def make_searches(comm, wuid, bhstates):
num_in_buffer = comm.get_queue_size() * config.comm_job_bundle_size
logger.info("%i searches in the queue" % num_in_buffer)
num_to_make = max(config.comm_job_buffer_size - num_in_buffer, 0)
logger.info("Making %i searches" % num_to_make)
if num_to_make == 0:
return wuid
searches = []
invariants = {}
f = open(os.path.join(config.path_root, 'pos.con'))
initial_react = StringIO(f.read())
f.close()
#invariants['reactant_passed.con']=reactIO
ini_changes = [('Main', 'job', 'basin_hopping')]
#invariants['config_passed.ini'] = io.modify_config(config.config_path, ini_changes)
#invariants['reactant_passed.con'] = reactIO
#Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
searches = []
for i in range(num_to_make):
search = {}
search['id'] = "%d" % wuid
ini_changes = [('Main', 'random_seed',
str(int(numpy.random.random() * 2**32)))]
#if config.bh_random_structure:
# reactIO = StringIO()
# io.savecon(reactIO, rs.generate())
#else:
# reactIO = initial_react
if config.bh_initial_state_pool_size == 0:
reactIO = initial_react
elif config.bh_initial_state_pool_size > 0:
reactIO = bhstates.get_random_minimum()
if reactIO is None:
reactIO = initial_react
else:
logger.fatal("Initial state pool size negative")
sys.exit(1)
search['pos.con'] = reactIO
search['config.ini'] = io.modify_config(config.config_path,
ini_changes)
searches.append(search)
wuid += 1
comm.submit_jobs(searches, invariants)
logger.info(str(num_to_make) + " searches created")
return wuid
def make_searches(comm, wuid, bhstates):
num_in_buffer = comm.get_queue_size()*config.comm_job_bundle_size
logger.info("%i searches in the queue" % num_in_buffer)
num_to_make = max(config.comm_job_buffer_size - num_in_buffer, 0)
logger.info("Making %i searches" % num_to_make)
if num_to_make == 0:
return wuid
searches = []
invariants = {}
f = open(os.path.join(config.path_root, 'pos.con'))
initial_react = StringIO(f.read())
f.close()
#invariants['reactant_passed.con']=reactIO
ini_changes = [ ('Main', 'job', 'basin_hopping') ]
#invariants['config_passed.ini'] = io.modify_config(config.config_path, ini_changes)
#invariants['reactant_passed.con'] = reactIO
#Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
searches = []
for i in range(num_to_make):
search = {}
search['id'] = "%d" % wuid
ini_changes = [ ('Main', 'random_seed', str(int(numpy.random.random()*2**32))) ]
#if config.bh_random_structure:
# reactIO = StringIO()
# io.savecon(reactIO, rs.generate())
#else:
# reactIO = initial_react
if config.bh_initial_state_pool_size == 0:
reactIO = initial_react
elif config.bh_initial_state_pool_size > 0:
reactIO = bhstates.get_random_minimum()
if reactIO is None:
reactIO = initial_react
else:
logger.fatal("Initial state pool size negative")
sys.exit(1)
search['pos.con'] = reactIO
search['config.ini'] = io.modify_config(config.config_path, ini_changes)
searches.append(search)
wuid += 1
comm.submit_jobs(searches, invariants)
logger.info( str(num_to_make) + " searches created")
return wuid
def main():
config.init()
# Should we have some kind of sanity-check module/function somewhere?
fnames = [
os.path.basename(f)
for f in glob.glob(os.path.join(config.path_pot, '*'))
]
if 'pos.con' in fnames:
print "WARNING: pos.con found in potfiles path. Are you sure you want this? It will overwrite the pos.con in the calculation directory when your jobs are being run."
job = config.main_job.lower()
if job == 'akmc':
akmc.main()
elif job == 'parallel_replica' or job == 'unbiased_parallel_replica':
parallelreplica.main()
elif job == 'basin_hopping':
basinhopping.main()
elif job == 'escape_rate':
escaperate.main()
else:
import communicator
import shutil
config.path_scratch = config.path_root
comm = communicator.get_communicator()
invariants = {}
# Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
job = {}
files = [f for f in os.listdir(".") if os.path.isfile(f)]
for f in files:
fh = open(f)
if (len(f.split('.')) > 1):
#f_passed = f.split('.')[0] + "_passed." + f.split('.')[1]
f_passed = f.split('.')[0] + "." + f.split('.')[1]
job[f_passed] = StringIO(fh.read())
fh.close()
job["id"] = "output"
if os.path.isdir("output_old"):
shutil.rmtree("output_old")
if os.path.isdir("output"):
shutil.move("output", "output_old")
comm.submit_jobs([job], invariants)
def main():
config.init()
# Should we have some kind of sanity-check module/function somewhere?
fnames = [os.path.basename(f) for f in glob.glob(os.path.join(config.path_pot, '*'))]
if 'pos.con' in fnames:
print "WARNING: pos.con found in potfiles path. Are you sure you want this? It will overwrite the pos.con in the calculation directory when your jobs are being run."
