def test_init(self):
f = self.tfp + 'logfiles/init.log'
logfile = LogFile(f, 200)
logfile.update_status()
self.assertEqual(logfile.pct, 0)
self.assertEqual(logfile.status, INITIALIZATION)
self.assertEqual(logfile.errors, [])
def test_simulation(self):
f = self.tfp + 'logfiles/simulating.log'
logfile = LogFile(f, 2)
logfile.update_status()
self.assertEqual(logfile.pct, 25)
self.assertEqual(logfile.status, SIMULATING)
self.assertEqual(logfile.errors, [])
def test_turbulence_generation(self):
f = self.tfp + 'logfiles/turbulence_generation.log'
logfile = LogFile(f, 200)
logfile.update_status()
self.assertEqual(logfile.pct, 0)
self.assertEqual(logfile.status, INITIALIZATION)
self.assertEqual(logfile.errors, [])
self.assertEqual(logfile.lastline, "Turbulence generation starts ...")
def test_simulation_init_error(self):
f = self.tfp + 'logfiles/init_error.log'
logfile = LogFile(f, 2)
logfile.update_status()
self.assertEqual(logfile.pct, 100)
self.assertEqual(logfile.status, DONE)
self.assertEqual(
logfile.errors,
['*** ERROR *** No line termination in command line 8'])
def test_simulation_error2(self):
f = self.tfp + 'logfiles/simulation_error2.log'
logfile = LogFile(f, 2)
self.assertEqual(logfile.pct, 100)
self.assertEqual(logfile.status, DONE)
self.assertEqual(
logfile.errors[0],
'*** ERROR *** Out of limits in user defined shear field - limit value used'
)
self.assertEqual(
logfile.error_str(),
'30 x *** ERROR *** Out of limits in user defined shear field - limit value used'
)
def test_remaining_str(self):
logfile = LogFile("f", 2)
logfile.remaining_time = 5
self.assertEqual(logfile.remaining_time_str(), "00:05")
logfile.remaining_time = 60 + 5
self.assertEqual(logfile.remaining_time_str(), "01:05")
logfile.remaining_time = 3600 + 120 + 5
self.assertEqual(logfile.remaining_time_str(), "1:02:05")
def test_simulation_error(self):
f = self.tfp + 'logfiles/simulation_error.log'
logfile = LogFile(f, 2)
self.assertEqual(logfile.pct, 100)
self.assertEqual(logfile.status, DONE)
self.assertEqual(logfile.errors,
['*** ERROR *** Error opening out .dat file'])
def test_finish(self):
f = self.tfp + 'logfiles/finish.log'
logfile = LogFile(f, 200)
self.assertEqual(logfile.pct, 100)
self.assertEqual(logfile.status, DONE)
self.assertEqual(logfile.errors, [])
self.assertEqual(logfile.elapsed_time, 0.8062344)
def _simulate(self):
"""starts blocking simulation"""
self.sim.logFile = LogInfo(log_file.MISSING, 0, "None", "")
self.pbsjob.submit("%s.in" % self.simulation_id, self.tmp_exepath,
self.sim.stdout_filename)
sleeptime = 1
while self.is_simulating:
time.sleep(sleeptime)
local_out_file = self.exepath + self.stdout_filename
with self.ssh:
try:
self.ssh.download(self.tmp_exepath + self.stdout_filename,
local_out_file)
with open(local_out_file) as fid:
_, self.stdout, returncode_str, _ = fid.read().split(
"---------------------")
self.returncode = returncode_str.strip() != "0"
except Exception:
self.returncode = 1
self.stdout = "error: Could not download and read stdout file"
try:
self.ssh.download(self.tmp_exepath + self.log_filename,
self.exepath + self.log_filename)
except Exception:
raise Warning("Logfile not found",
self.tmp_modelpath + self.log_filename)
self.sim.logFile = LogFile.from_htcfile(self.htcFile, self.exepath)
def test_from_htcfile(self):
htcfile = HTCFile(
self.tfp +
'logfiles/model/htc/dlc14_iec61400-1ed3/dlc14_wsp10_wdir000_s0000.htc',
"../")
logfile = LogFile.from_htcfile(htcfile, self.tfp + 'logfiles/model/')
