diff --git a/wetb/hawc2/cluster_simulation.py b/wetb/hawc2/cluster_simulation.py
new file mode 100644
index 0000000000000000000000000000000000000000..c67377f58a723b324b91f1cafe3665520770dcd1
--- /dev/null
+++ b/wetb/hawc2/cluster_simulation.py
@@ -0,0 +1,23 @@
+from wetb.hawc2.simulation import Simulation, SimulationThread
+import os
+import sys
+from threading import Thread
+class ClusterSimulation(Simulation):
+ def __init__(self, modelpath, htcfilename, hawc2exe="HAWC2MB.exe"):
+ Simulation.__init__(self, modelpath, htcfilename, hawc2exe=hawc2exe)
+
+ self.simulation_id = [f for f in os.listdir('.') if f.endswith('.in')][0][:-3]
+ self.host.simulationThread.low_priority = False
+ self.non_blocking_simulation_thread = Thread(target=self.simulate)
+ self.start(1)
+ self.wait()
+ print (self.host.simulationThread.res[1]) # print hawc2 output to stdout
+ sys.exit(self.host.simulationThread.res[0])
+
+ def update_status(self, *args, **kwargs):
+ Simulation.update_status(self, *args, **kwargs)
+ with open("/home/mmpe/.hawc2launcher/status_%s" % self.simulation_id, 'w') as fid:
+ fid.write (";".join([self.status] + [str(getattr(self.logFile, v)) for v in ['status', 'pct', 'remaining_time', 'lastline']]) + "\n")
+
+ def show_status(self):
+ pass
diff --git a/wetb/hawc2/hawc2_pbsjob.py b/wetb/hawc2/hawc2_pbsjob.py
deleted file mode 100755
index 1091786a8f939406c2fac23384111f3da3dd0460..0000000000000000000000000000000000000000
--- a/wetb/hawc2/hawc2_pbsjob.py
+++ /dev/null
@@ -1,63 +0,0 @@
-
-
-from wetb.hawc2.htc_file import HTCFile
-from wetb.utils.cluster_tools.pbsjob import PBSJob
-from wetb.hawc2.log_file import LogInterpreter
-import os
-import time
-from wetb.utils.cluster_tools import pbsjob
-class HAWC2PBSJob(PBSJob):
-
- def __init__(self, host, username, password):
- PBSJob.__init__(self, host, username, password)
-
-
- def submit(self, job, cwd, pbs_out_file):
- with open (cwd + job) as fid:
- htcfilename = [l for l in fid if l.startswith('wine')][0].rsplit(" ", 1)[1].strip()
- print (htcfilename)
- htcfile = HTCFile(cwd + htcfilename)
-
- self.log_filename = htcfile.simulation.logfile[0]
- self.loginterpreter = LogInterpreter(htcfile.simulation.time_stop[0])
- PBSJob.submit(self, job, cwd, pbs_out_file)
-
- def status_monitor(self, update=5):
- i = 0
- self.loglinenumber = 0
- while self.in_queue():
- i += 1
- print (i, self.status, self.get_nodeid())
- if self.status is pbsjob.RUNNING:
- #self.test()
- scratch_log_filename = "/scratch/%s/%s.g-000.risoe.dk/%s" % (self.client.username, self.jobid, self.log_filename)
- try:
- n, out, err = self.client.execute('tail --lines=+%d %s' % (self.loglinenumber, scratch_log_filename))
- self.loginterpreter.update_status(out)
- print (self.loginterpreter.status, self.loginterpreter.pct, self.loginterpreter.remaining_time, self.loginterpreter.lastline)
- with open("status" + self.jobid, 'w') as fid:
- fid.write(";".join([self.loginterpreter.status, str(self.loginterpreter.pct), str(self.loginterpreter.remaining_time), self.loginterpreter.lastline]))
- #print (out)
- self.loglinenumber += out.count ("\n")
- #print (err)
-
- except Warning as e:
- if not "tail: cannot open" in str(e):
- print (str(e))
-
- time.sleep(update)
- print (i, self.status, self.get_nodeid())
-
- def test(self):
- self.log_filename = "logfiles/short.log"
- scratch_log_filename = "/scratch/%s/%s.g-000.risoe.dk/%s" % (self.client.username, self.jobid, self.log_filename)
- print (scratch_log_filename)
- try:
- n, out, err = self.client.execute('tail --lines=+%d %s' % (self.loglinenumber, scratch_log_filename))
- print (n)
- print (out)
- self.loglinenumber += out.count ("\n")
- print (err)
-
- except Warning as e:
- print (str(e))
diff --git a/wetb/hawc2/htc_file.py b/wetb/hawc2/htc_file.py
index d539794e32d0f8107757e1e8b4e30b5f40d6f4c8..95e3fb7485eca3f670b95e98174977cffb617b31 100644
--- a/wetb/hawc2/htc_file.py
+++ b/wetb/hawc2/htc_file.py
@@ -169,7 +169,7 @@ class HTCFile(HTCContents, HTCDefaults):
return [f for f in files if f]
def turbulence_files(self):
- if self.wind.turb_format[0] == 0:
+ if 'wind' not in self.contents.keys() or self.wind.turb_format[0] == 0:
return []
elif self.wind.turb_format[0] == 1:
files = [self.get('wind.mann.filename_%s' % comp, [None])[0] for comp in ['u', 'v', 'w']]
diff --git a/wetb/hawc2/log_file.py b/wetb/hawc2/log_file.py
index 622bb6fc009df5834ecf6ab9f2ee3bfe26be5748..48a810c8455258c636a9f521835bfbb63ab6c8c8 100644
--- a/wetb/hawc2/log_file.py
+++ b/wetb/hawc2/log_file.py
@@ -169,6 +169,16 @@ class LogFile(LogInterpreter):
if txt != "":
LogInterpreter.update_status(self, txt)
+class LogInfo(LogFile):
+ def __init__(self, status, pct, remaining_time, lastline):
+ self.status = status
+ self.pct = int(pct)
+ try:
+ self.remaining_time = float(remaining_time)
+ except:
+ self.remaining_time = None
+ self.lastline = lastline
+ self.errors = []
-
-
+ def update_status(self):
+ pass
\ No newline at end of file
diff --git a/wetb/hawc2/simulation.py b/wetb/hawc2/simulation.py
old mode 100644
new mode 100755
index d1d20e698568c0f91786c47a954c9cdd942955c3..f7d8a444032777b06f4cec184426cac11f17bd64
--- a/wetb/hawc2/simulation.py
+++ b/wetb/hawc2/simulation.py
@@ -1,53 +1,90 @@
-from __future__ import print_function
+from __future__ import absolute_import
from __future__ import division
+from __future__ import print_function
from __future__ import unicode_literals
-from __future__ import absolute_import
-from io import open
+
from builtins import str
-from future import standard_library
-standard_library.install_aliases()
-import os
-from wetb.hawc2.htc_file import HTCFile
-from wetb.hawc2.log_file import LogFile
-from threading import Timer, Thread
-import sys
-from multiprocessing.process import Process
-import psutil
-from wetb.utils.process_exec import process, exec_process
-import subprocess
-import shutil
-import json
import glob
-from wetb.hawc2 import log_file