job = config.main_job.lower()
if job == 'akmc':
akmc.main()
elif job == 'parallel_replica' or job == 'unbiased_parallel_replica':
parallelreplica.main()
elif job == 'basin_hopping':
basinhopping.main()
elif job == 'escape_rate':
escaperate.main()
else:
import communicator
import shutil
config.path_scratch = config.path_root
comm = communicator.get_communicator()
invariants = {}
# Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
job = {}
files = [ f for f in os.listdir(".") if os.path.isfile(f) ]
for f in files:
fh = open(f)
if(len(f.split('.')) > 1):
#f_passed = f.split('.')[0] + "_passed." + f.split('.')[1]
f_passed = f.split('.')[0] + "." + f.split('.')[1]
job[f_passed] = StringIO(fh.read())
fh.close()
job["id"] = "output"
if os.path.isdir("output_old"):
shutil.rmtree("output_old")
if os.path.isdir("output"):
shutil.move("output", "output_old")
comm.submit_jobs([job], invariants)
def make_searches(comm, current_state, wuid):
reactant = current_state.get_reactant()
#XXX:what if the user changes the bundle size?
num_in_buffer = comm.get_queue_size() * config.comm_job_bundle_size
logger.info("Queue contains %i searches" % num_in_buffer)
num_to_make = max(config.comm_job_buffer_size - num_in_buffer, 0)
logger.info("Making %i searches" % num_to_make)
if num_to_make == 0:
return wuid
searches = []
invariants = {}
reactIO = StringIO()
io.savecon(reactIO, reactant)
# Merge potential files into invariants
#XXX: Should this be in our "science" maybe the communicator should
# handle this.
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
searches = []
for i in range(num_to_make):
search = {}
search['id'] = "%d_%d" % (current_state.number, wuid)
search['pos.con'] = reactIO
ini_changes = [
('Main', 'job', 'parallel_replica'),
('Main', 'random_seed', str(int(numpy.random.random() * 10**9))),
]
search['config.ini'] = io.modify_config(config.config_path,
ini_changes)
searches.append(search)
wuid += 1
comm.submit_jobs(searches, invariants)
logger.info("Created " + str(num_to_make) + " searches")
return wuid
def make_searches(comm, current_state, wuid):
reactant = current_state.get_reactant()
#XXX:what if the user changes the bundle size?
num_in_buffer = comm.get_queue_size()*config.comm_job_bundle_size
logger.info("Queue contains %i searches" % num_in_buffer)
num_to_make = max(config.comm_job_buffer_size - num_in_buffer, 0)
logger.info("Making %i searches" % num_to_make)
if num_to_make == 0:
return wuid
searches = []
invariants = {}
reactIO = StringIO()
io.savecon(reactIO, reactant)
# Merge potential files into invariants
#XXX: Should this be in our "science" maybe the communicator should
# handle this.
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
searches = []
for i in range(num_to_make):
search = {}
search['id'] = "%d_%d" % (current_state.number, wuid)
search['pos.con'] = reactIO
ini_changes = [
('Main', 'job', 'parallel_replica'),
('Main', 'random_seed',
str(int(numpy.random.random()*10**9))),
]
search['config.ini'] = io.modify_config(config.config_path, ini_changes)
searches.append(search)
wuid += 1
comm.submit_jobs(searches, invariants)
logger.info("Created " + str(num_to_make) + " searches")
return wuid
def make_jobs(self):
num_unsent = self.comm.get_queue_size()*config.comm_job_bundle_size
logger.info("Queued %i jobs" % num_unsent)
num_in_progress = self.comm.get_number_in_progress()*config.comm_job_bundle_size
logger.info("Running %i jobs" % num_in_progress)
num_total = num_unsent + num_in_progress
num_to_make = max(config.comm_job_buffer_size - num_unsent, 0)
if config.comm_job_max_size != 0:
if num_total + num_to_make>= config.comm_job_max_size:
num_to_make = max(0, config.comm_job_max_size - num_total)
logger.info("Reached max_jobs")
logger.info("Making %i jobs" % num_to_make)
if num_to_make == 0:
return
jobs = []
invariants = {}
# Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
t1 = time()
# start new searches
for i in range(num_to_make):
job = None
for ps in self.process_searches.values():
job, job_type = ps.get_job(self.state.number)
if job:
self.wuid_to_search_id[self.wuid] = ps.search_id
sid = ps.search_id
break
if not job:
displacement, mode, disp_type = self.generate_displacement()
reactant = self.state.get_reactant()
process_search = ProcessSearch(reactant, displacement, mode,
disp_type, self.search_id, self.state.number)
self.process_searches[self.search_id] = process_search
self.wuid_to_search_id[self.wuid] = self.search_id
job, job_type = process_search.get_job(self.state.number)
sid = self.search_id
self.search_id += 1
job['id'] = "%i_%i" % (self.state.number, self.wuid)
job_entry = {'type':job_type, 'status':'running'}
if sid not in self.job_info:
self.job_info[sid] = {}
self.job_info[sid][job['id']] = job_entry
self.wuid += 1
self.save_wuid()
jobs.append(job)
self.save()
if config.recycling_on and self.nrecycled > 0:
logger.info("Recycled %i saddles" % self.nrecycled)
try:
self.comm.submit_jobs(jobs, invariants)
t2 = time()
logger.info( "Created " + str(len(jobs)) + " searches")
logger.debug( "Created " + str(num_to_make/(t2-t1)) + " searches per second")
except:
logger.exception("Failed to submit searches")
def make_jobs(self):
#XXX:what if the user changes the bundle size?
