def run(self):
"""Runs the simulation.
Does all the simulation steps, and outputs data to the appropriate files
when necessary. Also deals with starting and cleaning up the threads used
in the communication between the driver and the PIMD code.
"""
# registers the softexit routine
softexit.register_function(self.softexit)
softexit.start(self.ttime)
# prints inital configuration -- only if we are not restarting
if self.step == 0:
self.step = -1
# must use multi-threading to avoid blocking in multi-system runs with WTE
if self.threading:
stepthreads = []
for o in self.outputs:
st = threading.Thread(target=o.write, name=o.filename)
st.daemon = True
st.start()
stepthreads.append(st)
for st in stepthreads:
while st.is_alive():
# This is necessary as join() without timeout prevents main from receiving signals.
st.join(2.0)
else:
for o in self.outputs:
o.write(
) # threaded output seems to cause random hang-ups. should make things properly thread-safe
self.step = 0
steptime = 0.0
simtime = time.time()
cstep = 0
# tptime = 0.0
# tqtime = 0.0
# tttime = 0.0
ttot = 0.0
# main MD loop
for self.step in range(self.step, self.tsteps):
# stores the state before doing a step.
# this is a bit time-consuming but makes sure that we can honor soft
# exit requests without screwing the trajectory
steptime = -time.time()
if softexit.triggered:
break
self.chk.store()
if self.threading:
stepthreads = []
# steps through all the systems
for s in self.syslist:
# creates separate threads for the different systems
st = threading.Thread(target=s.motion.step,
name=s.prefix,
kwargs={"step": self.step})
st.daemon = True
stepthreads.append(st)
for st in stepthreads:
st.start()
for st in stepthreads:
while st.is_alive():
# This is necessary as join() without timeout prevents main from receiving signals.
st.join(2.0)
else:
for s in self.syslist:
s.motion.step(step=self.step)
if softexit.triggered:
# Don't continue if we are about to exit.
break
# does the "super motion" step
if self.smotion is not None:
# TODO: We need a file where we store the exchanges
self.smotion.step(self.step)
if softexit.triggered:
# Don't write if we are about to exit.
break
if self.threading:
stepthreads = []
for o in self.outputs:
st = threading.Thread(target=o.write, name=o.filename)
st.daemon = True
st.start()
stepthreads.append(st)
for st in stepthreads:
while st.is_alive():
# This is necessary as join() without timeout prevents main from receiving signals.
st.join(2.0)
else:
for o in self.outputs:
o.write()
steptime += time.time()
ttot += steptime
cstep += 1
if (verbosity.high or (verbosity.medium and self.step % 100 == 0)
or (verbosity.low and self.step % 1000 == 0)):
info(" # Average timings at MD step % 7d. t/step: %10.5e" %
(self.step, ttot / cstep))
cstep = 0
ttot = 0.0
# info(" # MD diagnostics: V: %10.5e Kcv: %10.5e Ecns: %10.5e" %
# (self.properties["potential"], self.properties["kinetic_cv"], self.properties["conserved"] ) )
if os.path.exists("EXIT"):
info(" # EXIT file detected! Bye bye!", verbosity.low)
break
if (self.ttime > 0) and (time.time() - simtime > self.ttime):
info(" # Wall clock time expired! Bye bye!", verbosity.low)
break
self.rollback = False
def run(self):
"""Runs the simulation.
Does all the simulation steps, and outputs data to the appropriate files
when necessary. Also deals with starting and cleaning up the threads used
in the communication between the driver and the PIMD code.
"""
# registers the softexit routine
softexit.register_function(self.softexit)
softexit.start(self.ttime)
# for k, f in self.fflist.iteritems():
# f.run()
# prints inital configuration -- only if we are not restarting
if self.step == 0:
self.step = -1
# must use multi-threading to avoid blocking in multi-system runs with WTE
if self.threading:
stepthreads = []
for o in self.outputs:
st = threading.Thread(target=o.write, name=o.filename)
st.daemon = True
st.start()
stepthreads.append(st)
for st in stepthreads:
while st.isAlive():
# This is necessary as join() without timeout prevents main from receiving signals.
st.join(2.0)
else:
for o in self.outputs:
o.write() # threaded output seems to cause random hang-ups. should make things properly thread-safe
self.step = 0
steptime = 0.0
simtime = time.time()
cstep = 0
#tptime = 0.0
#tqtime = 0.0
#tttime = 0.0
ttot = 0.0
# main MD loop
for self.step in xrange(self.step, self.tsteps):
# stores the state before doing a step.
# this is a bit time-consuming but makes sure that we can honor soft
# exit requests without screwing the trajectory
steptime = -time.time()
if softexit.triggered:
break
self.chk.store()
if self.threading:
stepthreads = []
# steps through all the systems
for s in self.syslist:
# creates separate threads for the different systems
st = threading.Thread(target=s.motion.step, name=s.prefix, kwargs={"step": self.step})
st.daemon = True
stepthreads.append(st)
for st in stepthreads:
st.start()
for st in stepthreads:
while st.isAlive():
# This is necessary as join() without timeout prevents main from receiving signals.
st.join(2.0)
else:
for s in self.syslist:
s.motion.step(step=self.step)
if softexit.triggered:
# Don't continue if we are about to exit.
break
# does the "super motion" step
if self.smotion is not None:
# TODO: We need a file where we store the exchanges
self.smotion.step(self.step)
if softexit.triggered:
# Don't write if we are about to exit.
break
if self.threading:
stepthreads = []
for o in self.outputs:
st = threading.Thread(target=o.write, name=o.filename)
st.daemon = True
st.start()
stepthreads.append(st)
for st in stepthreads:
while st.isAlive():
