def __init__(self, **kw):
index = kw.get('index') #simulation index
# path_code=kw.get('path_code')
pr = kw.get('path_results')
# self.local_threads=10
self.p_subp_out = pr + "/std/subp/out{0:0>4}".format(index)
self.p_subp_err = pr + '/std/subp/err{0:0>4}'.format(index)
'''
self.p_sbatch_out=pr+"/std/sbatch/out{0:0>4}".format(index)
self.p_sbatch_err=pr+'/std/sbatch/err{0:0>4}'.format(index)
'''
self.p_tee_out = pr + '/std/tee/out{0:0>4}'.format(index)
self.p_par = pr + '/params/run{0:0>4}.pkl'.format(index)
self.p_script = dr.HOME_CODE + '/core/toolbox/parallel_excecution/simulation.py'
self.p_bash0 = dr.HOME_CODE + '/2ndManuscript/20paramsfree/checkRelSWAACT/jc1NoEqjc2/jobb0_jyotika.sh'
self.p_bash = pr + '/jobbs/jobb_{0:0>4}.sh'.format(index)
self.p_qsubout = '/users/bahuguna/2ndManuscript/20paramsfree/checkRelSWAACT/jc1NoEqjc2/'
# data_to_disk.mkdir('/'.join(self.p_subp_out.split('/')[0:-1]))
# data_to_disk.mkdir('/'.join(self.p_sbatch_out.split('/')[0:-1]))
data_to_disk.mkdir('/'.join(self.p_tee_out.split('/')[0:-1]))
for key, value in kw.items():
self.__dict__[key] = value
self.kw = kw
def __init__(self, **kw):
index = kw.get('index') #simulation index
# path_code=kw.get('path_code')
pr = kw.get('path_results')
self.num_mpi_task = kw.get('num-mpi-task')
# self.local_threads=10
self.p_subp_out = pr + "/std/subp/out{0:0>4}".format(index)
self.p_subp_err = pr + '/std/subp/err{0:0>4}'.format(index)
self.p_par = pr + '/params/run{0:0>4}.pkl'.format(index)
self.p_script = dr.HOME_CODE + '/core/toolbox/parallel_excecution/simulation.py'
data_to_disk.mkdir('/'.join(self.p_subp_out.split('/')[0:-1]))
for key, value in kw.items():
self.__dict__[key] = value
def setUp(self):
home=default_params.HOME
code=home+'/git/bgmodel/core/toolbox/test_milner_hybrid_mpi'
result=home+'/results/unittest/test_milner_hybrid_mpi/main'
path_bash=code+'/jobb.sh'
path_bash0=code+'/jobb0.sh'
path_err=result+'/jobb_err'
path_out=result+'/jobb_out'
path_simu=code+'/simulation.py'
path_data_nest=result+'/nest'
path_data_sd=result+'/spike_dic'
path_delme=result+'/delme_simulation'
mkdir(result)
cores=40*2 #multiple of 40
local_threads=10
d={'cores_hosting_OpenMP_threads':40/local_threads,
'memory_per_node':int(819*local_threads),
'num-mpi-task':cores/local_threads,
'num-of-nodes':cores/40,
'num-mpi-tasks-per-node':40/local_threads,
'num-threads-per-mpi-process':local_threads,
'output':path_delme,
'path_nest':path_data_nest,
'script':path_simu,
}
# if my_socket.determine_host()=='milner_login':
fun='sbatch'
# call='aprun -n 2 -N 1 -d 20 python {SCRIPT} 2>&1 | tee delme_simulation'
call=('aprun -n {num-mpi-task} '
+'-N {num-mpi-tasks-per-node} '
+'-d {num-threads-per-mpi-process} '
+'-m {memory_per_node} '
+'python {script} {num-threads-per-mpi-process} {path_nest} 2>&1 | tee {output}')
call=call.format(**d)
print call
# else:
# fun='batch'
# call='mpirun -np 2 python {script} 2>&1 | tee {output}'
call=call.format(**d)
on_milner=int(my_socket.determine_host() == 'milner_login')
k={
'path_err':path_err,
'path_out':path_out,
'call':call,
'home':home,
'on_milner':on_milner}
k.update(d)
make_bash_script(path_bash0,
path_bash,
**k)
# if my_socket.determine_host()=='milner_login':
args_call=[fun,
path_bash
]
# else:
# args_call=[
# path_bash
# ]
self.path_err=path_err