+from io import open
+import io
+import json
+import os
import re
+import shutil
+import subprocess
+import sys
import threading
+import time
+from wetb.hawc2 import log_file
+from wetb.hawc2.htc_file import HTCFile
+from wetb.hawc2.log_file import LogFile, LogInfo
+from future import standard_library
+import psutil
+from wetb.utils.cluster_tools import pbsjob
+from wetb.utils.cluster_tools.cluster_resource import LocalResource
+from wetb.utils.cluster_tools.pbsjob import SSHPBSJob
+from wetb.utils.cluster_tools.ssh_client import SSHClient
+standard_library.install_aliases()
+from threading import Thread
QUEUED = "queued" #until start
PREPARING = "Copy to host" # during prepare simulation
INITIALIZING = "Initializing" #when starting
SIMULATING = "Simulating" # when logfile.status=simulating
-FINISH = "Finish" # when finish
+FINISH = "Finish" # when HAWC2 finish
ERROR = "Error" # when hawc2 returns error
ABORTED = "Aborted" # when stopped and logfile.status != Done
CLEANED = "Cleaned" # after copy back
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
+ - updateStatusThread:
+ - 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
- _status = QUEUED
- def __init__(self, modelpath, htcfilename, hawc2exe="HAWC2MB.exe"):
+ status = QUEUED
+ def __init__(self, modelpath, htcfilename, hawc2exe="HAWC2MB.exe", copy_turbulence=True):
self.modelpath = os.path.abspath(modelpath) + "/"
self.folder = os.path.dirname(htcfilename)
if not os.path.isabs(htcfilename):
htcfilename = os.path.join(modelpath, htcfilename)
- self.htcfilename = htcfilename
self.filename = os.path.basename(htcfilename)
self.htcFile = HTCFile(htcfilename)
self.time_stop = self.htcFile.simulation.time_stop[0]
- self.copy_turbulence = True
- self.simulation_id = os.path.relpath(self.htcfilename, self.modelpath).replace("\\", "_") + "_%d" % id(self)
- self.stdout_filename = "%s.out" % self.simulation_id
+ self.hawc2exe = hawc2exe
+ self.copy_turbulence = copy_turbulence
+ self.simulation_id = os.path.relpath(htcfilename, self.modelpath).replace("\\", "_").replace("/", "_") + "_%d" % id(self)
+ self.stdout_filename = "stdout/%s.out" % self.simulation_id
if 'logfile' in self.htcFile.simulation:
self.log_filename = self.htcFile.simulation.logfile[0]
else:
@@ -60,35 +97,32 @@ class Simulation(object):
self.logFile = LogFile(os.path.join(self.modelpath, self.log_filename), self.time_stop)
self.logFile.clear()
- self.last_status = self._status
+ self.last_status = self.status
self.errors = []
- self.thread = Thread(target=self.simulate_distributed)
- self.dist_thread = Thread()
- self.hawc2exe = hawc2exe
- self.simulationThread = SimulationThread(self)
- self.timer = RepeatedTimer(self.update_status)
-
+ self.non_blocking_simulation_thread = Thread(target=self.simulate_distributed)
+ self.updateStatusThread = UpdateStatusThread(self)
+ self.host = LocalSimulationHost(self)
- def __str__(self):
- return "Simulation(%s)" % self.filename
- @property
- def status(self):
- return self._status
-
- @status.setter
- def status(self, status):
- self._status = status
- self.show_status()
+ def start(self, update_interval=1):
+ """Start non blocking distributed simulation"""
+ self.is_simulating = True
+ self.updateStatusThread.start()
+ self.non_blocking_simulation_thread.start()
- def update_status(self, *args, **kwargs):
- if self.status in [INITIALIZING, SIMULATING]:
- self.logFile.update_status()
+ def wait(self):
+ self.non_blocking_simulation_thread.join()
+ self.update_status()
- if self.logFile.status == log_file.SIMULATING:
- self._status = SIMULATING
- if self.logFile.status == log_file.DONE:
- self._status = FINISH
+ def abort(self):
+ self.host.stop()
+ for _ in range(100):
+ if self.is_simulating:
+ break
+ time.sleep(0.1)
+ if self.logFile.status not in [log_file.DONE]:
+ self.status = ABORTED
+ self.update_status()
def show_status(self):
#print ("log status:", self.logFile.status)
@@ -103,6 +137,8 @@ class Simulation(object):
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:
@@ -111,47 +147,37 @@ class Simulation(object):
self.last_status = self.logFile.status
-
- 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.load(fid)
- 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 prepare_simulation(self):
self.status = PREPARING
+ self.tmp_modelpath = os.path.join(".hawc2launcher/%s/" % self.simulation_id)
+ self.set_id(self.simulation_id, str(self.host), self.tmp_modelpath)
+ self.host._prepare_simulation()
- self.tmp_modelpath = os.path.join(self.modelpath, "tmp_%s/" % self.simulation_id)
-
-
- for src in self.htcFile.input_files() + self.htcFile.turbulence_files() + self.additional_files().get('input', []):
- if not os.path.isabs(src):
- src = os.path.join(self.modelpath, src)
- for src_file in glob.glob(src):
- 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)
- else:
- #print (dst)
- pass
-
-
- self.logFile.filename = os.path.join(self.tmp_modelpath, self.log_filename)
- self.simulationThread.modelpath = self.tmp_modelpath
+ def simulate(self):
+ #starts blocking simulation
+ self.is_simulating = True
+ self.errors = []
+ self.status = INITIALIZING
+ self.logFile.clear()
+ self.host._simulate()
+ if self.host.returncode or 'error' in self.host.stdout.lower():
+ 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()])))
+ 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:\n" + "\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):
@@ -160,56 +186,64 @@ class Simulation(object):
if self.status == CLEANED: return
if self.status != ERROR:
self.status = CLEANED
+ self.host._finish_simulation()
+ self.set_id(self.simulation_id)
- files = self.htcFile.output_files()
- if self.copy_turbulence:
- files.extend(self.htcFile.turbulence_files())
- for dst in files:
- if not os.path.isabs(dst):
- dst = os.path.join(self.modelpath, dst)
- src = os.path.join(self.tmp_modelpath, os.path.relpath(dst, self.modelpath))
- for src_file in glob.glob(src):
