log_file)
else:
config.stdout = None
config.stderr = None
# task hook
config = task.glite_job_config(config, job_num, branches)
# determine basenames of input files and add that list to the render data
input_basenames = [pf(os.path.basename(path)) for path in config.input_files]
config.render_variables["input_files"] = " ".join(input_basenames)
# build the job file and get the sanitized config
job_file, config = self.job_file_factory(**config.__dict__)
# determine the custom log file uri if set
abs_log_file = None
if config.custom_log_file:
abs_log_file = os.path.join(config.output_uri, config.custom_log_file)
# return job and log files
return {"job": job_file, "log": abs_log_file}
def create_job_file(self, job_num, branches):
task = self.task
config = self.job_file_factory.Config()
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2] -> "_0To3"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
config.postfix = postfix
_postfix = lambda path: self.job_file_factory.postfix_file(
path, postfix)
pf = lambda s: "postfix:{}".format(s)
# collect task parameters
task_params = task.as_branch(branches[0]).cli_args(exclude={"branch"})
task_params += global_cmdline_args()
# force the local scheduler?
ls_flag = "--local-scheduler"
if ls_flag not in task_params and task.lsf_use_local_scheduler():
task_params.append(ls_flag)
# job script arguments
job_args = JobArguments(
task_module=task.__class__.__module__,
task_family=task.task_family,
task_params=task_params,
start_branch=branches[0],
end_branch=branches[-1] + 1,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.attempts.get(job_num, 0)),
)
config.command = "bash {} {}".format(_postfix("job.sh"),
job_args.join())
# meta infos
config.job_name = task.task_id
config.emails = True
# prepare render variables
config.render_variables = {}
# input files
config.input_files = [law_src_path("job", "job.sh")]
# add the bootstrap file
bootstrap_file = task.lsf_bootstrap_file()
if bootstrap_file:
config.input_files.append(bootstrap_file)
config.render_variables["bootstrap_file"] = pf(
os.path.basename(bootstrap_file))
# add the stageout file
stageout_file = task.lsf_stageout_file()
if stageout_file:
config.input_files.append(stageout_file)
config.render_variables["stageout_file"] = pf(
os.path.basename(stageout_file))
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
config.input_files.append(dashboard_file)
config.render_variables["dashboard_file"] = pf(
os.path.basename(dashboard_file))
# determine basenames of input files and add that list to the render data
input_basenames = [
pf(os.path.basename(path)) for path in config.input_files
]
config.render_variables["input_files"] = " ".join(input_basenames)
# output files
config.output_files = []
# logging
# we do not use lsf's logging mechanism since it requires that the submission directory
# is present when it retrieves logs, and therefore we rely on the job.sh script
config.stdout = None
config.stderr = None
if task.transfer_logs:
log_file = "stdall.txt"
config.output_files.append(log_file)
config.render_variables["log_file"] = pf(log_file)
# we can use lsf's file stageout only when the output directory is local
# otherwise, one should use the stageout_file and stageout manually
output_dir = task.lsf_output_directory()
if not isinstance(output_dir, LocalDirectoryTarget):
del config.output_files[:]
else:
config.absolute_paths = True
config.cwd = output_dir.path
# task hook
config = task.lsf_job_config(config, job_num, branches)
return self.job_file_factory(**config.__dict__)
def create_job_file(self, job_num, branches):
task = self.task
# the file postfix is pythonic range made from branches, e.g. [0, 1, 2, 4] -> "_0To5"
postfix = "_{}To{}".format(branches[0], branches[-1] + 1)
# create the config
c = self.job_file_factory.Config()
c.input_files = DeprecatedInputFiles()
c.output_files = []
c.render_variables = {}
c.custom_content = []
# get the actual wrapper file that will be executed by the remote job
c.executable = get_path(task.htcondor_wrapper_file())
c.input_files["executable_file"] = c.executable
law_job_file = law_src_path("job", "law_job.sh")
if c.executable != law_job_file:
c.input_files["job_file"] = law_job_file
# collect task parameters
proxy_cmd = ProxyCommand(
task.as_branch(branches[0]),
exclude_task_args={"branch"},
exclude_global_args=["workers", "local-scheduler"])
if task.htcondor_use_local_scheduler():
proxy_cmd.add_arg("--local-scheduler", "True", overwrite=True)
for key, value in OrderedDict(task.htcondor_cmdline_args()).items():
proxy_cmd.add_arg(key, value, overwrite=True)
# job script arguments
job_args = JobArguments(
task_cls=task.__class__,
task_params=proxy_cmd.build(skip_run=True),
branches=branches,
auto_retry=False,
dashboard_data=self.dashboard.remote_hook_data(
job_num, self.submission_data.attempts.get(job_num, 0)),
)
c.arguments = job_args.join()
# add the bootstrap file
bootstrap_file = task.htcondor_bootstrap_file()
if bootstrap_file:
c.input_files["bootstrap_file"] = bootstrap_file
# add the stageout file
stageout_file = task.htcondor_stageout_file()
if stageout_file:
c.input_files["stageout_file"] = stageout_file
# does the dashboard have a hook file?
dashboard_file = self.dashboard.remote_hook_file()
if dashboard_file:
c.input_files["dashboard_file"] = dashboard_file
# logging
# we do not use htcondor's logging mechanism since it might require that the submission
# directory is present when it retrieves logs, and therefore we use a custom log file
c.log = None
c.stdout = None
c.stderr = None
if task.transfer_logs:
c.custom_log_file = "stdall.txt"
# when the output dir is local, we can run within this directory for easier output file
# handling and use absolute paths for input files
output_dir = task.htcondor_output_directory()
output_dir_is_local = isinstance(output_dir, LocalDirectoryTarget)
if output_dir_is_local:
c.absolute_paths = True
c.custom_content.append(("initialdir", output_dir.path))
# task hook
c = task.htcondor_job_config(c, job_num, branches)
# when the output dir is not local, direct output files are not possible
if not output_dir_is_local:
del c.output_files[:]
# build the job file and get the sanitized config
job_file, c = self.job_file_factory(postfix=postfix, **c.__dict__)
# get the location of the custom local log file if any
abs_log_file = None
if output_dir_is_local and c.custom_log_file:
abs_log_file = os.path.join(output_dir.path, c.custom_log_file)
# return job and log files
return {"job": job_file, "log": abs_log_file}