num_in_buffer = self.comm.get_queue_size()*config.comm_job_bundle_size
logger.info("Queue contains %i searches" % num_in_buffer)
num_to_make = max(config.comm_job_buffer_size - num_in_buffer, 0)
logger.info("Making %i process searches" % num_to_make)
if num_to_make == 0:
return
searches = []
invariants = {}
reactIO = StringIO.StringIO()
io.savecon(reactIO, self.reactant)
file_permission = os.stat("pos.con").st_mode
invariants['pos.con'] = (reactIO, file_permission)
t1 = time()
if config.saddle_method == 'dynamics' and \
config.recycling_on and \
config.disp_moved_only and \
self.state.number != 0:
moved_atoms = self.recycler.process_atoms
mass_weights = self.reactant.mass.copy()
mass_weights *= config.recycling_mass_weight_factor
for i in range(len(self.reactant)):
if i in moved_atoms:
mass_weights[i] = self.reactant.mass[i]
weightsIO = StringIO.StringIO()
numpy.savetxt(weightsIO, mass_weights)
file_permission = os.stat("masses.dat").st_mode
invariants['masses.dat'] = (weightsIO, file_permission)
# Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
for i in range(num_to_make):
search = {}
# The search dictionary contains the following key-value pairs:
# id - CurrentState_WUID
# displacement - an atoms object containing the point the saddle search will start at
# mode - an Nx3 numpy array containing the initial mode
search['id'] = "%d_%d" % (self.state.number, self.wuid)
displacement, mode, disp_type = self.generate_displacement()
self.job_table.add_row( {'state':self.state.number,
'wuid':self.wuid,
'type':disp_type } )
ini_changes = [ ('Main', 'job', 'process_search'),
('Main', 'random_seed',
str(int(numpy.random.random()*10**9))),
]
# if we are recycling a saddle, but using "dynamics saddle search" we need
# to switch to min_mode searches
if config.saddle_method == 'dynamics' and disp_type != 'dynamics':
ini_changes.append( ('Saddle Search', 'method', 'min_mode') )
search['config.ini'] = io.modify_config(config.config_path, ini_changes)
if displacement:
dispIO = StringIO.StringIO()
io.savecon(dispIO, displacement)
search['displacement.con'] = dispIO
modeIO = StringIO.StringIO()
io.save_mode(modeIO, mode)
search['direction.dat'] = modeIO
searches.append(search)
self.wuid += 1
# eager write
self.save_wuid()
if config.recycling_on and self.nrecycled > 0:
logger.info("Recycled %i saddles" % self.nrecycled)
try:
self.comm.submit_jobs(searches, invariants)
t2 = time()
logger.info( "Created " + str(len(searches)) + " searches")
logger.debug( "Created " + str(num_to_make/(t2-t1)) + " searches per second")
except:
logger.exception("Failed to submit searches")
self.job_table.write()
def make_jobs(self):
num_unsent = self.comm.get_queue_size() * config.comm_job_bundle_size
logger.info("Queued %i jobs" % num_unsent)
num_in_progress = self.comm.get_number_in_progress(
) * config.comm_job_bundle_size
logger.info("Running %i jobs" % num_in_progress)
num_total = num_unsent + num_in_progress
num_to_make = max(config.comm_job_buffer_size - num_unsent, 0)
if config.comm_job_max_size != 0:
if num_total + num_to_make >= config.comm_job_max_size:
num_to_make = max(0, config.comm_job_max_size - num_total)
logger.info("Reached max_jobs")
logger.info("Making %i jobs" % num_to_make)
if num_to_make == 0:
return
jobs = []
invariants = {}
# Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
t1 = time()
# start new searches
for i in range(num_to_make):
job = None
for ps in self.process_searches.values():
job, job_type = ps.get_job(self.state.number)
if job:
self.wuid_to_search_id[self.wuid] = ps.search_id
sid = ps.search_id
break
if not job:
displacement, mode, disp_type = self.generate_displacement()
reactant = self.state.get_reactant()