- dst_file = os.path.join(self.modelpath, os.path.relpath(src_file, self.tmp_modelpath))
- # exist_ok does not exist in Python27
- if not os.path.exists(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)
- self.logFile.filename = os.path.join(self.modelpath, self.log_filename)
+ 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 _input_sources(self):
+ def fmt(src):
+ if os.path.isabs(src):
+ src = os.path.relpath(os.path.abspath(src), self.modelpath)
+ 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
+ return [fmt(src) for src in self.htcFile.input_files() + self.htcFile.turbulence_files() + self.additional_files().get('input', [])]
+
+ def _output_sources(self):
+ def fmt(dst):
+ if os.path.isabs(dst):
+ dst = os.path.relpath(os.path.abspath(dst), self.modelpath)
+ else:
+ dst = os.path.relpath (dst)
+ dst = dst.replace("\\", "/")
+ assert not dst.startswith(".."), "%s referes to a file outside the model path\nAll input files be inside model path" % dst
+ return dst
+ return [fmt(dst) for dst in self.htcFile.output_files() + ([], self.htcFile.turbulence_files())[self.copy_turbulence] + [self.stdout_filename]]
- try:
- shutil.rmtree(self.tmp_modelpath)
- except (PermissionError, OSError) as e:
- raise Warning(str(e))
+ def __str__(self):
+ return "Simulation(%s)" % self.filename
- def simulate(self):
- #starts blocking simulation
- self.is_simulating = True
- self.errors = []
- self.logFile.clear()
- self.status = INITIALIZING
- self.returncode, self.stdout = 1, "Simulation failed"
- self.simulationThread.start()
- self.simulationThread.join()
- self.returncode, self.stdout = self.simulationThread.res
- if self.returncode or 'error' in self.stdout.lower():
- self.errors = list(set([l for l in self.stdout.split("\n") if 'error' in l.lower()]))
- self.status = ERROR
- self.is_simulating = False
- self.logFile.update_status()
- self.errors.extend(list(set(self.logFile.errors)))
- if self.returncode:
- raise Exception("Simulation error:\n" + "\n".join(self.errors))
- elif self.logFile.status != log_file.DONE or self.errors or self.logFile.errors:
- raise Warning("Simulation succeded with errors:\nLog status:%s\n" % self.logFile.status + "\n".join(self.logFile.errors))
- else:
- self.status = FINISH
+
+
+ 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.load(fid)
+ 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):
self.prepare_simulation()
@@ -217,7 +251,6 @@ class Simulation(object):
self.finish_simulation()
-
def fix_errors(self):
def confirm_add_additional_file(folder, file):
if os.path.isfile(os.path.join(self.modelpath, folder, file)):
@@ -243,102 +276,302 @@ class Simulation(object):
continue
def get_confirmation(self, title, msg):
+ """override in subclass"""
return True
+
def show_message(self, msg, title="Information"):
print (msg)
+
+
+class UpdateStatusThread(Thread):
+ def __init__(self, simulation, interval=1):
+ Thread.__init__(self)
+ self.simulation = simulation
+ self.interval = interval
+
def start(self):
- """Start non blocking distributed simulation"""
- self.timer.start(1000)
- self.thread.start()
+ Thread.start(self)
+
+ def run(self):
+ while self.simulation.is_simulating:
+ self.simulation.update_status()
+ time.sleep(self.interval)
+
+
+class SimulationResource(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)
+ tmp_modelpath = property(lambda self : self.sim.tmp_modelpath, lambda self, v: setattr(self.sim, "tmp_modelpath", 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.host
+class LocalSimulationHost(SimulationResource):
+ def __init__(self, simulation):
+ SimulationResource.__init__(self, simulation)
+ LocalResource.__init__(self, "hawc2mb")
+ self.simulationThread = SimulationThread(self.sim)
+
+ def _prepare_simulation(self):
+ # must be called through simulation object
+ self.tmp_modelpath = os.path.join(self.modelpath, self.tmp_modelpath)
+ self.sim.set_id(self.simulation_id, 'Localhost', self.tmp_modelpath)
+ for src in self._input_sources():
+ for src_file in glob.glob(os.path.join(self.modelpath, src)):
+ 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)
+
+ if not os.path.exists(os.path.join(self.tmp_modelpath, 'stdout')):
+ os.makedirs(os.path.join(self.tmp_modelpath, 'stdout')) #, exist_ok=True)
+ self.logFile.filename = os.path.join(self.tmp_modelpath, self.log_filename)
+ self.simulationThread.modelpath = self.tmp_modelpath
+
+
+ def _simulate(self):
+ #must be called through simulation object
+ self.returncode, self.stdout = 1, "Simulation failed"
+ self.simulationThread.start()
+ 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):
+ for dst in self._output_sources():
+ src = os.path.join(self.tmp_modelpath, dst)
+
+ for src_file in glob.glob(src):
+ dst_file = os.path.join(self.modelpath, os.path.relpath(src_file, self.tmp_modelpath))
+ # exist_ok does not exist in Python27
+ 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)
+
+ self.logFile.filename = os.path.join(self.modelpath, self.log_filename)
- def stop(self):
- self.timer.stop()
- self.simulationThread.process.kill()
try:
- self.finish_simulation()
- except:
- pass
- if self.logFile.status not in [log_file.DONE]:
- self.status = ABORTED
- self.update_status()
+ shutil.rmtree(self.tmp_modelpath)
+ except (PermissionError, OSError) as e:
+ raise Warning(str(e))
+
+ def update_logFile_status(self):
+ self.logFile.update_status()
+
+ def stop(self):
+ self.simulationThread.stop()
+ self.simulationThread.join()
-#class SimulationProcess(Process):
-#
-# def __init__(self, modelpath, htcfile, hawc2exe="HAWC2MB.exe"):
-# Process.__init__(self)
-# self.modelpath = modelpath
-# self.htcfile = os.path.abspath(htcfile)
-# self.hawc2exe = hawc2exe
-# self.res = [0, "", "", ""]
-# self.process = process([self.hawc2exe, self.htcfile] , self.modelpath)
-#
-#
-# def run(self):
-# p = psutil.Process(os.getpid())
-# p.nice = psutil.BELOW_NORMAL_PRIORITY_CLASS
-# exec_process(self.process)
