def prepare_pbs_files(self, pbs_module):
"""
:type pbs_module: scripts.pbs.modules.pbs_tarkil_cesnet_cz
:rtype: list[(str, PBSModule)]
"""
jobs = list()
for p in self.proc:
case = ConfigCase(dict(
proc=p,
time_limit=self.time_limit,
memory_limit=self.memory_limit,
tmp='exec-parallel'
), None)
pbs_run = pbs_module.Module(case)
pbs_run.queue = self.arg_options.get('queue', True)
pbs_run.ppn = self.arg_options.get('ppn', 1)
pbs_content = self.create_pbs_job_content(pbs_module, case)
IO.write(case.fs.pbs_script, pbs_content)
qsub_command = pbs_run.get_pbs_command(case.fs.pbs_script)
jobs.append((qsub_command, pbs_run))
return jobs
def finish_pbs_exec(job, batch):
"""
Upon PBS finish determine Job exit
:rtype: scripts.serialization.PyPyResult
:type job: scripts.pbs.job.Job
"""
job.is_active = False
try:
result = load_pypy(job.case.fs.dump_output)
except Exception as e:
# no output file was generated assuming it went wrong
job.status = JobState.EXIT_ERROR
Printer.all.err('Job {} ended (no output file found). Case: {}', job, job.full_name)
Printer.all.out(' pbs output: ')
Printer.all.raw(format_n_lines(IO.read(job.case.fs.pbs_output), False))
return
# check result
if result.returncode == 0:
job.status = JobState.EXIT_OK
Printer.all.suc('Job {}({}) ended', job, job.full_name)
else:
job.status = JobState.EXIT_ERROR
Printer.all.err('Job {}({}) ended', job, job.full_name)
if result.returncode != 0 or batch:
with Printer.all.with_level(1):
Printer.all.raw(format_n_lines(IO.read(result.output), result.returncode == 0))
return result
def finish_pbs_runtest(job, batch):
"""
Upon PBS runtest finish determine Job exit
:type job: scripts.pbs.job.Job
:rtype: ResultParallelThreads
"""
job.is_active = False
try:
runner = load_runtest(job.case.fs.dump_output)
except:
# no output file was generated assuming it went wrong
job.status = JobState.EXIT_ERROR
Printer.all.err('Job {} ended (no output file found). Case: {}', job, job.full_name)
Printer.all.out(' pbs output: ')
Printer.all.raw(format_n_lines(IO.read(job.case.fs.pbs_output), False))
return
job.status = JobState.EXIT_OK if runner.returncode == 0 else JobState.EXIT_ERROR
for thread in runner.threads:
StatusPrinter.print_test_result(thread)
if thread.returncode != 0 or batch:
with Printer.all.with_level():
Printer.all.out('Log file {}', job.case.fs.job_output)
Printer.all.raw(format_n_lines(IO.read(job.case.fs.job_output), thread.returncode == 0))
# print status line only if pbs job container more cases
if len(runner.threads) > 1:
Printer.all.sep()
StatusPrinter.print_runner_stat(runner)
Printer.all.sep()
return runner
def compare(self, reference_filepath, other_filepath, **kwargs):
"""
Method can do anything as long as int value is returned
:param reference_filepath:
:param other_filepath:
:param kwargs:
:return:
"""
reference_content = IO.read(
Paths.abspath(reference_filepath)
)
other_content = IO.read(
Paths.abspath(other_filepath)
)
self.output.write("In case of emergency,")
self.output.write(" you can provide details on what went wrong")
self.output.write(" using self.output.write method")
self.output.write("")
self.output.write("Error while comparing files \n{} \n{}"
.format(reference_filepath, other_filepath))