# This is necessary as join() without timeout prevents main from receiving signals.
st.join(2.0)
else:
for o in self.outputs:
o.write()
steptime += time.time()
ttot += steptime
cstep += 1
if (verbosity.high or (verbosity.medium and self.step % 100 == 0) or (verbosity.low and self.step % 1000 == 0)):
info(" # Average timings at MD step % 7d. t/step: %10.5e" % (self.step, ttot / cstep))
cstep = 0
ttot = 0.0
# info(" # MD diagnostics: V: %10.5e Kcv: %10.5e Ecns: %10.5e" %
# (self.properties["potential"], self.properties["kinetic_cv"], self.properties["conserved"] ) )
if os.path.exists("EXIT"):
info(" # EXIT file detected! Bye bye!", verbosity.low)
break
if (self.ttime > 0) and (time.time() - simtime > self.ttime):
info(" # Wall clock time expired! Bye bye!", verbosity.low)
break
self.rollback = False
def run(self):
"""Runs the simulation.
Does all the simulation steps, and outputs data to the appropriate files
when necessary. Also deals with starting and cleaning up the threads used
in the communication between the driver and the PIMD code.
"""
# registers the softexit routine
softexit.register_function(self.softexit)
softexit.start(self.ttime)
for k, f in self.fflist.iteritems():
f.run()
# prints inital configuration -- only if we are not restarting
info("Step:", self.step)
if self.step == 0:
print # me c*g
print "Waiting for all CP2K clients to connect before starting the simulation." # me c*g
trials_count = 0 # me c*g
trials_max = 2*self.syslist[0].beads.nbeads + 500 # me c*g
while self.syslist[0].beads.nbeads != len(self.fflist["cp2k"].socket.clients): # me c*g
trials_count += 1 # me c*g
print " * Currently " + str(len(self.fflist["cp2k"].socket.clients)) + " of " + str(self.syslist[0].beads.nbeads) + " CP2K clients have connected. Sleeping one second... (trial " + str(trials_count) + " of " + str(trials_max) + ")." # me c*g
if trials_count == trials_max: # me c*g
softexit.trigger("Sufficiently many CP2K clients failed to connect within the maximum waiting time of " + str(trials_max) + " seconds.") # me c*g
time.sleep(1) # me c*g
print "All CP2K clients have connected. Continuing..." # me c*g
self.step = -1
# must use multi-threading to avoid blocking in multi-system runs with WTE
stepthreads = []
for o in self.outputs:
o.write() # threaded output seems to cause random hang-ups. should make things properly thread-safe
#st = threading.Thread(target=o.write, name=o.filename)
#st.daemon = True
#st.start()
#stepthreads.append(st)
for st in stepthreads:
while st.isAlive():
# This is necessary as join() without timeout prevents main
# from receiving signals.
st.join(2.0)
if self.mode == "paratemp":
self.paratemp.parafile.write("%10d" % (self.step + 1))
for i in self.paratemp.temp_index:
self.paratemp.parafile.write(" %5d" % i)
self.paratemp.parafile.write("\n")
self.paratemp.parafile.flush()
os.fsync(self.paratemp.parafile)
self.step = 0
steptime = 0.0
simtime = time.time()
cstep = 0
#tptime = 0.0
#tqtime = 0.0
#tttime = 0.0
ttot = 0.0
# main MD loop
for self.step in range(self.step, self.tsteps):
# stores the state before doing a step.
# this is a bit time-consuming but makes sure that we can honor soft
# exit requests without screwing the trajectory
# Checking if no CP2K client has disconnected
steptime = -time.time()
if softexit.triggered:
break
self.chk.store()
stepthreads = []
# steps through all the systems
#for s in self.syslist:
# s.motion.step()
for s in self.syslist:
# creates separate threads for the different systems
#st = threading.Thread(target=s.motion.step, name=s.prefix, kwargs={"step":self.step})
#st.daemon = True
s.motion.step(step=self.step)
#st.start()
#stepthreads.append(st)
for st in stepthreads:
while st.isAlive():
# This is necessary as join() without timeout prevents main
# from receiving signals.
st.join(2.0)
if softexit.triggered:
# Don't continue if we are about to exit.
break
for o in self.outputs:
o.write()
# does parallel tempering
if self.mode == "paratemp":
# because of where this is in the loop, we must write out BEFORE doing the swaps.
self.paratemp.parafile.write("%10d" % (self.step + 1))
for i in self.paratemp.temp_index:
self.paratemp.parafile.write(" %5d" % i)
self.paratemp.parafile.write("\n")
self.paratemp.parafile.flush()
os.fsync(self.paratemp.parafile)
self.paratemp.swap(self.step)
if softexit.triggered:
# Don't write if we are about to exit.
break
steptime += time.time()
ttot += steptime
cstep += 1
if (verbosity.high or (verbosity.medium and self.step % 100 == 0) or (verbosity.low and self.step % 1000 == 0)):
info(" # Average timings at MD step % 7d. t/step: %10.5e" % (self.step, ttot / cstep))
cstep = 0
ttot = 0.0
#info(" # MD diagnostics: V: %10.5e Kcv: %10.5e Ecns: %10.5e" %
# (self.properties["potential"], self.properties["kinetic_cv"], self.properties["conserved"] ) )
if os.path.exists("EXIT"):
info(" # EXIT file detected! Bye bye!", verbosity.low)
break
if (self.ttime > 0) and (time.time() - simtime > self.ttime):
info(" # Wall clock time expired! Bye bye!", verbosity.low)
break
self.rollback = False