self.assertEqual(logfile.status, DONE)
def test_reset(self):
htcfile = HTCFile(
self.tfp +
'logfiles/model/htc/dlc14_iec61400-1ed3/dlc14_wsp10_wdir000_s0000.htc',
"../")
logfile = LogFile.from_htcfile(htcfile, self.tfp + 'logfiles/model/')
self.assertEqual(logfile.status, DONE)
logfile.reset()
self.assertEqual(logfile.status, UNKNOWN)
self.assertEqual(logfile.txt, "")
logfile.update_status()
self.assertEqual(logfile.status, DONE)
def test_remaining(self):
logfilename = self.tfp + 'logfiles/finish.log'
logfile = LogFile(logfilename + "_", 2)
logfile.clear()
if os.path.isfile(logfile.filename):
os.remove(logfile.filename)
t = threading.Thread(target=simulate, args=(logfilename, 0.01))
t.start()
last_status = None
last_pct = 0
estimated_simulation_time = None
while logfile.pct >= 0 and logfile.status != DONE:
if estimated_simulation_time is None and logfile.remaining_time is not None:
estimated_endtime = time.time() + logfile.remaining_time
#print (logfile.pct, logfile.remaining_time, logfile.lastline)
logfile.update_status()
if logfile.status != last_status or logfile.pct != last_pct:
last_status = logfile.status
last_pct = logfile.pct
time.sleep(0.1)
t.join()
self.assertLess(abs(time.time() - estimated_endtime), 0.15)
os.remove(logfile.filename)
def check(self, logfilename, phases, end_status, end_errors=[]):
logfile = LogFile(logfilename + "_", 2)
logfile.clear()
if os.path.isfile(logfile.filename):
os.remove(logfile.filename)
t = threading.Thread(target=simulate, args=(logfilename, 0.0001))
t.start()
last_status = None
last_pct = 0
while logfile.pct >= 0 and logfile.status != DONE:
logfile.update_status()
if logfile.status != last_status or logfile.pct != last_pct:
last_status = logfile.status
last_pct = logfile.pct
if logfile.status in phases:
phases.remove(logfile.status)
time.sleep(0.01)
self.assertEqual(logfile.pct, 100)
self.assertEqual(logfile.status, end_status)
self.assertEqual(logfile.errors, end_errors)
self.assertFalse(phases)
t.join()
os.remove(logfile.filename)
def __init__(self,
modelpath,
htcfilename,
hawc2exe="HAWC2MB.exe",
copy_turbulence=True):
self.modelpath = os.path.abspath(modelpath) + "/"
if os.path.isabs(htcfilename):
htcfilename = os.path.relpath(htcfilename, modelpath)
if htcfilename.startswith("input/"):
htcfilename = htcfilename[6:]
exists = [
os.path.isfile(os.path.join(modelpath, htcfilename)),
os.path.isfile(os.path.join(modelpath, "input/", htcfilename))
]
if all(exists):
raise Exception(
"Both standard and input/output file structure available for %s in %s. Delete one of the options"
% (htcfilename, modelpath))
if not any(exists):
raise Exception("%s not found in %s" % (htcfilename, modelpath))
else:
self.ios = exists[1] # input/output file structure
if self.ios:
self.exepath = self.modelpath + "input/"
else:
self.exepath = self.modelpath
# model_path: top level path containing all resources
# exepath: parent path for relative paths
htcfilename = fmt_path(htcfilename)
self.tmp_modelpath = self.exepath
self.folder = os.path.dirname(htcfilename)
self.filename = os.path.basename(htcfilename)
self.htcFile = HTCFile(os.path.join(self.exepath, htcfilename),
self.exepath)
self.time_stop = self.htcFile.simulation.time_stop[0]
self.hawc2exe = hawc2exe
self.copy_turbulence = copy_turbulence
self.simulation_id = (
htcfilename.replace("\\", "/").replace("/", "_")[:50] +
"_%d" % id(self))
if self.simulation_id.startswith("input_"):
self.simulation_id = self.simulation_id[6:]
self.stdout_filename = fmt_path(
