def simulate(spk_interval=1000, sim_time=2000):
nest.ResetKernel()
#ip=nest.Create('spike_generator',params={'spike_times':[10.,20.]})
sg = nest.Create('spike_generator', 1)
st = gen_spikes(3, 100, 900)
st = numpy.arange(20., sim_time, spk_interval)
pp(nest.SetStatus(sg, {'spike_times': st}))
# pp(nest.GetStatus(sg))
n = nest.Create('my_aeif_cond_exp', 1)
df = nest.GetDefaults('my_aeif_cond_exp')['receptor_types']
# df=nest.GetDefaults('my_aeif_cond_exp')['recordables']
receptor = 'AMPA_1'
recordables = ['g_AMPA_1']
print nest.version()
# nest.Connect(sg, n,model='tsodyks_synapse', params={
# 'U':0.0192,
# 'tau_fac': 623.,
# 'tau_rec':559. ,
# 'receptor_type':df[receptor]})
nest.Connect(sg,
n,
model='tsodyks_synapse',
params={
'U': 0.29,
'tau_fac': 53.,
'tau_rec': 902.0,
'tau_psc': 8.,
'receptor_type': df[receptor]
})
print nest.version()
# dic['nest']['M1_SN_gaba']['U'] = 0.0192
# dic['nest']['M1_SN_gaba']['tau_fac'] = 623.
# dic['nest']['M1_SN_gaba']['tau_rec'] = 559.
# dic['nest']['M1_SN_gaba']['tau_psc'] = 5.2
pp(df)
p_mm = {
"withgid": True,
'to_file': False,
'to_memory': True,
'record_from': recordables
}
mm = nest.Create('multimeter', params=p_mm)
pp(nest.GetStatus(mm))
nest.Connect(mm, n)
nest.Simulate(st[-1])
t = nest.GetStatus(mm)[0]['events']['times']
y = nest.GetStatus(mm)[0]['events']['g_AMPA_1']
return t, y
def simulate(spk_interval=1000, sim_time=2000):
nest.ResetKernel()
#ip=nest.Create('spike_generator',params={'spike_times':[10.,20.]})
sg=nest.Create('spike_generator',1)
st=gen_spikes(3, 100, 900)
st=numpy.arange(20.,sim_time,spk_interval)
pp(nest.SetStatus(sg, {'spike_times':st}))
# pp(nest.GetStatus(sg))
n=nest.Create('my_aeif_cond_exp',1)
df=nest.GetDefaults('my_aeif_cond_exp')['receptor_types']
# df=nest.GetDefaults('my_aeif_cond_exp')['recordables']
receptor='AMPA_1'
recordables=['g_AMPA_1']
print nest.version()
# nest.Connect(sg, n,model='tsodyks_synapse', params={
# 'U':0.0192,
# 'tau_fac': 623.,
# 'tau_rec':559. ,
# 'receptor_type':df[receptor]})
nest.Connect(sg, n,model='tsodyks_synapse', params={
'U':0.29,
'tau_fac': 53.,
'tau_rec':902.0,
'tau_psc':8. ,
'receptor_type':df[receptor]})
print nest.version()
# dic['nest']['M1_SN_gaba']['U'] = 0.0192
# dic['nest']['M1_SN_gaba']['tau_fac'] = 623.
# dic['nest']['M1_SN_gaba']['tau_rec'] = 559.
# dic['nest']['M1_SN_gaba']['tau_psc'] = 5.2
pp(df)
p_mm={"withgid": True,
'to_file':False,
'to_memory':True,
'record_from':recordables
}
mm=nest.Create('multimeter', params=p_mm)
pp(nest.GetStatus(mm))
nest.Connect(mm,n)
nest.Simulate(st[-1])
t=nest.GetStatus(mm)[0]['events']['times']
y=nest.GetStatus(mm)[0]['events']['g_AMPA_1']
return t,y
def save_data(sim_type, conn_type, output_dir):
"""Saves the expected results"""
from bmtk import __version__ as bmtk_version
import platform
if not os.path.exists('expected'):
os.mkdir('expected')
save_file = 'expected/sim_output_{}.h5'.format(sim_type)
sample_data = h5py.File(save_file, 'w')
root_group = sample_data['/']
root_group.attrs['bmtk'] = bmtk_version
root_group.attrs['date'] = str(datetime.datetime.now())
root_group.attrs['python'] = '{}.{}'.format(*sys.version_info[0:2])
root_group.attrs['NEST'] = nest.version()
root_group.attrs['system'] = platform.system()
root_group.attrs['arch'] = platform.machine()
# spikes data
input_spikes = SpikesFile(os.path.join(output_dir, 'spikes.h5'))
spikes_df = input_spikes.to_dataframe()
sample_data.create_dataset('/spikes/gids',
data=np.array(spikes_df['gids']))
sample_data.create_dataset('/spikes/timestamps',
data=np.array(spikes_df['timestamps']))
sample_data['/spikes/gids'].attrs['sorting'] = 'time'
def extract_nestvalid_dict(d, param_type='neuron'):
"""
Verify whether the parameters dictionary are in the correct format, with adequate keys, in agreement with the nest
parameters dictionaries so that they can later be passed as direct input to nest.