class SimulationThread(Thread):
- def __init__(self, simulation):
+ def __init__(self, simulation, low_priority=True):
Thread.__init__(self)
self.sim = simulation
self.modelpath = self.sim.modelpath
self.res = [0, "", ""]
+ self.low_priority = low_priority
def start(self):
- si = subprocess.STARTUPINFO()
- si.dwFlags |= subprocess.STARTF_USESHOWWINDOW
CREATE_NO_WINDOW = 0x08000000
modelpath = self.modelpath
htcfile = os.path.relpath(self.sim.htcFile.filename, self.sim.modelpath)
hawc2exe = self.sim.hawc2exe
stdout = self.sim.stdout_filename
- self.process = subprocess.Popen('"%s" %s 1> %s 2>&1' % (hawc2exe, htcfile, stdout), stdout=None, stderr=None, shell=True, cwd=modelpath, creationflags=CREATE_NO_WINDOW)
-
+ if os.name == "nt":
+ self.process = subprocess.Popen('"%s" %s 1> %s 2>&1' % (hawc2exe, htcfile, stdout), stdout=None, stderr=None, shell=True, cwd=modelpath) #, creationflags=CREATE_NO_WINDOW)
+ else:
+ self.process = subprocess.Popen('wine "%s" %s 1> %s 2>&1' % (hawc2exe, htcfile, stdout), stdout=None, stderr=None, shell=True, cwd=modelpath)
Thread.start(self)
def run(self):
p = psutil.Process(os.getpid())
- p.set_nice(psutil.BELOW_NORMAL_PRIORITY_CLASS)
+ if self.low_priority:
+ p.set_nice(psutil.BELOW_NORMAL_PRIORITY_CLASS)
self.process.communicate()
errorcode = self.process.returncode
+ if not os.path.isdir(os.path.dirname(self.modelpath + self.sim.stdout_filename)):
+ os.makedirs(os.path.dirname(self.modelpath + self.sim.stdout_filename))
with open(self.modelpath + self.sim.stdout_filename, encoding='utf-8') as fid:
stdout = fid.read()
self.res = errorcode, stdout
+ def stop(self):
+ subprocess.Popen("TASKKILL /F /PID {pid} /T".format(pid=self.process.pid))
+
+
+class PBSClusterSimulationHost(SimulationResource, SSHClient):
+ def __init__(self, simulation, host, username, password, port=22):
+ SimulationResource.__init__(self, simulation)
+ SSHClient.__init__(self, host, username, password, port=port)
+ self.pbsjob = SSHPBSJob(host, username, password, port)
+
+ hawc2exe = property(lambda self : os.path.basename(self.sim.hawc2exe))
+
+
+ def _prepare_simulation(self):
+ with self:
+ self.execute(["mkdir -p .hawc2launcher/%s" % self.simulation_id], verbose=False)
+ self.execute("mkdir -p %s%s" % (self.tmp_modelpath, os.path.dirname(self.log_filename)))
+
+ for src in self._input_sources():
+ for src_file in glob.glob(os.path.join(self.modelpath, src)):
+ dst = (self.tmp_modelpath + os.path.relpath(src_file, self.modelpath)).replace("\\", "/")
+ 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())
+ f.seek(0)
+ self.upload(f, self.tmp_modelpath + "%s.in" % self.simulation_id)
+ self.execute("mkdir -p .hawc2launcher/%s/stdout" % self.simulation_id)
+ remote_log_filename = "%s%s" % (self.tmp_modelpath, self.log_filename)
+ self.execute("rm -f %s" % remote_log_filename)
+
+
+
+ def _finish_simulation(self):
+ with self:
+ for dst in self._output_sources():
+
+ src = os.path.join(self.tmp_modelpath, dst).replace("\\", "/")
+ for src_file in self.glob(src):
+ 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, verbose=False)
+ self.execute('rm -r .hawc2launcher/%s' % self.simulation_id)
+ self.execute('rm .hawc2launcher/status_%s' % self.simulation_id)
+
+
+ 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_modelpath , self.sim.stdout_filename)
+ sleeptime = 1
+ while self.is_simulating:
+ #self.__update_logFile_status()
+ time.sleep(sleeptime)
+
+ local_out_file = self.modelpath + self.sim.stdout_filename
+ with self:
+ try:
+ self.download(self.tmp_modelpath + self.sim.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_modelpath + self.log_filename, self.modelpath + self.log_filename)
+ except Exception:
+ raise Exception ("Logfile not found")
+ self.sim.logFile = LogFile.from_htcfile(self.htcFile, self.modelpath)
+
+
+
+ def update_logFile_status(self):
+ status = self.pbsjob.status
+ if status == pbsjob.NOT_SUBMITTED:
+ pass
+ elif status == pbsjob.DONE:
+ self.is_simulating = False
+ pass
+ else:
+ try:
+ _, out, _ = self.execute("cat .hawc2launcher/status_%s" % self.simulation_id)
+ out = out.split(";")
+ if len(out) == 5:
+ self.status = out[0]
+ self.logFile = LogInfo(*out[1:])
+
+ except Exception as e:
+ if "No such file or directory" in str(e):
+ pass
+ else:
+ raise
-
-class RepeatedTimer(object):
- def __init__(self, function, *args, **kwargs):
- self._timer = None
- self.function = function
- self.args = args
- self.kwargs = kwargs
- self.is_running = False
+ def start(self):
+ """Start non blocking distributed simulation"""
+ self.non_blocking_simulation_thread.start()
- def _run(self):
- self.is_running = False
- self.start(self.interval)
- self.function(*self.args, **self.kwargs)
- def start(self, interval_ms=None):
- self.interval = interval_ms
- if not self.is_running:
- self._timer = Timer(interval_ms / 1000, self._run)
- self._timer.start()
- self.is_running = True
+ def abort(self):
+ self.pbsjob.stop()
+ self.stop()
+ try:
+ self.finish_simulation()
+ except:
+ pass
+ if self.status != ERROR and self.logFile.status not in [log_file.DONE]:
+ self.status = ABORTED
def stop(self):
- self._timer.cancel()
- self.is_running = False
+ self.is_simulating = False
+ self.pbsjob.stop()
+
+ def pbsjobfile(self):
+ cp_back = ""
+ for folder in set([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 = os.path.relpath(self.htcFile.filename, self.modelpath).replace("\\", "/")
+ return """
+### 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=01:00:00
+###PBS -a 201547.53
+#PBS -lnodes=1:ppn=1
+### Queue name
+#PBS -q workq
+### Create scratch directory and copy data to it
+cd $PBS_O_WORKDIR
+pwd
+cp -R . /scratch/$USER/$PBS_JOBID
+### Execute commands on scratch nodes
+cd /scratch/$USER/$PBS_JOBID
+pwd
+echo "---------------------"
+python -c "from wetb.hawc2.cluster_simulation import ClusterSimulation;ClusterSimulation('.','%s', '%s')"
+echo "---------------------"
+echo $?
