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'''
Created on 22. dec. 2016
@author: mmpe
'''
from datetime import datetime
import glob
import io
import os
import shutil
from subprocess import STDOUT
import subprocess
from threading import Thread
import time
from wetb.hawc2 import log_file
from wetb.hawc2.log_file import LogInfo, LogFile
from wetb.hawc2.simulation import ERROR, ABORTED
from wetb.utils.cluster_tools import pbsjob
from wetb.utils.cluster_tools.cluster_resource import LocalResource, \
SSHPBSClusterResource, unix_path
from wetb.utils.cluster_tools.pbsjob import SSHPBSJob, NOT_SUBMITTED, DONE
from wetb.utils.cluster_tools.ssh_client import SSHClient
from wetb.utils.timing import print_time
class SimulationHost(object):
def __init__(self, simulation):
self.sim = simulation
logFile = property(lambda self : self.sim.logFile, lambda self, v: setattr(self.sim, "logFile", v))
errors = property(lambda self : self.sim.errors)
modelpath = property(lambda self : self.sim.modelpath)
exepath = property(lambda self : self.sim.exepath)
tmp_modelpath = property(lambda self : self.sim.tmp_modelpath, lambda self, v: setattr(self.sim, "tmp_modelpath", v))
tmp_exepath = property(lambda self : self.sim.tmp_exepath, lambda self, v: setattr(self.sim, "tmp_exepath", v))
simulation_id = property(lambda self : self.sim.simulation_id)
stdout_filename = property(lambda self : self.sim.stdout_filename)
htcFile = property(lambda self : self.sim.htcFile)
additional_files = property(lambda self : self.sim.additional_files)
_input_sources = property(lambda self : self.sim._input_sources)
_output_sources = property(lambda self : self.sim._output_sources)
log_filename = property(lambda self : self.sim.log_filename)
status = property(lambda self : self.sim.status, lambda self, v: setattr(self.sim, "status", v))
is_simulating = property(lambda self : self.sim.is_simulating, lambda self, v: setattr(self.sim, "is_simulating", v))
def __str__(self):
return self.resource.host
class LocalSimulationHost(SimulationHost):
def __init__(self, simulation, resource=None):
SimulationHost.__init__(self, simulation)
if resource is None:
resource = LocalResource(1)
self.resource = resource
self.simulationThread = SimulationThread(self.sim)
def get_datetime(self):
return datetime.now()
def glob(self, path, recursive=False):
if recursive:
return [os.path.join(root, f) for root, _, files in os.walk(path) for f in files]
else:
return glob.glob(path)
def _prepare_simulation(self, input_files):
# must be called through simulation object
self.tmp_modelpath = os.path.join(self.modelpath, self.tmp_modelpath)
self.tmp_exepath = os.path.join(self.tmp_modelpath, os.path.relpath(self.sim.exepath, self.sim.modelpath) ) + "/"
self.sim.set_id(self.simulation_id, 'Localhost', self.tmp_modelpath)
for src_file in input_files:
dst = os.path.join(self.tmp_modelpath, os.path.relpath(src_file, self.modelpath))
# exist_ok does not exist in Python27
if not os.path.exists(os.path.dirname(dst)):
os.makedirs(os.path.dirname(dst)) #, exist_ok=True)
shutil.copy(src_file, dst)
if not os.path.isfile(dst) or os.stat(dst).st_size != os.stat(src_file).st_size:
print ("error copy ", dst)
stdout_folder = os.path.join(self.tmp_exepath, os.path.dirname(self.sim.stdout_filename))
if not os.path.exists(stdout_folder):
os.makedirs(stdout_folder) #, exist_ok=True)
self.logFile.filename = os.path.join(self.tmp_exepath, self.log_filename)
self.simulationThread.modelpath = self.tmp_modelpath
self.simulationThread.exepath = self.tmp_exepath
def _simulate(self):
#must be called through simulation object
self.returncode, self.stdout = 1, "Simulation failed"
self.simulationThread.start()
self.sim.set_id(self.sim.simulation_id, "Localhost(pid:%d)" % self.simulationThread.process.pid, self.tmp_modelpath)
self.simulationThread.join()
self.returncode, self.stdout = self.simulationThread.res
self.logFile.update_status()
self.errors.extend(list(set(self.logFile.errors)))
def _finish_simulation(self, output_files):
missing_result_files = []
for src_file in output_files:
dst_file = os.path.join(self.modelpath, os.path.relpath(src_file, self.tmp_modelpath))
# exist_ok does not exist in Python27
try:
if not os.path.isdir(os.path.dirname(dst_file)):
os.makedirs(os.path.dirname(dst_file)) #, exist_ok=True)
if not os.path.isfile(dst_file) or os.path.getmtime(dst_file) != os.path.getmtime(src_file):
shutil.copy(src_file, dst_file)
except:
missing_result_files.append(dst_file)
