# import ipdb
from neuron import h, gui
import numpy as np
from glob import glob as listdir
import os
from branch_setup import *
import h5py as h5
from protocol import *
import sys
def superrun(xxx_todo_changeme):
(run_index,delta_t, dep_dur, hyp_dur, n_BPAP, conf_n, activate_LTP,nstim,blk_RMBLK) = xxx_todo_changeme
global protocol, p , cell, rank
if p['check']:
print(('Started simulation %s run %g on CPU %g'%(conf_n, run_index,rank)))
# print protocol.stimulators['IC_dep'][0][0].delay,protocol.stimulators['IC_dep'][0][0].amp
for ic_idx,(dc,hc) in enumerate(zip(protocol.stimulators['IC_dep'],protocol.stimulators['IC_hyp'])):
if ic_idx < p['protocols'][conf_n]['nstim']:
for dcc,hcc in zip(dc,hc):
dcc.dur = dep_dur
hcc.dur = hyp_dur
hcc.delay = dcc.delay + dcc.dur # ms
if n_BPAP == 1:
for i in [1,2,3]:
dc[i].dur = 0
hc[i].dur = 0
if n_BPAP == 2:
for i in [2,3]:
dc[i].dur = 0
hc[i].dur = 0
else:
for i in [0,1,2,3]:
dc[i].dur = 0
hc[i].dur = 0
if activate_LTP:
protocol.stim.number = nstim
if p['check']:
print(('Stimulation is %s for %g times.'%(conf_n,nstim)))
else:
protocol.stim.number = 0
# Remove the RMBLK
if blk_RMBLK:
for s in cell.spines:
s.head.RMECB.alpha_cai_RMBLK = 0
# print s.name,s.head.RMECB.alpha_cai_RMBLK
# print "SPINE max_fused_vesicles", s.head.BDNF.max_fused_vesicles
if p['check']:
print(("Running for delta_t = %g"%delta_t))
protocol.stim.start = p['time_start_induction_stimuli'] + delta_t # ms
if p['check']:
print(('Initializing on run %g on CPU %g'%(run_index,rank)))
if p['override_tstop'] is not None:
h.tstop = p['override_tstop']
else:
h.tstop = protocol.p['tstop']#p['time_on_initialization']+p['time_to_begin_induction'] + 1000
if p['check']:
print(('Running for %g ms'%h.tstop))
# for seg in dend:
# mec = getattr(seg,'na3')
# mec.gbar = 0
# for dc in protocol.stimulators['IC_dep']:
# for d in dc:
# d.amp = 0
# for dc in protocol.stimulators['IC_hyp']:
# for d in dc:
# d.amp = 0
# print conf_n, dc[0].amp, dc[0].dur
# for s in cell.spines:
# print s.head.BDNF.alpha_gAMPA, s.head.BDNF.theta_gAMPA, s.head.BDNF.sigma_gAMPA
# print s.parent_sec,s.parent_seg
# s.head.AMPA.Pmax = 0
# s.head.NMDA.Pmax = 0
h.init()
if h.tstop > 1e3:
while h.t < h.tstop:
h.continuerun(h.t+5e3)
print((h.t))
sys.stdout.flush()
else:
h.run()
for s in cell.spines:
print((s.name, s.head.AMPA.Pmax, s.head.AMPA.g_factor, s.head.AMPA.glut_factor, 'lowindex', cell.MCell_Ran4_lowindex, 'cell highindex', cell.MCell_Ran4_highindex, 'spine highindex', s.highindex, 'delta t', delta_t))
store = h5.File(p['data_file']+'_%g.hdf5'%run_index, 'w')
# print "Opened data file on cpu %g"%rank
# Group for sim data
sim_data = store.create_group('Simulation_data')
conf_data = sim_data.create_group(conf_n)
# Group for single iteration
run_iteration = conf_data.create_group('delta_t_%g_%g'%(delta_t,run_index))
run_iteration.create_dataset('branches indexes',data=cell.seg_indexes)
run_iteration.create_dataset('branches indexes 2',data=cell.seg_indexes_2)
run_iteration.create_dataset('branch names',data=[str(ss) for ss in cell.branch_segments])
run_iteration.create_dataset('spiny branch names',data=[str(ss) for ss in cell.spine_segments])
run_iteration.create_dataset('delta_t',data=delta_t)
run_iteration.create_dataset('test_pre_spike_times',
data=np.array(protocol.stimulators['test_pre_spike_times']))
run_iteration.create_dataset('induction_spikes',
data=np.array(protocol.stimulators['induction_spikes']))
run_iteration.create_dataset('test_during_spike_times',
data=np.array(protocol.stimulators['test_during_spike_times']))
run_iteration.create_dataset('test_post_spike_times',
data=np.array(protocol.stimulators['test_post_spike_times']))
run_iteration.create_dataset('induction_injection_times',
data=np.array(protocol.stimulators['IC_delays']))
if p['check']:
for spine_index,spine in enumerate(cell.spines):
print((conf_n, spine.name, 'delta_t_%g'%delta_t, list(run_iteration.keys())))
for spine_index,spine in enumerate(cell.spines):
# Single spine group
# if spine.name in run_iteration.keys():
spine_group = run_iteration.create_group(spine.name)
spine.head.save_records(spine_group,
spine_index,
write_datasets = True)
spine.neck.save_records(spine_group,
spine_index,
write_datasets = True)
cell.cell.save_records(run_iteration, write_datasets = True)
tb.dig_dict_save('Parameters',p,store.create_group('Parameters'))
store.close()
return 'Completed sim on run %g on CPU %g time %g'%(run_index,rank,h.t)
pc = h.ParallelContext()
rank = int(pc.id())
CVOde = h.cvode
CVOde.active(1)
# h.nrnmainmenu()
p = {}
exec(compile(open('parameters.py').read(), 'parameters.py', 'exec'),p)
# global cell
cell = Spiny_branch(p,rank=rank)
# for s in cell.spines:
# print s.head.BDNF.alpha_gAMPA, s.head.BDNF.theta_gAMPA, s.head.BDNF.sigma_gAMPA
# global protocol
protocol = stim_protocol(cell,p, rank=rank)
pc.runworker()
print(('Starting %g'%rank))
sim_list = []
if rank == 0:
# Remove old data files
ls = listdir(p['data_file']+'_*.hdf5')
for f in ls:
if 'pulled' not in f:
os.remove(f)
# nnodes = world.size
run_index = 0
for conf_n,conf in list(p['protocols'].items()):
for delta_t in p['time_delta']:
blk_RMBLK = conf['Block_RMBLK'] if 'Block_RMBLK' in list(conf.keys()) else False
# print "Submitting jobs", delta_t
args = [
run_index,
delta_t,
conf['BPAP_dep_stimulus_duration'],
conf['BPAP_hyp_stimulus_duration'],
conf['n_BPAP'],
conf_n,
conf['activate_LTP_protocol'],
conf['nstim'],
blk_RMBLK]
# print(args)
sim_list.append(args)
run_index += 1
pc.submit(superrun, args)
while pc.working():
print((pc.pyret()))
pc.done()