# must return return-code!
return 1
def on_complete(self, pypy=None):
if pypy.executor.broken:
return
if self.log_file:
IO.write(self.log_file, self.content)
enabled = False
if self.policy == self.POLICY_ALWAYS:
enabled = True
elif self.policy == self.POLICY_BATCH_OR_ERROR:
enabled = pypy.with_error() or (not Printer.batched.is_muted())
elif self.policy == self.POLICY_ERROR_ONLY:
enabled = pypy.with_error()
if enabled:
with Printer.all.with_level():
if self.pypy.full_output:
Printer.all.sep()
Printer.all.out('Output from file {self.pypy.full_output}'.format(**locals()))
if not Printer.batched.is_muted():
Printer.batched.raw(format_n_lines(self.content, pypy.was_successful()))
if not Printer.console.is_muted():
Printer.console.raw(format_n_lines(self.content, pypy.was_successful()))
def on_complete(self, pypy=None):
if pypy.executor.broken:
return
if self.log_file:
IO.write(self.log_file, self.content)
enabled = False
if self.policy == self.POLICY_ALWAYS:
enabled = True
elif self.policy == self.POLICY_BATCH_OR_ERROR:
enabled = pypy.with_error() or (not Printer.batched.is_muted())
elif self.policy == self.POLICY_ERROR_ONLY:
enabled = pypy.with_error()
if enabled:
with Printer.all.with_level():
if self.pypy.full_output:
Printer.all.sep()
Printer.all.out(
'Output from file {self.pypy.full_output}'.format(
**locals()))
if not Printer.batched.is_muted():
Printer.batched.raw(
format_n_lines(self.content, pypy.was_successful()))
if not Printer.console.is_muted():
Printer.console.raw(
format_n_lines(self.content, pypy.was_successful()))
def test_pbs_mode(self):
# this test can be only tested on PBS server
do_work(parser, ['-q', '--', 'sleep', '1'], debug=True)
mpi_dirs = [f for f in os.listdir(__dir__) if f.startswith('exec-parallel-')]
self.assertGreaterEqual(len(mpi_dirs), 1)
# test that script were actually created and contain at least one file
# also remove them ...
for mpi in mpi_dirs:
self.assertGreaterEqual(len(os.listdir(os.path.join(__dir__, mpi))), 1)
IO.delete_all(os.path.join(__dir__, mpi))
def tearDownClass(cls):
super(UnitTest, cls).tearDownClass()
from scripts.core.base import IO
cls.end_state = os.listdir(cls.__dir__)
for f in cls.end_state:
if f not in cls.start_state:
full_path = os.path.join(cls.__dir__, f)
if os.path.isdir(full_path):
IO.delete_all(full_path)
else:
IO.delete(full_path)
def tearDownClass(cls):
super(UnitTest, cls).tearDownClass()
from scripts.core.base import IO
cls.end_state = os.listdir(cls.__dir__)
for f in cls.end_state:
if f not in cls.start_state:
full_path = os.path.join(cls.__dir__, f)
if os.path.isdir(full_path):
IO.delete_all(full_path)
else:
IO.delete(full_path)
def on_complete(self, pypy=None):
if self.log_file:
IO.write(self.log_file, self.content)
# finish after update
if self.update_format and (not self.complete_format
and not self.color_complete_format):
printf.finish_rewrite()
# print regular messages
for fmt in ensure_iterable(self.complete_format):
printf.out(fmt, monitor=self)
# print messages if error
if self.pypy.with_error():
for fmt in ensure_iterable(self.error_complete_format):
printf.error(fmt, monitor=self)
# print regular color messages based on result
for fmt in ensure_iterable(self.color_complete_format):
if self.pypy.returncode() == 0:
printf.success(fmt, monitor=self)
elif self.pypy.returncode() is None:
printf.warning(fmt, monitor=self)
else:
printf.error(fmt, monitor=self)
with printf:
if printf.verbosity() is printf.OutputVerbosity.FULL:
printf.sep()
printf.out('Output from file {self.pypy.full_output}'.format(
**locals()))
printf.opt(raw=True).stream(