:param d: parameter dictionary
:param param_type: type of parameters - kernel, neuron, population, network, connections, topology
:return: valid dictionary
"""
if param_type == 'neuron' or param_type == 'synapse' or param_type == 'device':
assert d['model'] in nest.Models(
), "Model %s not currently implemented in %s" % (d['model'],
nest.version())
accepted_keys = nest.GetDefaults(d['model']).keys()
accepted_keys.remove('model')
nest_dict = {k: v for k, v in d.iteritems() if k in accepted_keys}
elif param_type == 'kernel':
accepted_keys = nest.GetKernelStatus().keys()
nest_dict = {k: v for k, v in d.iteritems() if k in accepted_keys}
else:
# TODO
logger.error("{!s} not implemented yet".format(param_type))
exit(-1)
return nest_dict
def index():
response = {
'name': 'NEST server simulation',
'version': nest.version().split(' ')[1],
'ref': 'http://www.github.com/babsey/nest-server-simulation',
'env': dict(filter(lambda item: 'NEST' in item[0], os.environ.items()))
}
return jsonify(response)
def versions():
req = {}
try:
import nest
nest = nest.version()
except:
pass
nest = 'failed'
return jsonify(nest=nest)
def index():
response = {
'server': {
'version': __version__,
'git': {
'ref': 'http://www.github.com/babsey/nest-server',
'tag': 'v' + '.'.join(__version__.split('.')[:-1])
}
},
'simulator': {
'version': nest.version().split('-')[1],
},
}
return jsonify(response)
def get_version():
"""Trys to get NEST version major, minor, and patch (optional) of the current running version of nest. Will return
as a list of ints [major, minor, patch], although patch may be None.
:return: [major, minor, patch] if able to parse version, None if fails. 'patch' may be None value.
"""
# Try to get the version string
version_str = None
try:
# NEST 2.* uses .version() to get version string
version_str = nest.version()
except AttributeError:
pass
if version_str is None:
try:
# For NEST 3.1 it uses __version__ attribute to store string
version_str = nest.__version__
if version_str.upper() == 'UNKNOWN':
return [3, None, None]
except AttributeError:
pass
if version_str is None:
return None
# parse the version string to get major, minor and patch numbers
try:
version_pattern = re.compile(r'.*nest-(\d+)\.(\d+)(?:\.(\d+))?.*')
m = re.match(version_pattern, version_str)
n_groups = len(m.groups())
ver_major = int(m.group(1))
ver_minor = int(m.group(2))
ver_patch = int(
m.group(3)) if n_groups >= 3 and m.group(3) is not None else None
return [ver_major, ver_minor, ver_patch]
except (AttributeError, IndexError, ValueError, TypeError) as err:
return None
def get_default_module_paths(home_module):
# if nest.version()=='NEST 2.2.2':
# if my_socket.determine_computer()=='milner':
# s='nest-2.2.2-wo-music'
# else:
# s='nest-2.2.2'
# else:
# s='nest-'+nest.version()[-5:]
# if nest.version()=='NEST 2.4.1':
# s='nest-2.4.1'
# if nest.version()=='NEST 2.4.2':
# s='nest-2.4.2'
# if nest.version()=='NEST 2.4.2':
# s='nest-2.6.0'
if (nest.version() in ['NEST 2.2.2', 'NEST 2.12.0']):
path='ml_module'
sli_path=''
else:
path= (home_module+'/lib/nest/ml_module')
sli_path =(home_module+'/share/ml_module/sli')
return path, sli_path
def is_installed(version):
PyNestEngine.environment_vars = NestEngine.get_nest_environment()
ret = True
try:
import nest
try:
version = nest.version()
except:
version = '???'