os.path.join(os.path.relpath(self.exepath, self.modelpath),
(os.path.splitext(htcfilename)[0] + ".out").replace(
'htc', 'stdout', 1)))
if self.ios:
assert self.stdout_filename.startswith("input/")
self.stdout_filename = self.stdout_filename.replace(
"input/", "../output/")
# self.stdout_filename = "stdout/%s.out" % self.simulation_id
if 'logfile' in self.htcFile.simulation:
self.log_filename = self.htcFile.simulation.logfile[0]
else:
self.log_filename = self.stdout_filename
if os.path.isabs(self.log_filename):
self.log_filename = os.path.relpath(self.log_filename,
self.modelpath)
else:
self.log_filename = os.path.relpath(self.log_filename)
self.log_filename = fmt_path(self.log_filename)
self.logFile = LogFile(os.path.join(self.exepath, self.log_filename),
self.time_stop)
self.logFile.clear()
self.last_status = self.status
self.errors = []
self.non_blocking_simulation_thread = Thread(
target=lambda: self.simulate_distributed(raise_simulation_errors=
False))
self.updateSimStatusThread = UpdateSimStatusThread(self)
from wetb.hawc2.simulation_resources import LocalSimulationHost
self.host = LocalSimulationHost(self)
self.stdout = ""
self.returncode = 0
def test_HAWC2Version(self):
f = self.tfp + 'logfiles/finish.log'
logfile = LogFile(f, 200)
self.assertEqual(logfile.hawc2version, "HAWC2MB 11.8")
def test_missing_logfile(self):
f = self.tfp + 'logfiles/missing.log'
logfile = LogFile(f, 200)
logfile.update_status()
self.assertEqual(logfile.pct, 0)
self.assertEqual(logfile.status, log_file.MISSING)
class Simulation(object):
"""Class for doing hawc2 simulations
Examples
--------
>>> sim = Simulation("<path>/MyModel","htc/MyHtc")
Blocking inplace simulation
>>> sim.simulate()
Non-blocking distributed simulation(everything copied to temporary folder)\n
Starts two threads:
- non_blocking_simulation_thread:
- prepare_simulation() # copy to temporary folder
- simulate() # simulate
- finish_simulation # copy results back again
- updateSimStatusThread:
- update status every second
>>> sim.start()
>>> while sim.status!=CLEANED:
>>> sim.show_status()
The default host is LocalSimulationHost. To simulate on pbs featured cluster
>>> sim.host = PBSClusterSimulationHost(sim, <hostname>, <username>, <password>)
>>> sim.start()
>>> while sim.status!=CLEANED:
>>> sim.show_status()
"""
is_simulating = False
is_done = False
status = QUEUED
def __init__(self,
modelpath,
htcfilename,
hawc2exe="HAWC2MB.exe",
copy_turbulence=True):
self.modelpath = os.path.abspath(modelpath) + "/"
if os.path.isabs(htcfilename):
htcfilename = os.path.relpath(htcfilename, modelpath)
if htcfilename.startswith("input/"):
htcfilename = htcfilename[6:]
exists = [
os.path.isfile(os.path.join(modelpath, htcfilename)),
os.path.isfile(os.path.join(modelpath, "input/", htcfilename))
]
if all(exists):
raise Exception(
"Both standard and input/output file structure available for %s in %s. Delete one of the options"
% (htcfilename, modelpath))
if not any(exists):
raise Exception("%s not found in %s" % (htcfilename, modelpath))
else:
self.ios = exists[1] # input/output file structure
if self.ios:
self.exepath = self.modelpath + "input/"
else:
self.exepath = self.modelpath
# model_path: top level path containing all resources
# exepath: parent path for relative paths
htcfilename = fmt_path(htcfilename)
self.tmp_modelpath = self.exepath
self.folder = os.path.dirname(htcfilename)
self.filename = os.path.basename(htcfilename)
self.htcFile = HTCFile(os.path.join(self.exepath, htcfilename),
self.exepath)