format_n_lines(self.content, pypy.was_successful()))
elif printf.verbosity(
) is printf.OutputVerbosity.SMART and pypy.with_error():
printf.sep()
printf.out(
'Last 50 lines from file {self.pypy.full_output}'.format(
**locals()))
printf.opt(raw=True).stream(
format_n_lines(self.content, success=False, n_lines=-50))
elif printf.verbosity(
) is printf.OutputVerbosity.MINIMAL and pypy.with_error():
printf.sep()
printf.out(
'Last 50 lines from file {self.pypy.full_output}'.format(
**locals()))
printf.opt(raw=True).stream(
format_n_lines(self.content, success=False, n_lines=-50))
def on_thread_complete(self, thread):
"""
:type thread: scripts.core.pypy.PyPy
"""
super(ComparisonMultiThread, self).on_thread_complete(thread)
# append ndiff to file
content = list()
content.append('-' * 60 + '\n')
content.append(thread.name + '\n')
content.append('-' * 60 + '\n')
content.append(thread.executor.output.read())
content.append('\n' * 3)
IO.append(self.output, '\n'.join(content) or '')
def generate_status_file(cls, target):
"""
Will generate status file if target has option turned on
:type target: PyPy
"""
if target.status_file:
IO.write(target.status_file, json.dumps(target.status(), indent=4))
output_dir = Paths.dirname(target.status_file)
files = Paths.browse(
output_dir,
[PathFilters.filter_wildcards('*/profiler_info_*.log.json')])
# profiler json is missing?
if not files:
IO.write(
Paths.join(output_dir, 'profiler_info_dummy.log.json'),
'{}')
def prepare_pbs_files(self, pbs_module):
jobs = list()
""" :type: list[(str, PBSModule)] """
for yaml_file, yaml_config in self.configs.files.items():
for case in yaml_config.get_one(yaml_file):
pbs_run = pbs_module.Module(case)
pbs_run.queue = self.arg_options.get('queue', True)
pbs_run.ppn = self.arg_options.get('ppn', 1)
pbs_content = self.create_pbs_job_content(pbs_module, case)
IO.write(case.fs.pbs_script, pbs_content)
qsub_command = pbs_run.get_pbs_command(case.fs.pbs_script)
jobs.append((qsub_command, pbs_run))
return jobs
def finish_pbs_exec(job, batch):
"""
Upon PBS finish determine Job exit
:rtype: scripts.serialization.PyPyResult
:type job: scripts.pbs.job.Job
"""
job.is_active = False
try:
result = load_pypy(job.case.fs.dump_output)
except Exception as e:
# no output file was generated assuming it went wrong
job.status = JobState.EXIT_ERROR
Printer.all.err('Job {} ended (no output file found). Case: {}', job,
job.full_name)
Printer.all.out(' pbs output: ')
Printer.all.raw(format_n_lines(IO.read(job.case.fs.pbs_output), False))
return
# check result
if result.returncode == 0:
job.status = JobState.EXIT_OK
Printer.all.suc('Job {}({}) ended', job, job.full_name)
else:
job.status = JobState.EXIT_ERROR
Printer.all.err('Job {}({}) ended', job, job.full_name)
if result.returncode != 0 or batch:
with Printer.all.with_level(1):
Printer.all.raw(
format_n_lines(IO.read(result.output), result.returncode == 0))
return result
def read(self):
if self.mode is self.DUMMY:
return self.content
if self.filename:
if self.content is None:
self.content = IO.read(self.filename)
return self.content
def print_log_file(cls, f, n_lines):
log_file = IO.read(f)
if log_file:
if n_lines == 0:
Printer.out('Full log from file {}:', f)
else:
Printer.out('Last {} lines from file {}:', abs(n_lines), f)
Printer.wrn(format_n_lines(log_file.rstrip(), -n_lines, indent=Printer.indent * ' '))
def print_log_file(cls, f, n_lines):
log_file = IO.read(f)
if log_file:
if n_lines == 0:
printf.out('Full log from file {}:', f)
else:
printf.out('Last {} lines from file {}:', abs(n_lines), f)