if is_verbose():
inform("NEST version: %s is installed with Python support..." %
version,
indent=2)
inform("Env vars: %s" % PyNestEngine.environment_vars,
indent=2)
except Exception as err:
inform("Couldn't import NEST into Python: ", err, indent=1)
ret = False
return ret
def get_default_module_paths(home_module):
# if nest.version()=='NEST 2.2.2':
# if my_socket.determine_computer()=='milner':
# s='nest-2.2.2-wo-music'
# else:
# s='nest-2.2.2'
# else:
# s='nest-'+nest.version()[-5:]
# if nest.version()=='NEST 2.4.1':
# s='nest-2.4.1'
# if nest.version()=='NEST 2.4.2':
# s='nest-2.4.2'
# if nest.version()=='NEST 2.4.2':
# s='nest-2.6.0'
if (nest.version() in ['NEST 2.2.2', 'NEST 2.12.0']):
path = 'ml_module'
sli_path = ''
else:
path = (home_module + '/lib/nest/ml_module')
sli_path = (home_module + '/share/ml_module/sli')
return path, sli_path
M_INFO = 10
########################### PARAMETER SECTION #################################
if len(sys.argv) != 5:
raise ValueError(
"user arguments should be scale, num_vp, plastic and user_rule")
user_scale = int(sys.argv[1])
user_nvp = int(sys.argv[2])
user_plastic = bool(sys.argv[3])
user_rule = str(sys.argv[4])
print(
'GIT: ({}) \nuser_scale: {:>3} \nuser_nvp: {:>5} \nuser_plastic: {} \nuser_rule: {:>5}'
.format(nest.version(), user_scale, user_nvp, user_plastic, user_rule))
if user_rule not in ['all', 'in', 'out', 'tot', 'bern']:
raise ValueError("User rule not valid.")
# define all relevant parameters: changes should be made here
params = {
'nvp': user_nvp, # total number of virtual processes
'scale': user_scale, # scaling factor of the network size,
# total network size = scale*5000*20 neurons
'plastic': user_plastic,
'd_min': 1.5,
'd_max': 1.5,
'rule': user_rule,
'inisimtime': 10., # initial simulation time given in ms: calibration etc
'dt': 0.1, # simulation step
def __init__(self, network, sim_spec):
"""
Simulation class.
An instance of the simulation class with the given parameters.
Can be created as a member class of a multiarea_model instance
or standalone.
Parameters
----------
network : multiarea_model
An instance of the multiarea_model class that specifies
the network to be simulated.
params : dict
custom simulation parameters that overwrite the
default parameters defined in default_params.py
"""
print('GIT: ({})'.format(nest.version()))
self.params = deepcopy(sim_params)
if isinstance(sim_spec, dict):
check_custom_params(sim_spec, self.params)
self.custom_params = sim_spec
else:
fn = os.path.join(data_path, sim_spec, '_'.join(
('custom_params', sim_spec)))
with open(fn, 'r') as f:
self.custom_params = json.load(f)['sim_params']
nested_update(self.params, self.custom_params)
self.network = network
self.label = dicthash.generate_hash_from_dict({
'params':
self.params,
'network_label':
self.network.label
})
print("Simulation label: {}".format(self.label))
self.data_dir = os.path.join(data_path, self.label)
try:
os.mkdir(self.data_dir)
os.mkdir(os.path.join(self.data_dir, 'recordings'))
except OSError:
pass
self.copy_files()
print("Copied files.")
d = {
'sim_params': self.custom_params,
'network_params': self.network.custom_params,
'network_label': self.network.label
}
with open(
os.path.join(self.data_dir, '_'.join(
('custom_params', self.label))), 'w') as f:
json.dump(d, f)
print("Initialized simulation class.")
self.areas_simulated = self.params['areas_simulated']
self.areas_recorded = self.params['recording_dict']['areas_recorded']
self.T = self.params['t_sim']
self.time_create = 0
self.time_connect = 0
except:
print("No PyNN...")
print('\n========================================================\n')
try:
import neuron
print(">> NEURON: version %s"%neuron.h.nrnversion())
except:
print("No NEURON...")
print('\n========================================================\n')
try:
import nest
print(">> NEST: version %s"%nest.version())
except:
print("No PyNEST...")
print('\n========================================================\n')
try:
import brian
print(">> Brian: version %s"%brian.__version__)
except:
print("No Brian v1...")