self.time_stop = self.htcFile.simulation.time_stop[0]
self.hawc2exe = hawc2exe
self.copy_turbulence = copy_turbulence
self.simulation_id = (
htcfilename.replace("\\", "/").replace("/", "_")[:50] +
"_%d" % id(self))
if self.simulation_id.startswith("input_"):
self.simulation_id = self.simulation_id[6:]
self.stdout_filename = fmt_path(
os.path.join(os.path.relpath(self.exepath, self.modelpath),
(os.path.splitext(htcfilename)[0] + ".out").replace(
'htc', 'stdout', 1)))
if self.ios:
assert self.stdout_filename.startswith("input/")
self.stdout_filename = self.stdout_filename.replace(
"input/", "../output/")
# self.stdout_filename = "stdout/%s.out" % self.simulation_id
if 'logfile' in self.htcFile.simulation:
self.log_filename = self.htcFile.simulation.logfile[0]
else:
self.log_filename = self.stdout_filename
if os.path.isabs(self.log_filename):
self.log_filename = os.path.relpath(self.log_filename,
self.modelpath)
else:
self.log_filename = os.path.relpath(self.log_filename)
self.log_filename = fmt_path(self.log_filename)
self.logFile = LogFile(os.path.join(self.exepath, self.log_filename),
self.time_stop)
self.logFile.clear()
self.last_status = self.status
self.errors = []
self.non_blocking_simulation_thread = Thread(
target=lambda: self.simulate_distributed(raise_simulation_errors=
False))
self.updateSimStatusThread = UpdateSimStatusThread(self)
from wetb.hawc2.simulation_resources import LocalSimulationHost
self.host = LocalSimulationHost(self)
self.stdout = ""
self.returncode = 0
def start(self, update_interval=1):
"""Start non blocking distributed simulation"""
self.is_simulating = True
if update_interval > 0:
self.updateSimStatusThread.interval = update_interval
self.updateSimStatusThread.start()
self.non_blocking_simulation_thread.start()
def wait(self):
self.non_blocking_simulation_thread.join()
self.update_status()
def abort(self, update_status=True):
self.status = ABORTED
self.is_simulating = False
self.is_done = True
self.host.stop()
if update_status:
self.update_status()
# if self.status != QUEUED:
# self.host.stop()
# for _ in range(50):
# if self.is_simulating is False:
# break
# time.sleep(0.1)
# if self.logFile.status not in [log_file.DONE]:
# self.status = ABORTED
# self.is_simulating = False
# self.is_done = True
# if update_status:
# self.update_status()
def show_status(self):
# print ("log status:", self.logFile.status)
if self.logFile.status == log_file.SIMULATING:
if self.last_status != log_file.SIMULATING:
print("|" + ("-" * 50) + "|" + ("-" * 49) + "|")
sys.stdout.write("|")
sys.stdout.write("." *
(self.logFile.pct - getattr(self, 'last_pct', 0)))
sys.stdout.flush()
self.last_pct = self.logFile.pct
elif self.last_status == log_file.SIMULATING:
sys.stdout.write("." * (100 - self.last_pct) + "|")
sys.stdout.flush()
print("\n")
elif self.logFile.status == log_file.UNKNOWN:
print(self.status)
else:
print(self.logFile.status)
if self.logFile.status != log_file.SIMULATING:
if self.logFile.errors:
print(self.logFile.errors)
self.last_status = self.logFile.status
def prepare_simulation(self):
self.status = PREPARING
# self.tmp_modelpath = os.path.join(".hawc2launcher/%s/" % self.simulation_id)
# self.tmp_exepath = os.path.join(self.tmp_modelpath, os.path.relpath(self.exepath, self.modelpath) ) + "/"
self.set_id(self.simulation_id, str(self.host), self.tmp_modelpath)
def fmt(src):
if os.path.isabs(src):
src = os.path.relpath(os.path.abspath(src), self.exepath)
else:
src = os.path.relpath(src)
assert not src.startswith(
".."