process_search = ProcessSearch(reactant, displacement, mode,
disp_type, self.search_id,
self.state.number)
self.process_searches[self.search_id] = process_search
self.wuid_to_search_id[self.wuid] = self.search_id
job, job_type = process_search.get_job(self.state.number)
sid = self.search_id
self.search_id += 1
job['id'] = "%i_%i" % (self.state.number, self.wuid)
job_entry = {'type': job_type, 'status': 'running'}
if sid not in self.job_info:
self.job_info[sid] = {}
self.job_info[sid][job['id']] = job_entry
self.wuid += 1
self.save_wuid()
jobs.append(job)
self.save()
if config.recycling_on and self.nrecycled > 0:
logger.info("Recycled %i saddles" % self.nrecycled)
try:
self.comm.submit_jobs(jobs, invariants)
t2 = time()
logger.info("Created " + str(len(jobs)) + " searches")
logger.debug("Created " + str(num_to_make / (t2 - t1)) +
" searches per second")
except:
logger.exception("Failed to submit searches")
def make_jobs(self):
#XXX:what if the user changes the bundle size?
num_in_buffer = self.comm.get_queue_size(
) * config.comm_job_bundle_size
logger.info("Queue contains %i searches" % num_in_buffer)
num_to_make = max(config.comm_job_buffer_size - num_in_buffer, 0)
logger.info("Making %i process searches" % num_to_make)
if num_to_make == 0:
return
searches = []
invariants = {}
reactIO = StringIO.StringIO()
io.savecon(reactIO, self.reactant)
file_permission = os.stat("pos.con").st_mode
invariants['pos.con'] = (reactIO, file_permission)
t1 = time()
if config.saddle_method == 'dynamics' and \
config.recycling_on and \
config.disp_moved_only and \
self.state.number != 0:
moved_atoms = self.recycler.process_atoms
mass_weights = self.reactant.mass.copy()
mass_weights *= config.recycling_mass_weight_factor
for i in range(len(self.reactant)):
if i in moved_atoms:
mass_weights[i] = self.reactant.mass[i]
weightsIO = StringIO.StringIO()
numpy.savetxt(weightsIO, mass_weights)
file_permission = os.stat("masses.dat").st_mode
invariants['masses.dat'] = (weightsIO, file_permission)
# Merge potential files into invariants
invariants = dict(invariants, **io.load_potfiles(config.path_pot))
for i in range(num_to_make):
search = {}
# The search dictionary contains the following key-value pairs:
# id - CurrentState_WUID
# displacement - an atoms object containing the point the saddle search will start at
# mode - an Nx3 numpy array containing the initial mode
search['id'] = "%d_%d" % (self.state.number, self.wuid)
displacement, mode, disp_type = self.generate_displacement()
self.job_table.add_row({
'state': self.state.number,
'wuid': self.wuid,
'type': disp_type
})
ini_changes = [
('Main', 'job', 'process_search'),
('Main', 'random_seed',
str(int(numpy.random.random() * 10**9))),
]
# if we are recycling a saddle, but using "dynamics saddle search" we need
# to switch to min_mode searches
if config.saddle_method == 'dynamics' and disp_type != 'dynamics':
ini_changes.append(('Saddle Search', 'method', 'min_mode'))
search['config.ini'] = io.modify_config(config.config_path,
ini_changes)
if displacement:
dispIO = StringIO.StringIO()
io.savecon(dispIO, displacement)
search['displacement.con'] = dispIO
modeIO = StringIO.StringIO()
io.save_mode(modeIO, mode)
search['direction.dat'] = modeIO
searches.append(search)
self.wuid += 1
# eager write
self.save_wuid()
if config.recycling_on and self.nrecycled > 0:
logger.info("Recycled %i saddles" % self.nrecycled)
try:
self.comm.submit_jobs(searches, invariants)
t2 = time()
logger.info("Created " + str(len(searches)) + " searches")
logger.debug("Created " + str(num_to_make / (t2 - t1)) +
" searches per second")
except:
logger.exception("Failed to submit searches")
self.job_table.write()