print('\n========================================================\n')
try:
import brian2
import nest
print("Version: %s" % nest.version())
import nest
print("Test 2: NEST version: %s"%nest.version())
path = dirname(dirname(dirname(__file__)))
dotenv_path = join(path, '.env')
f=open(dotenv_path)
for l in f.readlines():
l=l.strip('\n').strip('\r')
key, val=l.split('=')
os.environ[key]=val
# load_dotenv(dotenv_path)
os.environ['BGMODEL_HOME']=path
os.environ['BGMODEL_HOME_CODE']=join(path, 'python')
# Add library path
if nest.version()=='NEST 2.2.2':
os.environ['LD_LIBRARY_PATH'] = (os.environ['LD_LIBRARY_PATH']
+ os.path.join(path,
'nest',
'dist',
'install',
'nest-2.2.2',
'lib',
'nest'))
# import misc
# import data_to_disk
# import network
# import my_axes
# import my_nest
# import my_population
import nest
from distutils.version import LooseVersion
from dipde.internals.internalpopulation import InternalPopulation
from dipde.internals.externalpopulation import ExternalPopulation
from dipde.internals.network import Network
from dipde.internals.connection import Connection as Connection
from dipde.examples.potjans_diesmann_cortical_column import population_list,\
connection_list
assert LooseVersion(nest.version().split()[1]) >= LooseVersion("2.6.0")
class Kernel(object):
def __init__(self, population_list=[], connection_list=[]):
self.simulation = Network(population_list, connection_list)
# def Create("poisson_generator", number_of_neurons, params={"rate": float(firing_rate), 'start':float(start)/.001})
#
#
# def Connect(self):
if __name__ == "__main__":
kernel = Kernel()
# # Settings:
# t0 = 0.
# dt = .0001
# dv = .0001
# tf = .1
_config['with_plot'] = True
__all__.append('plot')
except ImportError as e:
_log_message(_logger, "DEBUG",
"An error occured, plot module will not be loaded: " + str(e))
_config['with_plot'] = False
# look for nest
if _config['load_nest']:
try:
# silence nest
_sys.argv.append('--quiet')
import nest
from . import simulation
_config['with_nest'] = nest.version()
__all__.append("simulation")
# remove quiet from sys.argv
try:
idx = _sys.argv.index('--quiet')
del _sys.argv[idx]
except ValueError:
pass
except ImportError as e:
_log_message(_logger, "DEBUG",
"NEST not found; nngt.simulation not loaded: " + str(e))
_config["with_nest"] = False
# load database module if required
if _config["use_database"]:
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
import numpy as np
import re
try:
import nest
m = re.search(r'.*(\d+)\.(\d+)\.(\d+).*', nest.version())
ver_major = int(m.group(1))
ver_minor = int(m.group(2))
built_in_glifs = ver_major >= 2 and ver_minor >= 20
except Exception as e:
built_in_glifs = False
def lif_aibs_converter(config, tau_syn=[5.5, 8.5, 2.8, 5.8]):
"""
:param config:
:return:
"""
coeffs = config['coeffs']
sim_time, seed, {}, threads,
start_rec)
misc.pickle_save([layer_dic, mr], save_result_at)
else:
layer_dic, mr = misc.pickle_load(save_result_at)
save_result_at = OUTPUT_PATH + '/simulate_15000.plk'
if 1:
layer_dic2, mr = simulate_15000(params_msn_d1, params_msn_d2, params_stn,
synapse_models, sim_time, seed, {},
threads, start_rec)
misc.pickle_save([layer_dic2, mr], save_result_at)
else:
layer_dic2, mr = misc.pickle_load(save_result_at)
save_result_at = OUTPUT_PATH + '/simulate_1500.plk2' + nest.version()
if 1:
layer_dic3, mr = simulate_1500(params_msn_d1, params_msn_d2, params_stn,
synapse_models, sim_time, seed, {}, threads,
start_rec)
misc.pickle_save([layer_dic3, mr], save_result_at)
else:
layer_dic3, mr = misc.pickle_load(save_result_at)
#Inspect results
plot_settings.set_mode(pylab,
mode='by_fontsize',
w=1100.0,
h=450.0 + 275.0,
fontsize=12)
font_size_text = 8
import future.utils
import warnings
import nest
if future.utils.PY3 and nest.version().split()[1] == '2.12.0':
# Undo monkey patch of warning performed by pyNEST 2.12.0 as it
# isn't compatible with Python 3
warnings.showwarning = warnings._showwarning_orig
from .cells import Cell, CellMetaClass # @IgnorePep8
from .code_gen import CodeGenerator # @IgnorePep8
from .simulation import Simulation # @IgnorePep8
from .network import ( # @IgnorePep8
Network, ComponentArray, Selection, ConnectionGroup,
PyNNCellWrapperMetaClass)
from .units import UnitHandler # @IgnorePep8
def index():
return jsonify({'nest': nest.version()})
import nest
print("Test 2: NEST version: %s" % nest.version())
import nest
import nest.pynestkernel as _kernel
import os
import time
import core.directories as dr
from copy import deepcopy
from core.parallelization import comm, Barrier
from core.misc import Stopwatch
from core import my_socket
import pprint
pp = pprint.pprint
kernal_time = None
ver = int(''.join(nest.version().split(' ')[1].split('.')))