self.path_out=path_out
self.path_simu=path_simu
self.path_data_nest=path_data_nest
self.path_data_sd=path_data_sd
self.path_delme=path_delme
self.args_call=args_call
datadir = home + '/nest'
datadir_sd = home + '/spike_dic'
data_path = '/'.join(datadir.split('/')[0:-1])
for path in [datadir, datadir_sd]:
if os.path.isdir(path):
if comm.rank() == 0:
shutil.rmtree(path)
for path in [datadir_sd + '.pkl', datadir_sd + '.svg']:
if os.path.isfile(path):
if comm.rank() == 0:
os.remove(path)
if comm.rank() == 0:
data_to_disk.mkdir(datadir)
comm.barrier()
print comm.obj
my_nest.SetKernelStatus({'data_path': datadir, 'overwrite_files': True})
g = sim_group(10, 1, t)
ss = g.get_spike_signal()
fr = ss.get_firing_rate()
mr = ss.get_mean_rate()
sd = data_to_disk.Storage_dic.load(datadir_sd)
sd_figs = data_to_disk.Storage_dic.load(datadir_sd)
sd.save_dic({'fr': fr, 'mr': mr})
datadir=home+'/nest'
datadir_sd=home+'/spike_dic'
data_path='/'.join(datadir.split('/')[0:-1])
for path in [datadir, datadir_sd]:
if os.path.isdir(path):
if comm.rank()==0:
shutil.rmtree(path)
for path in [datadir_sd+'.pkl', datadir_sd+'.svg']:
if os.path.isfile(path):
if comm.rank()==0:
os.remove(path)
if comm.rank()==0:
data_to_disk.mkdir(datadir)
comm.barrier()
print comm.obj
my_nest.SetKernelStatus({'data_path':datadir,
'overwrite_files': True})
g=sim_group(10, 1, t)
ss=g.get_spike_signal()
fr=ss.get_firing_rate()
mr=ss.get_mean_rate()
sd=data_to_disk.Storage_dic.load(datadir_sd)
with Barrier():
if comm.rank()==0:
out=pickle_load(fileName, all_mpi=True)
else:
out=None
out=comm.bcast(out, root=0)
sim_time, args, kwargs=out
d={'sd':{'active':True,
'params':{'to_memory':False,
'to_file':True}}}
kwargs=misc.dict_update(kwargs, d)
mkdir(data_path+'nest/')
my_nest.ResetKernel(display=False,
data_path=data_path+'nest/',
**{'threads_local': np_local})
import pprint
pp=pprint.pprint
d=my_nest.GetKernelStatus()
if comm.rank()==0:
print comm.size()
pp(d)
import threading
print threading.active_count()
# comm.obj.
my_nest.SetKernelStatus({'overwrite_files':True,})
g=sim_group(sim_time, *args, **kwargs)
@author: mikael
'''
import numpy
import pickle
import sys
from toolbox.data_to_disk import mkdir
from toolbox.my_nest import collect_spikes_mpi
from toolbox.parallelization import comm
print sys.argv
fileName, = sys.argv[1:]
fileName += 'data'
s, e = numpy.ones(2) * comm.rank(), numpy.ones(2) * comm.rank() + 1
s, e = collect_spikes_mpi(s, e)
mkdir('/'.join(fileName.split('/')[0:-1]))
if comm.rank() == 0:
print 'File name'
print fileName
if 4 < len(fileName) and fileName[-4:] != '.pkl':
fileName = fileName + '.pkl'
f = open(fileName, 'wb') #open in binary mode
pickle.dump([s, e], f, -1)
f.close()
import pickle
import sys
from toolbox.data_to_disk import mkdir
from toolbox.my_nest import collect_spikes_mpi
from toolbox.parallelization import comm
print sys.argv
fileName, =sys.argv[1:]
fileName+='data'
s,e=numpy.ones(2)*comm.rank(),numpy.ones(2)*comm.rank()+1
s, e= collect_spikes_mpi(s, e)
mkdir('/'.join(fileName.split('/')[0:-1]))
if comm.rank()==0:
print 'File name'
print fileName
if 4<len(fileName) and fileName[-4:]!='.pkl':
fileName=fileName+'.pkl'
f=open(fileName, 'wb') #open in binary mode
pickle.dump([s,e], f, -1)
f.close()