printf.stream(format_n_lines(log_file.rstrip(), -n_lines))
def print_log_file(cls, f, n_lines):
log_file = IO.read(f)
if log_file:
if n_lines == 0:
Printer.out('Full log from file {}:', f)
else:
Printer.out('Last {} lines from file {}:', abs(n_lines), f)
Printer.wrn(
format_n_lines(log_file.rstrip(),
-n_lines,
indent=Printer.indent * ' '))
def close(self):
if self.mode in {self.WRITE, self.APPEND, self.VARIABLE}:
if self.fp is not None:
if type(self.fp) is int:
os.close(self.fp)
else:
self.fp.close()
self.fp = None
# remove temp file
if self.mode in {self.VARIABLE}:
self.content = IO.read(self.filename)
os.unlink(self.filename)
def run_local_mode_one(proc, time_limit, memory_limit):
if proc == 0:
command = arg_rest[1:]
else:
command = [arg_rest[0], '-np', proc] + arg_rest[1:]
n_lines = 0 if arg_options.batch else 10
pypy = PyPy(BinExecutor(command))
# set limits
pypy.limit_monitor.time_limit = time_limit
pypy.limit_monitor.memory_limit = memory_limit
pypy.progress = not arg_options.batch
pypy.info_monitor.deactivate()
pypy.error_monitor.deactivate()
# catch output to variable
# in batch mode we will keep the files
# otherwise we will keep logs only on error
log_file = Paths.temp_file('exec-parallel-{date}-{time}-{rnd}.log')
pypy.executor.output = OutputMode.variable_output()
pypy.full_output = log_file
# start and wait for exit
pypy.start()
pypy.join()
# add result to global json result
GlobalResult.add(pypy)
# in batch mode or on error
if not pypy.with_success() or arg_options.batch:
content = pypy.executor.output.read()
IO.write(log_file, content)
Printer.close()
Printer.out(format_n_lines(content, indent=' ', n_lines=-n_lines))
Printer.open()
return pypy
def finish_pbs_job(job, batch):
"""
:type job: scripts.pbs.job.Job
"""
# try to get more detailed job status
job.is_active = False
job_output = IO.read(job.case.fs.json_output)
if job_output:
job_json = JsonParser(json.loads(job_output), batch)
if job_json.returncode == 0:
job.status = JobState.EXIT_OK
Printer.out('OK: Job {}({}) ended', job, job.full_name)
Printer.open()
# in batch mode print all logs
if batch:
Printer.open()
for test in job_json.tests:
test.get_result()
Printer.close()
Printer.close()
else:
job.status = JobState.EXIT_ERROR
Printer.out('ERROR: Job {}({}) ended', job, job.full_name)
# in batch mode print all logs
Printer.open()
for test in job_json.tests:
test.get_result()
Printer.close()
else:
# no output file was generated assuming it went wrong
job.status = JobState.EXIT_ERROR
Printer.out('ERROR: Job {} ended (no output file found). Case: {}', job, job.full_name)
Printer.out(' pbs output: ')
Printer.out(format_n_lines(IO.read(job.case.fs.pbs_output), 0))
return 0 if job.status == JobState.EXIT_OK else 1
def close(self):
if self.mode is self.DUMMY:
return
if self.mode in {self.WRITE, self.APPEND, self.VARIABLE}:
if self.fp is not None:
if type(self.fp) is int:
os.close(self.fp)
else:
self.fp.close()
self.fp = None
# remove temp file
if self.mode in {self.VARIABLE}:
self.content = IO.read(self.filename)
os.unlink(self.filename)
def read(self):
if self.filename:
if self.content is None:
self.content = IO.read(self.filename)
return self.content
def run_pbs_mode(configs, debug=False):
"""
:type debug: bool
:type configs: scripts.config.yaml_config.ConfigPool
"""
global arg_options, arg_others, arg_rest
pbs_module = get_pbs_module(arg_options.host)
Printer.dynamic_output = not arg_options.batch
Printer.dyn('Parsing yaml files')
jobs = list()
""" :type: list[(str, PBSModule)] """
for yaml_file, yaml_config in configs.files.items():
for case in yaml_config.get_one(yaml_file):