if ver < 242:
pushsli = _kernel.pushsli
runsli = _kernel.runsli
else:
pushsli = nest.engine.push
runsli = nest.engine.run
def _Create_mpi(*args, **kwargs):
with Barrier():
return nest.Create(*args, **kwargs)
def Create(*args, **kwargs):
if comm.is_mpi_used():
import nest
import numpy as np
import nest.topology as ntop
print(nest.version())
nest.ResetKernel()
import configparser
import shelve
from simu_fun import *
from vLSPS_fun import *
import pickle
nest.ResetKernel()
#read configure file
config = configparser.ConfigParser()
config.read('simu.conf')
local_num_threads = int(config['parallel_computing']['local_num_threads'])
if local_num_threads != 1:
print('Setlocal_num_threads')
nest.SetKernelStatus({"local_num_threads": local_num_threads})
save_filename = 'BrainSimu.pickle'
# flag c means if the file doesn't exist, then create a new file
with open(save_filename, 'rb') as handle:
pickle_file = pickle.load(handle)
handle.close()
simulate_region = pickle_file['cerebralcortex']['vS1']
vS1_Layer_Name = simulate_region['structure_info']['Layer_Name']
vS1_layer_size = simulate_region['structure_info']['region_size']
vS1_Layer_Thickness = simulate_region['structure_info']['layer_thickness']
'allow_multapses': False,
'allow_autapses': False,
'connection_type': 'convergent',
'mask': {
'rectangular': {
'lower_left': [-0.5, -0.5],
'upper_right': [0.5, 0.5]
}
},
'kernel': 0.5,
'sources': {
'model': 'iaf_neuron'
},
'targets': {
'model': 'iaf_neuron'
}
}
tp.ConnectLayers(l, l, projections)
tp.ConnectLayers(l_dummy1, l, projections)
tp.ConnectLayers(l_dummy2, l, projections)
if nest.version() == 'NEST 2.0.0':
sources = nest.GetChildren(l)
if nest.version() == 'NEST 2.2.1':
sources = nest.GetChildren(l)[0]
t = time.time()
targets = tp.GetTargetNodes(sources, l)
print time.time() - t
nest.SetStatus(multimeter, {"withtime":True, "record_from":["V_m"]})
spikedetector = nest.Create("spike_detector",
params={"withgid": True, "withtime": True})
nest.CopyModel("static_synapse", "excitatory",
{
"weight": 0.25,
"delay": 0.5,
# "receptor_type": rec["AMPA_1"]
"receptor_type": 0
})
nest.Connect(multimeter, [m[0]])
if nest.version()=='NEST 2.12.0':
syn_dict = {
"model": 'excitatory',
}
conn_dict = {
"rule": "one_to_one",
}
nest.Connect(n, m, conn_dict, syn_dict)
nest.Connect(m, spikedetector)
# print 'Connecting ' + ' my_nest.GetConnections ', len(nest.GetConnections(n)), len(n)
if nest.version()=='NEST 2.2.2':
nest.Connect(n, m, **{
"model":"excitatory"
class CodeGenerator(BaseCodeGenerator):
SIMULATOR_NAME = 'nest'
SIMULATOR_VERSION = nest.version().split()[1]
ODE_SOLVER_DEFAULT = 'gsl'
REGIME_VARNAME = '__regime__'
SS_SOLVER_DEFAULT = None
MAX_STEP_SIZE_DEFAULT = 0.01 # Used for CVODE/IDA, FIXME: not sure best value!!! @IgnorePep8
ABS_TOLERANCE_DEFAULT = 1e-3
REL_TOLERANCE_DEFAULT = 0.0
GSL_JACOBIAN_APPROX_STEP_DEFAULT = 0.01
V_THRESHOLD_DEFAULT = 0.0
MAX_SIMULTANEOUS_TRANSITIONS = 1000
BASE_TMPL_PATH = path.abspath(
path.join(path.dirname(__file__), 'templates'))
UnitHandler = UnitHandler
_inline_random_implementations = {}
def __init__(self, build_cores=1, **kwargs):
super(CodeGenerator, self).__init__(**kwargs)
self._build_cores = build_cores
self.nest_config = os.path.join(self.get_nest_install_prefix(), 'bin',
'nest-config')
compiler, _ = self.run_command(
[self.nest_config, '--compiler'],
fail_msg=("Could not run nest-config at '{}': {{}}".format(
self.nest_config)))
self._compiler = compiler.strip() # strip trailing \n
def generate_source_files(self,
component_class,
src_dir,
name=None,
debug_print=None,
**kwargs):
if name is None:
name = component_class.name