+echo "---------------------"
+### Copy back from scratch directory
+cd /scratch/$USER/$PBS_JOBID
+%s
+echo $PBS_JOBID
+cd /scratch/
+### rm -r $PBS_JOBID
+exit""" % (self.simulation_id, self.stdout_filename, rel_htcfilename, self.hawc2exe, cp_back)
+
+
-if __name__ == "__main__":
- sim = Simulation('C:\mmpe\HAWC2\Hawc2_model/', 'htc/error.htc')
- sim.simulate()
diff --git a/wetb/prepost/Simulations.py b/wetb/prepost/Simulations.py
index 164aa1866638be0fce68b42f14bddeb9f5db2f35..a8abd120fc7b0bebedb5994d95d327bf82e6833b 100755
--- a/wetb/prepost/Simulations.py
+++ b/wetb/prepost/Simulations.py
@@ -3379,7 +3379,6 @@ class Cases(object):
self.loadstats = kwargs.get('loadstats', False)
self.rem_failed = kwargs.get('rem_failed', True)
self.config = kwargs.get('config', {})
- print(self.config)
# determine the input argument scenario
if len(args) == 1:
if type(args[0]).__name__ == 'dict':
@@ -5202,5 +5201,4 @@ def eigenstructure(cases, debug=False):
return cases
if __name__ == '__main__':
- pass
-
+ pass
\ No newline at end of file
diff --git a/wetb/utils/cluster_tools/cluster_resource.py b/wetb/utils/cluster_tools/cluster_resource.py
new file mode 100644
index 0000000000000000000000000000000000000000..804c6ed904e531b4e025ba5c8d3d22ee3386d925
--- /dev/null
+++ b/wetb/utils/cluster_tools/cluster_resource.py
@@ -0,0 +1,77 @@
+'''
+Created on 04/04/2016
+
+@author: MMPE
+'''
+from wetb.utils.cluster_tools.ssh_client import SSHClient
+from wetb.utils.cluster_tools import pbswrap
+import multiprocessing
+import psutil
+
+class Resource(object):
+
+ def __init__(self, min_cpu, min_free):
+ self.min_cpu = min_cpu
+ self.min_free = min_free
+
+ def ok2submit(self):
+ """Always ok to have min_cpu cpus and ok to have more if there are min_free free cpus"""
+ total, free, user = self.check_resources()
+
+ if user < self.min_cpu:
+ return True
+ elif free > self.min_free:
+ return True
+ else:
+ return False
+
+
+
+
+class SSHPBSClusterResource(Resource, SSHClient):
+ def __init__(self, host, username, password, port, min_cpu, min_free):
+ Resource.__init__(self, min_cpu, min_free)
+ SSHClient.__init__(self, host, username, password, port=port)
+
+ def new_ssh_connection(self):
+ return SSHClient(self.host, self.username, self.password, self.port)
+
+ def check_resources(self):
+ with self:
+ _, output, _ = self.execute('pbsnodes -l all')
+ pbsnodes, nodes = pbswrap.parse_pbsnode_lall(output.split("\n"))
+
+ _, output, _ = self.execute('qstat -n1')
+ users, host, nodesload = pbswrap.parse_qstat_n1(output.split("\n"))
+
+
+ # if the user does not have any jobs, this will not exist
+ try:
+ cpu_user = users[self.username]['cpus']
+ cpu_user += users[self.username]['Q']
+ except KeyError:
+ cpu_user = 0
+ cpu_free, nodeSum = pbswrap.count_cpus(users, host, pbsnodes)
+
+ return nodeSum['used_cpu'] + cpu_free, cpu_free, cpu_user
+
+
+
+class LocalResource(Resource):
+ def __init__(self, process_name):
+ N = max(1, multiprocessing.cpu_count() / 4)
+ Resource.__init__(self, N, N)
+ self.process_name = process_name
+ self.host = 'Localhost'
+
+ def check_resources(self):
+ def name(i):
+ try:
+ return psutil.Process(i).name
+ except psutil._error.AccessDenied:
+ return ""
+
+ no_cpu = multiprocessing.cpu_count()
+ cpu_free = (1 - psutil.cpu_percent(.5) / 100) * no_cpu
+ no_current_process = len([i for i in psutil.get_pid_list() if name(i).lower().startswith(self.process_name.lower())])
+ return no_cpu, cpu_free, no_current_process
diff --git a/wetb/utils/cluster_tools/pbsjob.py b/wetb/utils/cluster_tools/pbsjob.py
index ae18eaf8ccd00bf8c0129c65d5743900b0ba0dad..7b6d6f8e8827eecad29c19fab91f6e3ca280577c 100644
--- a/wetb/utils/cluster_tools/pbsjob.py
+++ b/wetb/utils/cluster_tools/pbsjob.py
@@ -3,42 +3,35 @@ Created on 04/12/2015
@author: mmpe
'''
-
-#import x
-import time
-from wetb.utils.cluster_tools.ssh_client import SSHClient
import os
-import paramiko
-import subprocess
-
-
+from wetb.utils.cluster_tools.ssh_client import SSHClient
NOT_SUBMITTED = "Job not submitted"
PENDING = "Pending"
RUNNING = "Running"
DONE = "Done"
-class PBSJob(object):
+
+
+class SSHPBSJob(SSHClient):
_status = NOT_SUBMITTED
nodeid = None
- def __init__(self, host, username, password):
- self.client = SSHClient(host, username, password, port=22)
+ jobid = None
- def execute(self, cmd, cwd="./"):
- proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, cwd=cwd)
- stdout, stderr = proc.communicate()
- errorcode = proc.returncode
- return errorcode, stdout.decode(), stderr.decode()
+ def __init__(self, host, username, password, port=22):
+ SSHClient.__init__(self, host, username, password, port=port)
def submit(self, job, cwd, pbs_out_file):