self.logFile.filename = os.path.join(self.sim.exepath, self.log_filename)
if missing_result_files:
raise Warning("Failed to copy %s from %s"%(",".join(missing_result_files), self.resource.host))
try:
shutil.rmtree(self.tmp_modelpath, ignore_errors=False)
except (PermissionError, OSError) as e:
raise Warning("Fail to remove temporary files and folders on %s\n%s"%(self.resource.host, str(e)))
def update_logFile_status(self):
self.logFile.update_status()
def stop(self):
self.simulationThread.stop()
self.simulationThread.join()
class SimulationThread(Thread):
def __init__(self, simulation, low_priority=True):
Thread.__init__(self)
self.sim = simulation
self.modelpath = self.sim.modelpath
self.exepath = self.sim.exepath
self.res = [0, "", ""]
self.low_priority = low_priority
def start(self):
CREATE_NO_WINDOW = 0x08000000
exepath = self.exepath #overwritten in _prepare_simulation
modelpath = self.modelpath #overwritten in _prepare_simulation
htcfile = os.path.relpath(self.sim.htcFile.filename, self.sim.exepath)
hawc2exe = self.sim.hawc2exe
stdout = self.sim.stdout_filename
if not os.path.isdir(os.path.dirname(exepath + self.sim.stdout_filename)):
os.makedirs(os.path.dirname(exepath + self.sim.stdout_filename))
with open (os.path.join(exepath, stdout), 'wb') as stdout:
if isinstance(hawc2exe, tuple):
wine, hawc2exe = hawc2exe
self.process = subprocess.Popen(" ".join([wine, hawc2exe, htcfile]), stdout=stdout, stderr=STDOUT, shell=True, cwd=exepath) #shell must be True to inwoke wine
else:
self.process = subprocess.Popen([hawc2exe, htcfile], stdout=stdout, stderr=STDOUT, shell=False, cwd=exepath, creationflags=CREATE_NO_WINDOW)
self.process.communicate()
import psutil
try:
self.sim.host.resource.process_name = psutil.Process(self.process.pid).name()
except:
pass
Thread.start(self)
def run(self):
import psutil
p = psutil.Process(os.getpid())
try:
if self.low_priority:
p.set_nice(psutil.BELOW_NORMAL_PRIORITY_CLASS)
except:
pass
self.process.communicate()
errorcode = self.process.returncode
with open(self.exepath + self.sim.stdout_filename, encoding='cp1252') as fid:
stdout = fid.read()
self.res = errorcode, stdout
def stop(self):
if hasattr(self, 'process'):
subprocess.Popen("TASKKILL /F /PID {pid} /T".format(pid=self.process.pid))
class PBSClusterSimulationResource(SSHPBSClusterResource):
def __init__(self, host, username, password, port, min_cpu, min_free, init_cmd, wine_cmd, python_cmd):
SSHPBSClusterResource.__init__(self, host, username, password, port, min_cpu, min_free, init_cmd, wine_cmd, python_cmd)
def is_clean(self):
return self.execute("find .hawc2launcher/ -type f | wc -l")[1] > 0
def clean(self):
try:
self.execute('rm .hawc2launcher -r -f')
except:
pass
try:
self.shared_ssh.close()
except:
pass
def update_status(self):
try:
_, out, _ = self.execute("find .hawc2launcher/ -name '*.out'")
self.finished = set([f.split("/")[1] for f in out.split("\n") if "/" in f])
except Exception:
#print ("resource_manager.update_status, out", str(e))
pass
try:
_, out, _ = self.execute("find .hawc2launcher -name 'status*' -exec cat {} \;")
self.loglines = {l.split(";")[0] : l.split(";")[1:] for l in out.split("\n") if ";" in l}
except Exception:
#print ("resource_manager.update_status, status file", str(e))
pass
try:
_, out, _ = self.execute("qstat -u %s" % self.username)
self.is_executing = set([j.split(".")[0] for j in out.split("\n")[5:] if "." in j])
except Exception:
#print ("resource_manager.update_status, qstat", str(e))
pass
class GormSimulationResource(PBSClusterSimulationResource):
def __init__(self, username, password, wine_cmd="WINEARCH=win32 WINEPREFIX=~/.wine32 wine"):
init_cmd = """export PATH=/home/python/miniconda3/bin:$PATH
source activate wetb_py3"""
PBSClusterSimulationResource.__init__(self, "gorm.risoe.dk", username, password, 22, 25, 100, init_cmd, wine_cmd, "python")
class PBSClusterSimulationHost(SimulationHost, SSHClient):
def __init__(self, simulation, resource):
SimulationHost.__init__(self, simulation)
SSHClient.__init__(self, resource.host, resource.username, resource.password, resource.port)
self.pbsjob = SSHPBSJob(resource.shared_ssh)
self.resource = resource
hawc2exe = property(lambda self : os.path.basename(self.sim.hawc2exe))
def get_datetime(self):
v, out, err = self.execute('date "+%Y,%m,%d,%H,%M,%S"')
if v == 0:
return datetime.strptime(out.strip(), "%Y,%m,%d,%H,%M,%S")
@print_time
def _prepare_simulation(self, input_files):
with self:
self.execute(["mkdir -p .hawc2launcher/%s" % self.simulation_id], verbose=False)