# Get the initial regime and check that it refers to a regime in the
# component class
tmpl_args = {
'component_name':
name,
'component_class':
component_class,
'version':
pype9.__version__,
'src_dir':
src_dir,
'timestamp':
datetime.now().strftime('%a %d %b %y %I:%M:%S%p'),
'unit_handler':
UnitHandler(component_class),
'sorted_regimes':
sorted(component_class.regimes,
key=lambda r: component_class.index_of(r)),
'jacobian_approx_step':
kwargs.get('jacobian_approx_step',
self.GSL_JACOBIAN_APPROX_STEP_DEFAULT),
'max_step_size':
kwargs.get('max_step_size', self.MAX_STEP_SIZE_DEFAULT),
'abs_tolerance':
kwargs.get('max_step_size', self.ABS_TOLERANCE_DEFAULT),
'rel_tolerance':
kwargs.get('max_step_size', self.REL_TOLERANCE_DEFAULT),
'max_simultaneous_transitions':
kwargs.get('max_simultaneous_transitions',
self.MAX_SIMULTANEOUS_TRANSITIONS),
'parameter_scales': [],
'v_threshold':
kwargs.get('v_threshold', self.V_THRESHOLD_DEFAULT),
'regime_varname':
self.REGIME_VARNAME,
'debug_print': [] if debug_print is None else debug_print
}
ode_solver = kwargs.get('ode_solver', self.ODE_SOLVER_DEFAULT)
ss_solver = kwargs.get('ss_solver', self.SS_SOLVER_DEFAULT)
if ode_solver is None:
raise Pype9BuildError("'ode_solver' cannot be None")
switches = {'ode_solver': ode_solver, 'ss_solver': ss_solver}
# Render C++ header file
self.render_to_file('header.tmpl',
tmpl_args,
name + '.h',
src_dir,
switches=switches)
# Render C++ class file
self.render_to_file('main.tmpl',
tmpl_args,
name + '.cpp',
src_dir,
switches=switches,
post_hoc_subs=self._inline_random_implementations)
# Render Loader header file
self.render_to_file('module-header.tmpl', tmpl_args, name + 'Module.h',
src_dir)
# Render Loader C++ class
self.render_to_file('module-cpp.tmpl', tmpl_args, name + 'Module.cpp',
src_dir)
# Render SLI initializer
self.render_to_file('module_sli_init.tmpl',
tmpl_args, name + 'Module-init.sli',
path.join(src_dir, 'sli'))
def configure_build_files(self, name, src_dir, compile_dir, install_dir,
**kwargs): # @UnusedVariable
# Generate Makefile if it is not present
if not path.exists(path.join(compile_dir, 'Makefile')):
if not path.exists(compile_dir):
os.mkdir(compile_dir)
logger.info("Configuring build files in '{}' directory".format(
compile_dir))
orig_dir = os.getcwd()
config_args = {
'name': name,
'src_dir': src_dir,
# NB: ODE solver currently ignored
# 'ode_solver': kwargs.get('ode_solver',
# self.ODE_SOLVER_DEFAULT),
'version': pype9.__version__,
'executable': sys.executable
}
self.render_to_file('CMakeLists.txt.tmpl', config_args,
'CMakeLists.txt', src_dir)
os.chdir(compile_dir)
stdout, stderr = self.run_command(
[
'cmake', '-Dwith-nest={}'.format(self.nest_config),
'-DCMAKE_INSTALL_PREFIX={}'.format(install_dir), src_dir
],
fail_msg=("Cmake of '{}' NEST module failed (see src "
"directory '{}'):\n\n {{}}".format(name, src_dir)))
if stderr:
raise Pype9BuildError(
"Configure of '{}' NEST module failed (see src "
"directory '{}'):\n\n{}\n{}".format(
name or src_dir, src_dir, stdout, stderr))
logger.debug("cmake '{}':\nstdout:\n{}stderr:\n{}\n".format(
compile_dir, stdout, stderr))
os.chdir(orig_dir)
def compile_source_files(self, compile_dir, component_name):
# Run configure script, make and make install
os.chdir(compile_dir)
logger.info("Compiling NEST model class in '{}' directory.".format(
compile_dir))
stdout, stderr = self.run_command(
['make', '-j{}'.format(self._build_cores)],
fail_msg=("Compilation of '{}' NEST module failed (see compile "
"directory '{}'):\n\n {{}}".format(
component_name, compile_dir)))
if re.search(r'error:', stderr): # Ignores warnings
raise Pype9BuildError(
"Compilation of '{}' NEST module directory failed:\n\n{}\n{}".