self.cwd = cwd
self.pbs_out_file = os.path.relpath(cwd + pbs_out_file).replace("\\", "/")
self.nodeid = None
- try:
- os.remove (self.pbs_out_file)
- except FileNotFoundError:
- pass
- _, out, _ = self.execute("qsub %s" % job, cwd)
+ #self.execute()
+
+ cmds = ['rm -f %s' % self.pbs_out_file]
+ if cwd != "":
+ cmds.append("cd %s" % cwd)
+ cmds.append("qsub %s" % job)
+ _, out, _ = self.execute(";".join(cmds))
self.jobid = out.split(".")[0]
self._status = PENDING
@@ -46,44 +39,38 @@ class PBSJob(object):
def status(self):
if self._status in [NOT_SUBMITTED, DONE]:
return self._status
-
- if self.nodeid is None:
- self.nodeid = self.get_nodeid()
- if self.nodeid is not None:
+ with self:
+ if self.is_executing():
self._status = RUNNING
-
- if self.in_queue() and self.nodeid is None:
- self._status = PENDING
- elif os.path.isfile(self.pbs_out_file):
- self._status = DONE
+ elif self.file_exists(self.pbs_out_file):
+ self._status = DONE
+ self.jobid = None
return self._status
def get_nodeid(self):
- errorcode, out, err = self.execute("qstat -f %s | grep exec_host" % self.jobid)
- if errorcode == 0:
- return out.strip().replace("exec_host = ", "").split(".")[0]
- elif errorcode == 1 and out == "":
- return None
- elif errorcode == 153 and 'qstat: Unknown Job Id' in err:
+ try:
+ _, out, _ = self.execute("qstat -f %s | grep exec_host" % self.jobid)
+ return out.strip().replace("exec_host = ", "").split(".")[0]
+ except Warning as e:
+ if 'qstat: Unknown Job Id' in str(e):
return None
- else:
- raise Exception(str(errorcode) + out + err)
+ #raise e
def stop(self):
- try:
- self.execute("qdel %s" % self.jobid)
- except Warning as e:
- if 'qdel: Unknown Job Id' in str(e):
- return
- raise e
+ if self.jobid:
+ try:
+ self.execute("qdel %s" % self.jobid)
+ except Warning as e:
+ if 'qdel: Unknown Job Id' in str(e):
+ return
+ raise e
- def in_queue(self):
- errorcode, out, err = self.execute("qstat %s" % self.jobid)
- if errorcode == 0:
+ def is_executing(self):
+ try:
+ self.execute("qstat %s" % self.jobid)
return True
- elif 'qstat: Unknown Job Id' in str(err):
- return False
- else:
- raise Exception(str(errorcode) + out + err)
-
+ except Warning as e:
+ if 'qstat: Unknown Job Id' in str(e):
+ return False
+ raise e
diff --git a/wetb/utils/cluster_tools/pbswrap.py b/wetb/utils/cluster_tools/pbswrap.py
new file mode 100644
index 0000000000000000000000000000000000000000..5eb3f37091f97405676dac4fd4347c12050bbbe2
--- /dev/null
+++ b/wetb/utils/cluster_tools/pbswrap.py
@@ -0,0 +1,389 @@
+#!/usr/bin/python
+#-----------------------------------------------------------------------------
+# Author: David Verelst - david.verelst@gmail.com
+# Version: 0.10 - 15/03/2010
+# Version: 0.11 - 13/04/2010 : adding nodes down, offline to the total
+# overview of available nodes
+# version: 0.20 - 17/11/2011 : major rewrite, support added for gorm
+# version: 0.30 - 19/12/2012 : refactoring, added the node overview
+# version: 0.40 - 26/03/2014 : removed Thyra, added support for Jess
+#-----------------------------------------------------------------------------
+
+import os
+import socket
+
+def print_dashboard(users, host, pbsnodes):
+
+ # print nicely
+ # the header
+ # ---------------------------------------------
+ # User Running Queued Waiting Other
+ # ---------------------------------------------
+ # jber 3 0 0 0
+
+ print
+ print ('-' * 54)
+ print ('cpus'.rjust(18) + 'nodes'.rjust(9))
+ print ('User'.rjust(9) + 'Running'.rjust(9) + 'Running'.rjust(9) \
+ + 'Queued'.rjust(9) + 'Waiting'.rjust(9) + 'Other'.rjust(9))
+ # nodeSum: overview (summation of all jobs) nodes per user:
+ # nodeSum = [running, queued, waiting, other, cpus]
+ nodeSum = [0, 0, 0, 0, 0]
+ print ('-' * 54)
+ # print all values in the table: the nodes used per user
+ #userlist = users['users'].keys()
+ #userlist.sort()
+ for uid in sorted(users):
+
+ # or get the unique nodes the user is on
+ try:
+ R = len(users[uid]['nodes'])
+ except KeyError:
+ # means it is not running yet but queued, waiting or otherwise
+ R = users[uid]['R']
+ Q = users[uid]['Q']
+ W = users[uid]['W']
+ O = users[uid]['E'] + users[uid]['H'] + users[uid]['T'] \
+ + users[uid]['S'] + users[uid]['O'] + users[uid]['C']
+
+ cpus = users[uid]['cpus']
+ print (uid.rjust(9) + str(cpus).rjust(9) + str(R).rjust(9) \
+ + str(Q).rjust(9) + str(W).rjust(9) + str(O).rjust(9))
+ nodeSum[0] += R
+ nodeSum[1] += Q
+ nodeSum[2] += W
+ nodeSum[3] += O
+ nodeSum[4] += cpus
+
+ nr_nodes = pbsnodes['nr_nodes']
+ down = pbsnodes['down']
+ others = pbsnodes['others']
+ total_cpu = host['cpu_per_node'] * nr_nodes
+
+ # the summed up for each node status (queued, running,...)
