def save_fig(self, *args):
if comm.is_mpi_used():
with Barrier():
if comm.rank() == 0:
self._save_fig(*args)
else:
self._save_fig(*args)
def save_fig(self, *args):
if comm.is_mpi_used():
with Barrier():
if comm.rank()==0:
self._save_fig(*args)
else:
self._save_fig(*args)
def clear_paths(self, cb):
for key in [
'p_tee_out', 'p_subp_out', 'p_subp_err', 'p_bash',
'p_sbatch_out', 'p_sbatch_err'
]:
if cb.get(key) and os.path.isdir(cb.get(key)):
if comm.rank() == 0:
os.remove(cb.get(key))
def _get_spikes_from_file_mpi(file_names):
with Barrier():
if comm.rank()==0:
data=_get_spikes_from_file(file_names)
else:
data=None
with Barrier():
data=comm.bcast(data, root=0)
return data
def _get_spikes_from_file_mpi(file_names):
with Barrier():
if comm.rank() == 0:
data = _get_spikes_from_file(file_names)
else:
data = None
with Barrier():
data = comm.bcast(data, root=0)
return data
def _text_load_mpi(f):
with Barrier():
if comm.rank()==0:
data=_text_load(f)
else:
data=None
with Barrier():
data=comm.bcast(data, root=0)
return data
def _text_load_mpi(f):
with Barrier():
if comm.rank() == 0:
data = _text_load(f)
else:
data = None
with Barrier():
data = comm.bcast(data, root=0)
return data
def collect_spikes_mpi(*args):
args = list(args)
for i in range(len(args)):
with Barrier():
if comm.rank() == 0:
for i_proc in xrange(1, comm.size()):
args[i] = numpy.r_[args[i], comm.recv(source=i_proc)]
else:
comm.send(args[i], dest=0)
args[i] = comm.bcast(args[i], root=0)
return args
def collect_spikes_mpi(*args):
args=list(args)
for i in range(len(args)):
with Barrier():
if comm.rank()==0:
for i_proc in xrange(1, comm.size()):
args[i] = numpy.r_[args[i],
comm.recv(source=i_proc)]
else:
comm.send(args[i],dest=0)
args[i]=comm.bcast(args[i], root=0)
return args
def set(self, surfs, display_print=True):
t=time.time()
# Convergent connections when driver = target and pool = source.
# The for each node driver not surfs from the pool is considered
# Divergent connections when driver = source and pool = target.
# Then for each node driver not surfs from the pool is considered
driver=surfs[self.target]
pool=surfs[self.source]
if not (self.save['active']
and not self.save['overwrite']
and os.path.isfile(self.save['path'] +'.pkl')):
self._set(driver, pool)
self._save()
else:
d=data_to_disk.pickle_load(self.save['path'] )
self.pre=sparse.coo_matrix(d[0])
self.post=sparse.coo_matrix(d[1])
self.sets=d[2]
# self.pre=numpy.array([[0]])#sparse.coo_matrix(d[0])
# self.post=numpy.array([[0]])#sparse.coo_matrix(d[1])
# self.sets=[0]#d[2]
#
t=time.time()-t
if display_print and comm.rank()==0:
s='Conn: {0:18} Connections: {1:8} Fan pool:{2:6} ({3:6}) Time:{4:5} sec Rule:{5}'
a=[self.name,
self.n,
round(float(self.n)/driver.get_n(),0),
self.fan_in,
round(t,2),
self.rule]
print s.format(*a)
def set(self, surfs, display_print=True):
t = time.time()