self.execute("mkdir -p %s%s" % (self.tmp_exepath, os.path.dirname(self.log_filename)))
self.upload_files(self.modelpath, self.tmp_modelpath, file_lst = [os.path.relpath(f, self.modelpath) for f in input_files])
# for src_file in input_files:
# dst = unix_path(self.tmp_modelpath + os.path.relpath(src_file, self.modelpath))
# self.execute("mkdir -p %s" % os.path.dirname(dst), verbose=False)
# self.upload(src_file, dst, verbose=False)
# ##assert self.ssh.file_exists(dst)
f = io.StringIO(self.pbsjobfile(self.sim.ios))
f.seek(0)
self.upload(f, self.tmp_exepath + "%s.in" % self.simulation_id)
self.execute("mkdir -p %s%s" % (self.tmp_exepath, os.path.dirname(self.stdout_filename)))
remote_log_filename = "%s%s" % (self.tmp_exepath, self.log_filename)
self.execute("rm -f %s" % remote_log_filename)
@print_time
def _finish_simulation(self, output_files):
with self:
download_failed = []
try:
self.download_files(self.tmp_modelpath, self.modelpath, file_lst = [os.path.relpath(f, self.tmp_modelpath) for f in output_files] )
except:
#
# for src_file in output_files:
# try:
# dst_file = os.path.join(self.modelpath, os.path.relpath(src_file, self.tmp_modelpath))
# os.makedirs(os.path.dirname(dst_file), exist_ok=True)
# self.download(src_file, dst_file, retry=10)
# except Exception as e:
# download_failed.append(dst_file)
# if download_failed:
raise Warning("Failed to download %s from %s"%(",".join(download_failed), self.host))
else:
try:
self.execute('rm -r .hawc2launcher/%s' % self.simulation_id)
finally:
try:
self.execute('rm .hawc2launcher/status_%s' % self.simulation_id)
except:
raise Warning("Fail to remove temporary files and folders on %s"%self.host)
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:
try:
self.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.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 update_logFile_status(self):
def pbsjob_status():
if self.pbsjob._status in [NOT_SUBMITTED, DONE]:
return self.pbsjob._status
if self.pbsjob.jobid in self.resource.is_executing:
self.pbsjob._status = pbsjob.RUNNING
elif self.simulation_id in self.resource.finished:
self.pbsjob._status = DONE
self.pbsjob.jobid = None
return self.pbsjob._status
def set_status():
if self.simulation_id in self.resource.loglines:
self.logline = self.resource.loglines[self.simulation_id]
self.status = self.logline[0]
self.logFile = LogInfo(*self.logline[1:])
status = pbsjob_status()
if status == pbsjob.NOT_SUBMITTED:
pass
elif status == pbsjob.DONE:
if self.is_simulating:
set_status()
self.is_simulating = False
else:
set_status()
def start(self):
"""Start non blocking distributed simulation"""
self.non_blocking_simulation_thread.start()
def abort(self):
self.pbsjob.stop()
self.stop()
try:
self.finish_simulation()
except:
pass
self.is_simulating = False
self.is_done = True
if self.status != ERROR and self.logFile.status not in [log_file.DONE]:
self.status = ABORTED
def stop(self):
self.is_simulating = False
self.pbsjob.stop()
def pbsjobfile(self, ios=False):
cp_back = ""
for folder in set([unix_path(os.path.relpath(os.path.dirname(f))) for f in self.htcFile.output_files() + self.htcFile.turbulence_files()]):
cp_back += "mkdir -p $PBS_O_WORKDIR/%s/. \n" % folder
cp_back += "cp -R -f %s/. $PBS_O_WORKDIR/%s/.\n" % (folder, folder)
rel_htcfilename = unix_path(os.path.relpath(self.htcFile.filename, self.exepath))
init="""
### Standard Output
#PBS -N h2l_%s
### merge stderr into stdout
#PBS -j oe
#PBS -o %s
### Maximum wallclock time format HOURS:MINUTES:SECONDS
#PBS -l walltime=04:00:00
###PBS -a 201547.53
#PBS -lnodes=1:ppn=1
### Queue name
#PBS -q workq
### Create scratch directory and copy data to it
cd $PBS_O_WORKDIR
pwd"""% (self.simulation_id, self.stdout_filename)
copy_to="""
cp -R %s /scratch/$USER/$PBS_JOBID
### Execute commands on scratch nodes
cd /scratch/$USER/$PBS_JOBID%s
pwd"""%((".","../")[ios], ("", "/input")[ios])
run='''
%s
### modelpath: %s
### htc: %s
echo "---------------------"
%s -c "from wetb.hawc2.cluster_simulation import ClusterSimulation;ClusterSimulation('.','%s', ('%s','%s'))"
echo "---------------------"
echo $?
echo "---------------------"'''% (self.resource.init_cmd, self.modelpath, self.htcFile.filename, self.resource.python_cmd, rel_htcfilename, self.resource.wine_cmd, self.hawc2exe)
copy_back = """
### Copy back from scratch directory
cd /scratch/$USER/$PBS_JOBID%s
%s
echo $PBS_JOBID
cd /scratch/
### rm -r $PBS_JOBID
exit""" % (("", "/input")[ios], cp_back)
return init+copy_to+run+copy_back