+ print ('-' * 54)
+ print ('total'.rjust(9) + str(nodeSum[4]).rjust(9) + str(nodeSum[0]).rjust(9) \
+ + str(nodeSum[1]).rjust(9) + str(nodeSum[2]).rjust(9)\
+ + str(nodeSum[3]).rjust(9))
+ print ('-' * 54)
+ print ('free'.rjust(9) + str(total_cpu - nodeSum[4]).rjust(9) \
+ + str(nr_nodes - nodeSum[0] - others - down).rjust(9))
+ print ('down'.rjust(9) + str(down).rjust(18))
+ print ('-' * 54)
+ print
+
+
+def print_node_loading(users, host, nodes, nodesload):
+ """
+ Give an overview of how each node is loaded
+ """
+
+ if len(host) < 1:
+ print ('It is very quit, nobody is working on the cluster.')
+ return
+
+ hostname = host['name']
+ cpunode = host['cpu_per_node']
+
+ print
+ # print a header
+ if hostname == 'gorm':
+ print ('-' * 79)
+ header = '|'.join([str(k).center(5) for k in range(1, 13, 1)]) + '|'
+ print ('id'.center(5), header)
+ print ('-' * 79)
+ elif hostname == 'jess':
+ print ('-' * 126)
+ header = '|'.join([str(k).center(5) for k in range(1, 21, 1)]) + '|'
+ print ('id'.center(5), header)
+ print ('-' * 126)
+
+ # print who is using the nodes
+ for node in sorted(nodes):
+ status = nodes[node]
+ # now we have a list of user on this node
+ try:
+ users = sorted(nodesload[node])
+ for kk in range(len(users), cpunode):
+ users.append('')
+ # limit uid names to 5 characters
+ printlist = '|'.join([k[:5].center(5) for k in users]) + '|'
+ # if it doesn't exist in the nodesload, just print the status
+ except KeyError:
+ printlist = status.center(5)
+
+ print (node, printlist)
+
+ # print a header
+ if hostname == 'gorm':
+ print ('-' * 79)
+ print ('id'.center(5), header)
+ print ('-' * 79)
+ elif hostname == 'jess':
+ print ('-' * 126)
+ print ('id'.center(5), header)
+ print ('-' * 126)
+ #print
+
+
+def parse_pbsnode_lall(output):
+ # read the qstat output
+ frees, exclusives, others, down = 0, 0, 0, 0
+ nr_nodes = 0
+
+ nodes = {}
+
+ for k in output:
+ if len(k) > 2:
+ line = k.split()
+ status = line[1]
+ node = line[0].split('.')[0]
+
+ if node.startswith('v-'):
+ #host = 'valde'
+ # uglye monkey patch: ignore any valde nodes
+ continue
+
+ #elif node.startswith('g-'):
+ #host = 'gorm'
+ #elif node.startswith('th-'):
+ #host = 'thyra'
+
+ if status == 'free':
+ frees += 1
+ nr_nodes += 1
+ elif status == 'job-exclusive':
+ exclusives += 1
+ nr_nodes += 1
+ elif status == 'down,offline':
+ down += 1
+ elif status == 'offline':
+ down += 1
+ elif status == 'down':
+ down += 1
+ else:
+ others += 1
+
+ nodes[node] = status
+
+ #check = frees + exclusives + down + others
+
+ pbsnodes = {'frees' : frees, 'nr_nodes' : nr_nodes, 'others' : others,
+ 'exclusives' : exclusives, 'down' : down}
+
+ return pbsnodes, nodes
+
+
+def parse_qstat_n1(output):
+ """
+ Parse the output of qstat -n1
+ """
+
+ # for global node usage, keep track of how many processes are running on
+ # each of the nodes
+ nodesload = {}
+ # store it all in dictionaries
+ host = {}
+ users = {}
+ # get the hostname
+ hostname = output[1]
+ if hostname[:5] == 'g-000':
+ host['name'] = 'gorm'
+ host['cpu_per_node'] = 12
+ else:
+ # 272 nodes are 2 x 10 core (twenty) processors
+ host['name'] = 'jess'
+ #total_nodes = 80
+ host['cpu_per_node'] = 20
+ # take the available nodes in nr_nodes: it excludes the ones
+ # who are down
+ #queue['_total_cpu_'] = cpu_node*nr_nodes
+
+ for line in output[5:]: # first 5 are not relevant
+ if line == "":
+ continue
+ items = line.split()
+ queue = items[2]
+
+ # uglye monkey patch: ignore any valde nodes
+ if queue == 'valdeq':
+ continue
+
+ jobid = items[0]
+ # valid line starts with the jobid, which is an int
+ jobid = jobid.split('.')[0]
+ userid = items[1]
+ # nr nodes used by the job
+ job_nodes = int(items[5])
+ # status of the job
+ job_status = items[9]
+ # is the user already in the queue dict?