format(compile_dir, stdout, stderr))
logger.debug("make '{}':\nstdout:\n{}stderr:\n{}\n".format(
compile_dir, stdout, stderr))
stdout, stderr = self.run_command(
['make', 'install'],
fail_msg=("Installation of '{}' NEST module failed (see compile "
"directory '{}'):\n\n {{}}".format(
component_name, compile_dir)))
if stderr:
raise Pype9BuildError(
"Installation of '{}' NEST module directory failed:\n\n{}\n{}".
format(compile_dir, stdout, stderr))
logger.debug("make install'{}':\nstdout:\n{}stderr:\n{}\n".format(
compile_dir, stdout, stderr))
logger.info("Compilation of '{}' NEST module completed "
"successfully".format(component_name))
def clean_src_dir(self, src_dir, name):
# Clean existing src directories from previous builds.
prefix = path.join(src_dir, name)
if path.exists(src_dir):
remove_ignore_missing(prefix + '.h')
remove_ignore_missing(prefix + '.cpp')
remove_ignore_missing(prefix + 'Module.h')
remove_ignore_missing(prefix + 'Module.cpp')
remove_ignore_missing(
path.join(src_dir, 'sli', name + 'Module-init.sli'))
sli_path = path.join(src_dir, 'sli')
if not path.exists(sli_path):
os.makedirs(sli_path)
def clean_compile_dir(self,
compile_dir,
purge=False,
**kwargs): # @UnusedVariable @IgnorePep8
if purge:
try:
shutil.rmtree(compile_dir)
except OSError as e:
if e.errno != errno.ENOENT: # Ignore if missing
raise
if not path.exists(compile_dir):
try:
os.makedirs(compile_dir)
except OSError as e:
raise Pype9BuildError(
"Could not make compile directory '{}': {}".format(
compile_dir, e))
else:
orig_dir = os.getcwd()
os.chdir(compile_dir)
try:
stdout, stderr = self.run_command(['make', 'clean'])
os.chdir(orig_dir)
except (sp.CalledProcessError, OSError):
os.chdir(orig_dir)
shutil.rmtree(compile_dir, ignore_errors=True)
try:
os.makedirs(compile_dir)
except OSError as e:
raise Pype9BuildError(
"Could not create build directory ({}), please check "
"the required permissions or specify a different "
"build directory:\n{}".format(e))
if stderr and 'No rule to make target' not in stderr:
raise Pype9BuildError(
"Clean of '{}' NEST module directory failed:\n\n{}\n{}".
format(compile_dir, stdout, stderr))
logger.debug("make clean '{}':\nstdout:\n{}stderr:\n{}\n".format(
compile_dir, stdout, stderr))
def simulator_specific_paths(self):
path = []
if 'NEST_INSTALL_DIR' in os.environ:
path.append(path.join(os.environ['NEST_INSTALL_DIR'], 'bin'))
return path
def load_libraries(self, name, url, **kwargs): # @UnusedVariable
install_dir = self.get_install_dir(name, url)
lib_dir = os.path.join(install_dir, 'lib')
add_lib_path(lib_dir)
# Add module install directory to NEST path
nest.sli_run('({}) addpath'.format(
os.path.join(install_dir, 'share', 'sli')))
# Install nest module
nest.Install(name + 'Module')
@classmethod
def get_nest_install_prefix(cls):
# Make doubly sure that the loaded nest install appears first on the
# PYTHONPATH (not sure if this is necessary, but can't hurt)
pynest_install_dir = os.path.join(os.path.dirname(nest.__file__), '..')
env = os.environ.copy()
env['PYTHONPATH'] = os.pathsep.join(
(pynest_install_dir, env.get('PYTHONPATH', '')))
try:
process = sp.Popen(
[sys.executable, '-c', "import nest; nest.sysinfo()"],
stdout=sp.PIPE,
stderr=sp.PIPE,
env=env)
stdout, _ = process.communicate()
except sp.CalledProcessError as e:
raise Pype9BuildError(
"Error trying to run 'import nest; nest.sysinfo()' in "
"subprocess:\n{}".format(e))
if PY3:
stdout = str(stdout.decode('utf-8'))
match = re.search(r'\(([^\)]+)/share/nest/sli\)', stdout)
if match is None:
raise Pype9BuildError(
"Could not find nest install prefix by searching for "
"'share/nest/sli' in output from nest.sysinfo:\n{}".format(
stdout))
return match.group(1)
print('\n========================================================\n')
import neuron
print(">> NEURON: version %s"%neuron.h.nrnversion())
print('\n========================================================\n')
try:
import nest
print(">> NEST: version %s"%nest.version())
except:
print("No PyNEST...")