), "%s referes to a file outside the model path\nAll input files be inside model path" % src
return src
if self.ios:
input_folder_files = []
for root, _, filenames in os.walk(
os.path.join(self.modelpath, "input/")):
for filename in filenames:
input_folder_files.append(os.path.join(root, filename))
input_patterns = [
fmt(src) for src in input_folder_files +
([], self.htcFile.turbulence_files())[self.copy_turbulence] +
self.additional_files().get('input', [])
]
else:
input_patterns = [
fmt(src) for src in self.htcFile.input_files() +
([], self.htcFile.turbulence_files())[self.copy_turbulence] +
self.additional_files().get('input', [])
]
input_files = set([
f for pattern in input_patterns
for f in glob.glob(os.path.join(self.exepath, pattern))
if os.path.isfile(f) and ".hawc2launcher" not in f
])
self.host._prepare_simulation(input_files)
# return [fmt(src) for src in self.htcFile.input_files() + self.htcFile.turbulence_files() + self.additional_files().get('input', [])]
#
# for src in self._input_sources():
# for src_file in glob.glob(os.path.join(self.modelpath, src)):
#
#
# self.host._prepare_simulation()
def simulate(self):
# starts blocking simulation
self.is_simulating = True
self.errors = []
self.status = INITIALIZING
self.logFile.clear()
self.host._simulate()
self.returncode, self.stdout = self.host.returncode, self.host.stdout
if self.host.returncode or 'error' in self.host.stdout.lower():
if self.status == ABORTED:
return
if "error" in self.host.stdout.lower():
self.errors = (list(
set([
l for l in self.host.stdout.split("\n")
if 'error' in l.lower() and not 'rms error' in l
])))
self.status = ERROR
if 'HAWC2MB version:' not in self.host.stdout:
self.errors.append(self.host.stdout)
self.status = ERROR
self.logFile.update_status()
self.errors.extend(list(set(self.logFile.errors)))
self.update_status()
self.is_simulating = False
if self.host.returncode or self.errors:
raise Exception("Simulation error:\nReturn code: %d\n%s" %
(self.host.returncode, "\n".join(self.errors)))
elif self.logFile.status != log_file.DONE or self.logFile.errors:
raise Warning(
"Simulation succeded with errors:\nLog status:%s\nErrors:\n%s"
% (self.logFile.status, "\n".join(self.logFile.errors)))
else:
self.status = FINISH
def finish_simulation(self):
if self.status == ABORTED:
return
if self.status != ERROR:
self.status = FINISHING
def fmt(dst):
if os.path.isabs(dst):
dst = os.path.relpath(os.path.abspath(dst), self.exepath)
else:
dst = os.path.relpath(dst)
dst = fmt_path(dst)
assert not os.path.relpath(
os.path.join(self.exepath, dst), self.modelpath
).startswith(
".."