+ try:
+ users[userid]['jobs'].append(jobid)
+ users[userid][job_status] += job_nodes
+ # if the user wasn't added before, create the sub dictionaries
+ except KeyError:
+ # initialise the users dictionary and job list
+ users[userid] = dict()
+ users[userid]['C'] = 0
+ users[userid]['E'] = 0
+ users[userid]['H'] = 0
+ users[userid]['Q'] = 0
+ users[userid]['R'] = 0
+ users[userid]['T'] = 0
+ users[userid]['W'] = 0
+ users[userid]['S'] = 0
+ users[userid]['O'] = 0
+ users[userid]['cpus'] = 0
+ users[userid]['jobs'] = []
+ users[userid]['nodes'] = set()
+ # set the values
+ users[userid]['jobs'].append(jobid)
+ users[userid][job_status] += job_nodes
+
+ if job_status == 'R':
+ # each occurance of the node name is seprated by a + and
+ # indicates a process running on a CPU of that node
+ nodes = items[11].split('+')
+ # TODO: take into account cpu number for jess: j-304/5
+ # on jess, the cpu number of the node is indicated, ignore for now
+ if host['name'].startswith('jess'):
+ for i, node in enumerate(nodes):
+ nodes[i] = node.split('/')[0]
+ # keep track of the number of processes the user running
+ users[userid]['cpus'] += len(nodes)
+ # for the number of used nodes, keep track of the unique nodes used
+ users[userid]['nodes'].update(set(nodes))
+ # remember all the nodes the user is on in a dictionary
+ for node in nodes:
+ try:
+ nodesload[node].append(userid)
+ except KeyError:
+ nodesload[node] = [userid]
+
+ return users, host, nodesload
+
+
+def count_cpus(users, host, pbsnodes):
+ """
+ See how many cpu's are actually free
+ """
+ nodeSum = {'R':0, 'Q':0, 'W':0, 'O':0, 'used_cpu':0, 'H':0}
+
+ for uid in users:
+
+ # or get the unique nodes the user is on
+ try:
+ nodeSum['R'] = len(users[uid]['nodes'])
+ except KeyError:
+ # means it is not running yet but queued, waiting or otherwise
+ nodeSum['R'] = users[uid]['R']
+
+ nodeSum['Q'] += users[uid]['Q']
+ nodeSum['W'] += users[uid]['W']
+ nodeSum['H'] += users[uid]['H']
+ nodeSum['used_cpu'] += users[uid]['cpus']
+ nodeSum['O'] += users[uid]['E'] + users[uid]['T'] + users[uid]['S'] \
+ + users[uid]['O'] + users[uid]['C']
+
+ # free cpus
+ down_cpu = host['cpu_per_node'] * pbsnodes['down']
+ total_cpu = host['cpu_per_node'] * pbsnodes['nr_nodes']
+ cpu_free = total_cpu - down_cpu - nodeSum['used_cpu']
+
+ return cpu_free, nodeSum
+
+
+PBS_TEMP = """
+### Standard Output
+#PBS -N [jobname]
+#PBS -o ./[pbs_out_file]
+### Standard Error
+#PBS -e ./[pbs_err_file]
+#PBS -W umask=003
+### Maximum wallclock time format HOURS:MINUTES:SECONDS
+#PBS -l walltime=[walltime]
+#PBS -lnodes=[lnodes]:ppn=[ppn]
+### Queue name
+#PBS -q [queue]
+### Browse to current working dir
+cd $PBS_O_WORKDIR
+pwd
+### ===========================================================================
+### set environment variables, activate python virtual environment, execute
+[commands]
+
+### ===========================================================================
+### wait for jobs to finish
+wait
+exit
+"""
+# TODO: this is very similar compared to what happens in qsub-wrap
+def create_input(walltime='00:59:59', queue='xpresq', pbs_in='pbs_in/', ppn=1,
+ pbs_out='pbs_out/', jobname=None, commands=None, lnodes=1):
+ """
+ Create a PBS script for a command. Optionally, define a python environment.
+ """
+
+ pbs_err_file = os.path.join(pbs_out, jobname + '.err')
+ pbs_out_file = os.path.join(pbs_out, jobname + '.out')
+ pbs_in_file = os.path.join(pbs_in, jobname + '.pbswrap')
+
+ pbs_script = PBS_TEMP
+ pbs_script = pbs_script.replace('[jobname]', jobname)
+ pbs_script = pbs_script.replace('[pbs_out_file]', pbs_out_file)
+ pbs_script = pbs_script.replace('[pbs_err_file]', pbs_err_file)
+ pbs_script = pbs_script.replace('[walltime]', walltime)
+ pbs_script = pbs_script.replace('[lnodes]', str(lnodes))
+ pbs_script = pbs_script.replace('[ppn]', str(ppn))
+ pbs_script = pbs_script.replace('[queue]', queue)
+ pbs_script = pbs_script.replace('[commands]', commands)
+
+ print ('following commands will be executed on the cluster:')
+ print ('%s' % (commands))
+
+ # make sure a pbs_in and pbs_out directory exists
+ if not os.path.exists(pbs_in):
+ os.makedirs(pbs_in)
+ if not os.path.exists(pbs_out):
+ os.makedirs(pbs_out)
+
+ # write the pbs_script
+ FILE = open(pbs_in_file, 'w')
+ FILE.write(pbs_script)
+ FILE.close()
+
+ return pbs_in_file
+
+
+def test():
+
+ # sample output
+ FILE = open('tests/sampleoutput_pbsnodes', 'rb')
+ output = FILE.readlines()
+ FILE.close()
+ pbsnodes, nodes = parse_pbsnode_lall(output)
+
+ # sample output
+ FILE = open('tests/sampleoutput_qstat', 'rb')
+ output = FILE.readlines()
+ FILE.close()
+ users, host, nodesload = parse_qstat_n1(output)
+
+ print_node_loading(users, host, nodes, nodesload)
+ print_dashboard(users, host, pbsnodes)
+
+
+if __name__ == '__main__':
+
+ #command = 'pbsnodes -l all' # | cut -c 22-35
+
+ output = os.popen('pbsnodes -l all').readlines()
+ pbsnodes, nodes = parse_pbsnode_lall(output)
+
+ output = os.popen('qstat -n1').readlines()
+ users, host, nodesload = parse_qstat_n1(output)
+
+ print_node_loading(users, host, nodes, nodesload)
+ print_dashboard(users, host, pbsnodes)
+
diff --git a/wetb/utils/cluster_tools/ssh_client.py b/wetb/utils/cluster_tools/ssh_client.py
index 1d70e472b1aed1705b436038bed2d5ff42e4b564..ea125bb77ade4aeeb662d91e9701ce201d552b8e 100644
--- a/wetb/utils/cluster_tools/ssh_client.py
+++ b/wetb/utils/cluster_tools/ssh_client.py
@@ -19,6 +19,8 @@ class SSHClient(object):
self.password = password
self.port = port
self.key = key
+ self.disconnect = 0
+ self.client = None
if key is not None:
self.key = paramiko.RSAKey.from_private_key(StringIO(key), password=passphrase)
@@ -26,6 +28,11 @@ class SSHClient(object):
return self.host, self.username, self.password, self.port
def __enter__(self):
+ self.disconnect += 1
+ if self.client is None:
+ self.connect()
+
+ def connect(self):
self.client = paramiko.SSHClient()
self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
self.client.connect(self.host, self.port, username=self.username, password=self.password, pkey=self.key, timeout=self.TIMEOUT)
@@ -36,7 +43,9 @@ class SSHClient(object):
return self
def __exit__(self, *args):
- self.close()
+ self.disconnect -= 1
+ if self.disconnect == 0:
+ self.close()
def download(self, remotefilepath, localfile, verbose=False):
@@ -68,6 +77,7 @@ class SSHClient(object):
self.client = None
self.sftp.close()
self.transport.close()
+ self.disconnect = False
def file_exists(self, filename):
_, out, _ = (self.execute('[ -f %s ] && echo "File exists" || echo "File does not exists"' % filename.replace("\\", "/")))
@@ -133,7 +143,7 @@ class SSHClient(object):
if __name__ == "__main__":
from mmpe.ui.qt_ui import QtInputUI
q = QtInputUI(None)
- import x
+ x = None
username, password = "mmpe", x.password #q.get_login("mmpe")