pbs_run = pbs_module.Module(case)
pbs_run.queue = arg_options.get('queue', True)
pbs_run.ppn = arg_options.get('ppn', 1)
pbs_content = create_pbs_job_content(pbs_module, case)
IO.write(case.fs.pbs_script, pbs_content)
qsub_command = pbs_run.get_pbs_command(case.fs.pbs_script)
jobs.append((qsub_command, pbs_run))
# start jobs
Printer.dyn('Starting jobs')
total = len(jobs)
job_id = 0
multijob = MultiJob(pbs_module.ModuleJob)
for qsub_command, pbs_run in jobs:
job_id += 1
Printer.dyn('Starting jobs {:02d} of {:02d}', job_id, total)
output = subprocess.check_output(qsub_command)
job = pbs_module.ModuleJob.create(output, pbs_run.case)
job.full_name = "Case {}".format(pbs_run.case)
multijob.add(job)
Printer.out()
Printer.out('{} job/s inserted into queue', total)
# # first update to get more info about multijob jobs
Printer.out()
Printer.separator()
Printer.dyn('Updating job status')
multijob.update()
# print jobs statuses
Printer.out()
if not arg_options.batch:
multijob.print_status()
Printer.separator()
Printer.dyn(multijob.get_status_line())
returncodes = dict()
# wait for finish
while multijob.is_running():
Printer.dyn('Updating job status')
multijob.update()
Printer.dyn(multijob.get_status_line())
# if some jobs changed status add new line to dynamic output remains
jobs_changed = multijob.get_all(status=JobState.COMPLETED)
if jobs_changed:
Printer.out()
Printer.separator()
# get all jobs where was status update to COMPLETE state
for job in jobs_changed:
returncodes[job] = finish_pbs_job(job, arg_options.batch)
if jobs_changed:
Printer.separator()
Printer.out()
# after printing update status lets sleep for a bit
if multijob.is_running():
time.sleep(5)
Printer.out(multijob.get_status_line())
Printer.out('All jobs finished')
# get max return code or number 2 if there are no returncodes
returncode = max(returncodes.values()) if returncodes else 2
sys.exit(returncode)
def compare(self, reference_filepath, other_filepath, **kwargs):
"""
Method can do anything as long as int value is returned
:param reference_filepath:
:param other_filepath:
:param kwargs:
:return:
"""
regex = kwargs.get('regex', None)
substr = kwargs.get('substr', None)
if regex is None and substr is None:
self.output.write(
"Invalid check rule! Specify either 'regex' or 'substr' keyword."
)
return 1
# convert to str or compile to regex
if substr is not None:
substr = str(substr)
if regex is not None:
regex = re.compile(str(regex))
# for regex comparison we ignore reference file
# read job_output.log
content = IO.read(Paths.abspath(other_filepath))
# substr find
if substr:
found = False
for line in content.splitlines():
if line.find(substr) != -1:
found = True
self.output.write(
'[OK] Found substr "{substr}" in line:'.format(
**locals()))
self.output.write(' ' + line)
break
if not found:
self.output.write(
'[ERROR] Could not find substr "{substr}":'.format(
**locals()))
return 1
# regex match
if regex:
found = False
for line in content.splitlines():
if regex.findall(line):
found = True
self.output.write(
'[OK] Found regex "{regex.pattern}" in line:'.format(
**locals()))
self.output.write(' ' + line)
break
if not found:
self.output.write(
'[ERROR] Could not find regex {regex.pattern}:'.format(
**locals()))
return 1
# self.output.write("In case of emergency,")
# self.output.write(" you can provide details on what went wrong")
# self.output.write(" using self.output.write method")
# self.output.write("")
# self.output.write("Error while comparing files \n{} \n{}"
# .format(reference_filepath, other_filepath))
# must return return-code!
return 0