), "%s referes to a file outside the model path\nAll input files be inside model path" % dst
return dst
turb_files = [
f for f in self.htcFile.turbulence_files() if self.copy_turbulence
and not os.path.isfile(os.path.join(self.exepath, f))
]
if self.ios:
output_patterns = ["../output/*", "../output/"] + turb_files + \
[os.path.join(self.exepath, self.stdout_filename)]
else:
output_patterns = self.htcFile.output_files() + turb_files + \
[os.path.join(self.exepath, self.stdout_filename)]
output_files = set(
self.host.glob([
fmt_path(os.path.join(self.tmp_exepath, fmt(p)))
for p in output_patterns
],
recursive=self.ios))
if not os.path.isdir(
os.path.dirname(self.exepath + self.stdout_filename)):
os.makedirs(os.path.dirname(self.exepath + self.stdout_filename))
try:
self.host._finish_simulation(output_files)
if self.status != ERROR:
self.status = CLEANED
except Warning as e:
self.errors.append(str(e))
if self.status != ERROR:
self.status = CLEANED
except Exception as e:
self.errors.append(str(e))
raise
finally:
self.set_id(self.filename)
self.logFile.reset()
self.htcFile.reset()
def update_status(self, *args, **kwargs):
self.host.update_logFile_status()
if self.status in [INITIALIZING, SIMULATING]:
if self.logFile.status == log_file.SIMULATING:
self.status = SIMULATING
if self.logFile.status == log_file.DONE and self.is_simulating is False:
self.status = FINISH
def __str__(self):
return "Simulation(%s)" % self.filename
def additional_files(self):
additional_files_file = os.path.join(self.modelpath,
'additional_files.txt')
additional_files = {}
if os.path.isfile(additional_files_file):
with open(additional_files_file, encoding='utf-8') as fid:
additional_files = json.loads(fid.read().replace("\\", "/"))
return additional_files
def add_additional_input_file(self, file):
additional_files = self.additional_files()
additional_files['input'] = list(
set(additional_files.get('input', []) + [file]))
additional_files_file = os.path.join(self.modelpath,
'additional_files.txt')
with open(additional_files_file, 'w', encoding='utf-8') as fid:
json.dump(additional_files, fid)
def simulate_distributed(self, raise_simulation_errors=True):
try:
tmpdirname = tempfile.TemporaryDirectory(
prefix="h2launcher_%s_" % os.path.basename(self.filename)).name
self.tmp_modelpath = tmpdirname + "/"
self.tmp_exepath = os.path.join(
self.tmp_modelpath,
os.path.relpath(self.exepath, self.modelpath)) + "/"
self.prepare_simulation()
try:
self.simulate()
except Warning as e:
print("simulation failed", str(self))
print("Trying to finish")
raise
finally:
try:
if self.status != ABORTED:
self.finish_simulation()
except Exception:
print("finish_simulation failed", str(self))
raise
finally:
def remove_readonly(fn, path, excinfo):
try:
os.chmod(path, stat.S_IWRITE)
fn(path)
except Exception as exc:
print("Skipped:", path, "because:\n", exc)
shutil.rmtree(tmpdirname, onerror=remove_readonly)
except Exception as e:
self.status = ERROR
self.errors.append(str(e))
if raise_simulation_errors:
raise e
finally:
self.is_done = True
def fix_errors(self):
def confirm_add_additional_file(folder, file):
if os.path.isfile(os.path.join(self.modelpath, folder, file)):
filename = fmt_path(os.path.join(folder, file))
if self.get_confirmation(
"File missing",
"'%s' seems to be missing in the temporary working directory. \n\nDo you want to add it to additional_files.txt"
% filename):
self.add_additional_input_file(filename)
self.show_message(
"'%s' is now added to additional_files.txt.\n\nPlease restart the simulation"
% filename)
for error in self.errors:
for regex in [
r".*\*\*\* ERROR \*\*\* File '(.*)' does not exist in the (.*) folder",
r".*\*\*\* ERROR \*\*\* DLL (.*)()"
]:
m = re.compile(regex).match(error.strip())
if m is not None:
file, folder = m.groups()
confirm_add_additional_file(folder, file)
continue
m = re.compile(
r".*\*\*\* ERROR \*\*\* File '(.*)' does not exist in the working directory"
).match(error.strip())
if m is not None:
file = m.groups()[0]
for root, folder, files in os.walk(self.modelpath):
if "__Thread" not in root and file in files:
folder = os.path.relpath(root, self.modelpath)
confirm_add_additional_file(folder, file)
continue
def get_confirmation(self, title, msg):
"""override in subclass"""
return True
def show_message(self, msg, title="Information"):
print(msg)
def set_id(self, *args, **kwargs):
pass
def progress_callback(self, *args, **kwargs):
pass