print('\n========================================================\n')
try:
import brian
print(">> Brian: version %s"%brian.__version__)
except:
import nest
import nest.pynestkernel as _kernel
import os
import time
import core.directories as dr
from copy import deepcopy
from core.parallelization import comm, Barrier
from core.misc import Stopwatch
from core import my_socket
import pprint
pp=pprint.pprint
kernal_time=None
ver=int(''.join(nest.version().split(' ')[1].split('.')))
if ver<242:
pushsli=_kernel.pushsli
runsli=_kernel.runsli
else:
pushsli=nest.engine.push
runsli=nest.engine.run
def _Create_mpi(*args, **kwargs):
with Barrier():
return nest.Create(*args, **kwargs)
def Create(*args, **kwargs):
if comm.is_mpi_used():
return _Create_mpi(*args, **kwargs)
else:
Created on Sep 11, 2014
@author: mikael
'''
import nest
import numpy
import pylab
from os.path import expanduser
import mpi4py
import pprint
pp=pprint.pprint
if nest.version()=='NEST 2.2.2':
s='nest-2.2.2'
if nest.version()=='NEST 2.4.1':
s='nest-2.4.1'
if nest.version()=='NEST 2.4.2':
s='nest-2.4.2'
pp(nest.Models())
HOME = expanduser("~")
MODULE_PATH= (HOME+'/opt/NEST/module/'
+'install-module-130701-'+s+'/lib/nest/ml_module')
MODULE_SLI_PATH= (HOME+'/opt/NEST/module/'
+'install-module-130701-'+s+'/share/ml_module/sli')
nest.sr('('+MODULE_SLI_PATH+') addpath')
import nest
print("Version: %s"%nest.version())
Created on Sep 11, 2014
@author: mikael
'''
import nest
import numpy
import pylab
from os.path import expanduser
import mpi4py
import pprint
pp=pprint.pprint
if nest.version()=='NEST 2.2.2':
s='nest-2.2.2'
if nest.version()=='NEST 2.4.1':
s='nest-2.4.1'
if nest.version()=='NEST 2.4.2':
s='nest-2.4.2'
pp(nest.Models())
HOME = expanduser("~")
MODULE_PATH= (HOME+'/opt/NEST/module/'
+'install-module-130701-'+s+'/lib/nest/ml_module')
MODULE_SLI_PATH= (HOME+'/opt/NEST/module/'
+'install-module-130701-'+s+'/share/ml_module/sli')
nest.sr('('+MODULE_SLI_PATH+') addpath')
import warnings
import numpy as np
import matplotlib.pyplot as plt
import nest
from .. import lib as _plib
from ..analysis import (activity_types, find_idx_nearest, data_from_nest,
interburst_properties, spiking_properties)
# ------------------ #
# Check NEST version #
# ------------------ #
nest_version = nest.version()
while not nest_version[0].isdigit():
nest_version = nest_version[1:]
dot_pos = nest_version.find('.')
dot_pos2 = nest_version[dot_pos + 1:].find('.')
version_major = int(nest_version[:dot_pos])
version_minor = int(nest_version[dot_pos + 1:dot_pos + 1 + dot_pos2])
useGIDCollection = False
if version_major > 2:
useGIDCollection = True
elif version_minor <= 11:
raise ImportError("NEST >= 2.12.0 required!")
'edge_wrap': True, 'extent':[1.,1.], 'center' : [0.,0.] } )
projections = {'allow_multapses': False,
'allow_autapses' : False,
'delays':{'uniform':{'min':(1-dev)*delay,'max':(1.+dev)*delay}},
'weights':{'uniform':{'min':(1+dev)*weight,'max':(1-dev)*weight}},
'connection_type' : 'convergent',
'mask':{'rectangular' : { 'lower_left' : [ -0.5 , -0.5 ],
'upper_right' : [ 0.5, 0.5 ]}},
'kernel': 0.5,
'sources': {'model' : 'iaf_neuron' },
'targets': {'model' : 'iaf_neuron' }}
tp.ConnectLayers(l, l, projections)
if nest.version()=='NEST 2.0.0':
sources=nest.GetChildren(l)
if nest.version()=='NEST 2.2.1':
sources=nest.GetChildren(l)[0]
sd=nest.Create('spike_detector')
nest.SetStatus(sd, {"withgid": True,'start':start_rec })
nest.ConvergentConnect(sources, sd)
mm=nest.Create('multimeter')
recodables=['V_m']
nest.SetStatus(mm, {'interval': 0.1, 'record_from': recodables, 'start':start_rec})
nest.Connect(mm, [sources[0]])
nest.Simulate(sim_time)