# Convergent connections when driver = target and pool = source.
# The for each node driver not surfs from the pool is considered
# Divergent connections when driver = source and pool = target.
# Then for each node driver not surfs from the pool is considered
driver = surfs[self.target]
pool = surfs[self.source]
if not (self.save['active'] and not self.save['overwrite']
and os.path.isfile(self.save['path'] + '.pkl')):
self._set(driver, pool)
self._save()
else:
d = data_to_disk.pickle_load(self.save['path'])
self.pre = sparse.coo_matrix(d[0])
self.post = sparse.coo_matrix(d[1])
self.sets = d[2]
# self.pre=numpy.array([[0]])#sparse.coo_matrix(d[0])
# self.post=numpy.array([[0]])#sparse.coo_matrix(d[1])
# self.sets=[0]#d[2]
#
t = time.time() - t
if display_print and comm.rank() == 0:
s = 'Conn: {0:18} Connections: {1:8} Fan pool:{2:6} ({3:6}) Time:{4:5} sec Rule:{5}'
a = [
self.name, self.n,
round(float(self.n) / driver.get_n(), 0), self.fan_in,
round(t, 2), self.rule
]
print s.format(*a)
def _save_mpi(self):
with Barrier():
if comm.rank()==0:
self._save()
def connect_conns(params_nest, conns, popus, display_print=False):
for c in conns:
# if c.name[0] not in ['E','C']:
# if c.name[0:5] not in ['C1_M1', 'C2_M2']:
#if c.name[0:5] not in ['E']:
#
# continue
if display_print and comm.rank() == 0:
print 'Connecting ' + str(c)
my_nest.MyCopyModel(params_nest[c.get_syn()], c.get_syn())
#c.copy_model( params_nest )
sr_ids = numpy.array(popus[c.get_source()].ids)
tr_ids = numpy.array(popus[c.get_target()].ids)
c.set_local_lockup(tr_ids)
weights = list(c.get_weights_local())
delays = list(c.get_delays_local())
pre = list(sr_ids[c.get_pre_local()])
post = list(tr_ids[c.get_post_local()])
import time
# time.sleep(0.1*my_nest.Rank())
# print c,'lu',c._get_local_lockup()
# print c,'pre', c.get_pre_local()[0:10], len(pre)
# print c,'post', c.get_post_local()[0:10], len(pre)
# print sr_ids[0:10]
# print tr_ids[0:10]
# print c,'pre2', pre[0:10], len(pre)
# print c,'pos2t', post[0:10], len(pre)
# comm.barrier()
# weights_input_rates=list(c.get_weights())
# delays=list(c.get_delays())
# pre=list(sr_ids[c.get_pre()])
# post=list(tr_ids[c.get_post()])
model = c.get_syn()
c.clear()
del c
gc.collect()
# delete_and_gc_collect(c)
# my_nest.Connect_DC(pre, post , weights_input_rates, delays, model, only_local=True)
my_nest.Connect_speed(pre, post, weights, delays, model=model)
#
# syn_dict={
# "model":model,
# "weight":weights,
# "delay":delays,
# }
# conn_dict={
# "rule": "one_to_one",
# }
# import nest
# nest.Connect(pre, post, conn_dict, syn_dict)
# pp(my_nest.GetConnections(list(set(pre)))[0])
# pp(my_nest.GetConnections(post)[0])
# print pre[0], post[0]
# print model, len(pre), len(post), len(weights), len(delays)
# print 'Connecting ' + ' my_nest.GetConnections ', len(my_nest.GetConnections(list(set(pre)))), len(pre)
# print 'Connecting ' + ' my_nest.GetConnections ', len(my_nest.GetConnections(post)), len(post)
# delete_and_gc_collect(weights_input_rates, delays, pre, post)
#
del weights
del delays
del pre
del post
gc.collect()
def _set_mpi(self, *args):
# with Barrier(True):
if comm.rank() == 0:
self._set(*args)
comm.barrier()
def _garbage_collect_mpi(self):
with Barrier():
if comm.rank() == 0:
self._garbage_collect()
def _text_save_mpi(*args):
with Barrier():
if comm.rank()==0:
_text_save(*args)
def _mkdir_mpi(*args):
with Barrier():
if comm.rank()==0:
_mkdir(*args)
def _set_mpi(self, *args):
# with Barrier(True):
if comm.rank()==0:
self._set(*args)
comm.barrier()
def _text_save_mpi(*args):
with Barrier():
if comm.rank() == 0:
_text_save(*args)
def _pickle_save_mpi(*args):
with Barrier():
if comm.rank() == 0:
# OBS!!! watch out for having barriers inside here.
# Will stall program
_pickle_save(*args)
def _mkdir_mpi(*args):
with Barrier():
if comm.rank() == 0:
_mkdir(*args)
def connect_conns(params_nest, conns, popus, display_print=False):
for c in conns:
# if c.name[0] not in ['E','C']:
# if c.name[0:5] not in ['C1_M1', 'C2_M2']:
#if c.name[0:5] not in ['E']:
#
# continue
if display_print and comm.rank()==0:
print 'Connecting '+str(c)
my_nest.MyCopyModel( params_nest[c.get_syn()], c.get_syn())
#c.copy_model( params_nest )
sr_ids=numpy.array(popus[c.get_source()].ids)
tr_ids=numpy.array(popus[c.get_target()].ids)
c.set_local_lockup(tr_ids)
weights=list(c.get_weights_local())
delays=list(c.get_delays_local())
pre=list(sr_ids[c.get_pre_local()])
post=list(tr_ids[c.get_post_local()])
import time
# time.sleep(0.1*my_nest.Rank())
# print c,'lu',c._get_local_lockup()
# print c,'pre', c.get_pre_local()[0:10], len(pre)
# print c,'post', c.get_post_local()[0:10], len(pre)
# print sr_ids[0:10]
# print tr_ids[0:10]
# print c,'pre2', pre[0:10], len(pre)
# print c,'pos2t', post[0:10], len(pre)
# comm.barrier()
# weights_input_rates=list(c.get_weights())
# delays=list(c.get_delays())
# pre=list(sr_ids[c.get_pre()])
# post=list(tr_ids[c.get_post()])
model=c.get_syn()
c.clear()
del c
gc.collect()
# delete_and_gc_collect(c)
# my_nest.Connect_DC(pre, post , weights_input_rates, delays, model, only_local=True)
my_nest.Connect_speed(pre, post , weights, delays, model=model)
#
# syn_dict={
# "model":model,
# "weight":weights,
# "delay":delays,
# }
# conn_dict={
# "rule": "one_to_one",
# }
# import nest
# nest.Connect(pre, post, conn_dict, syn_dict)
# pp(my_nest.GetConnections(list(set(pre)))[0])
# pp(my_nest.GetConnections(post)[0])
# print pre[0], post[0]
# print model, len(pre), len(post), len(weights), len(delays)
# print 'Connecting ' + ' my_nest.GetConnections ', len(my_nest.GetConnections(list(set(pre)))), len(pre)
# print 'Connecting ' + ' my_nest.GetConnections ', len(my_nest.GetConnections(post)), len(post)
# delete_and_gc_collect(weights_input_rates, delays, pre, post)
#
del weights
del delays
del pre
del post
gc.collect()
def _delete_data_mpi(path, **kwargs):
with Barrier():
if comm.rank()==0:
_delete_data(path, **kwargs)
def _delete_data_mpi(path, **kwargs):
with Barrier():
if comm.rank() == 0:
_delete_data(path, **kwargs)
def _garbage_collect_mpi(self):
with Barrier():
if comm.rank()==0:
self._garbage_collect()
def _save_mpi(self):
with Barrier():
if comm.rank() == 0:
self._save()
def _pickle_save_mpi(*args):
with Barrier():
if comm.rank()==0:
# OBS!!! watch out for having barriers inside here.
# Will stall program
_pickle_save(*args)
def clear_paths(self, cb):
for key in ['p_tee_out', 'p_subp_out','p_subp_err',
'p_bash','p_sbatch_out', 'p_sbatch_err']:
if cb.get(key) and os.path.isdir(cb.get(key)):
if comm.rank()==0:
os.remove(cb.get(key))
''' Created on Jul 15, 2014 @author: mikael ''' from core.data_to_disk import pickle_load from core.parallelization import comm import sys path=sys.argv[1]+str(comm.rank()) # path='/home/mikael/git/bgmodel/core_old/misc_folder/test_subprocess/00' print path fun, args, kwargs=pickle_load(path) fun(*args, **kwargs)
