Add code for prallel execution

dev/issues/issue179_speedup/speed_up/code/MushroomBody/MBody_cuda.py

@@ -0,0 +1,204 @@
+import random as py_random
+
+from brian2 import *
+import brian2genn
+import sys
+from utils import get_directory
+
+MB_scaling = float(sys.argv[1])
+
+extra_args = {}
+device = sys.argv[2]
+threads = int(sys.argv[3])
+use_spikemon = sys.argv[4] == 'true'
+do_run = sys.argv[5] == 'true'
+if threads == -1:
+ extra_args = {'use_GPU': False}
+else:
+ prefs.devices.cpp_standalone.openmp_threads = threads
+
+prefs.devices.genn.path = "/cognition/home/subora/Documents/github_repository/brian2cuda/frozen_repos/genn"
+
+codefolder = get_directory(device, delete_dir=False)
+
+set_device(device,directory=codefolder,**extra_args)
+
+print('Running with arguments: ', sys.argv)
+
+# defaultclock.dt = 0.025*ms
+# Constants
+g_Na = 7.15*uS
+E_Na = 50*mV
+g_K = 1.43*uS
+E_K = -95*mV
+g_leak = 0.0267*uS
+E_leak = -63.56*mV
+C = 0.3*nF
+# Those two constants are dummy constants, only used when populations only have
+# either inhibitory or excitatory inputs
+E_e = 0*mV
+E_i = -92*mV
+# Actual constants used for synapses
+tau_PN_LHI = 1*ms
+tau_LHI_iKC = 3*ms
+tau_PN_iKC = 2*ms
+tau_iKC_eKC = 10*ms
+tau_eKC_eKC = 5*ms
+w_LHI_iKC = 8.75*nS
+w_eKC_eKC = 75*nS
+tau_pre = tau_post = 10*ms
+dApre = 0.1*nS/MB_scaling
+dApost = -dApre
+# tau_STDP = 10*ms
+# g_0 = 0.125*nS
+g_max = 3.75*nS/MB_scaling
+# g_mid = g_max/2
+# g_slope = g_mid
+# tau_decay = 10e5*ms
+# A = g_max/4
+# offset = 0.01*A
+
+scale = .675
+
+# Number of neurons
+N_AL = 100
+N_MB = int(2500*MB_scaling)
+N_LB = 100
+
+traub_miles = '''
+dV/dt = -(1/C)*(g_Na*m**3*h*(V - E_Na) +
+ g_K*n**4*(V - E_K) +
+ g_leak*(V - E_leak) +
+ I_syn) : volt
+dm/dt = alpha_m*(1 - m) - beta_m*m : 1
+dn/dt = alpha_n*(1 - n) - beta_n*n : 1
+dh/dt = alpha_h*(1 - h) - beta_h*h : 1
+
+alpha_m = 0.32*(-52 - V/mV)/(exp((-52 - V/mV)/4) - 1)/ms: Hz
+beta_m = 0.28*(25 + V/mV)/(exp((25 + V/mV)/5) - 1)/ms: Hz
+alpha_h = 0.128*exp((-48 - V/mV)/18)/ms: Hz
+beta_h = 4/(exp((-25 - V/mV)/5) + 1)/ms : Hz
+alpha_n = 0.032*(-50 - V/mV)/(exp((-50 - V/mV)/5) - 1)/ms: Hz
+beta_n = 0.5*exp((-55 - V/mV)/40)/ms : Hz
+'''
+
+# Principal neurons (Antennal Lobe)
+n_patterns = 10
+n_repeats = 10
+p_perturb = 0.1
+patterns = np.repeat(np.array([np.random.choice(N_AL, int(0.2*N_AL), replace=False) for _ in range(n_patterns)]), n_repeats, axis=0)
+# Make variants of the patterns
+to_replace = np.random.binomial(int(0.2*N_AL), p=p_perturb, size=n_patterns*n_repeats)
+variants = []
+for idx, variant in enumerate(patterns):
+ np.random.shuffle(variant)
+ if to_replace[idx] > 0:
+ variant = variant[:-to_replace[idx]]
+ new_indices = np.random.randint(N_AL, size=to_replace[idx])
+ variant = np.unique(np.concatenate([variant, new_indices]))
+ variants.append(variant)
+
+training_size = (n_repeats-10)
+training_variants = []
+for p in range(n_patterns):
+ training_variants.extend(variants[n_repeats * p:n_repeats * p + training_size])
+py_random.shuffle(training_variants)
+sorted_variants = list(training_variants)
+for p in range(n_patterns):
+ sorted_variants.extend(variants[n_repeats * p + training_size:n_repeats * (p + 1)])
+
+# all_patterns = np.zeros((n_patterns*n_repeats, N_AL))
+# for idx, p in enumerate(sorted_variants):
+# all_patterns[idx, p] = 1
+# plt.imshow(all_patterns[-10*n_patterns:, :], interpolation='none')
+# plt.show()
+
+spike_times = np.arange(n_patterns*n_repeats)*50*ms + 1*ms + rand(n_patterns*n_repeats)*2*ms
+spike_times = spike_times.repeat([len(p) for p in sorted_variants])
+spike_indices = np.concatenate(sorted_variants)
+
+PN = SpikeGeneratorGroup(N_AL, spike_indices, spike_times)
+
+# iKC of the mushroom body
+I_syn = '''I_syn = g_PN_iKC*(V - E_e): amp
+ dg_PN_iKC/dt = -g_PN_iKC/tau_PN_iKC : siemens'''
+eqs_iKC = Equations(traub_miles) + Equations(I_syn)
+iKC = NeuronGroup(N_MB, eqs_iKC, threshold='V>0*mV', refractory='V>0*mV',
+ method='exponential_euler')
+iKC.V = E_leak
+iKC.h = 1
+iKC.m = 0
+iKC.n = .5
+
+# eKCs of the mushroom body lobe
+I_syn = '''I_syn = g_iKC_eKC*(V - E_e) + g_eKC_eKC*(V - E_i): amp
+ dg_iKC_eKC/dt = -g_iKC_eKC/tau_iKC_eKC : siemens
+ dg_eKC_eKC/dt = -g_eKC_eKC/tau_eKC_eKC : siemens'''
+eqs_eKC = Equations(traub_miles) + Equations(I_syn)
+eKC = NeuronGroup(N_LB, eqs_eKC, threshold='V>0*mV', refractory='V>0*mV',
+ method='exponential_euler')
+eKC.V = E_leak
+eKC.h = 1
+eKC.m = 0
+eKC.n = .5
+
+# Synapses
+PN_iKC = Synapses(PN, iKC, 'weight : siemens', on_pre='g_PN_iKC += scale*weight')
+PN_iKC.connect(p=0.15)
+PN_iKC.weight = '4.545*nS + 1.25*nS*randn()'
+
+# iKC_eKC = Synapses(iKC, eKC,
+# '''
+# dg_raw/dt = (g_0 - g_raw)/tau_decay : siemens (event-driven)
+# g_syn = g_max*(tanh((g_raw - g_mid)/g_slope) + 1)/2 : siemens
+# dapre/dt = -apre/tau_stdp : siemens (event-driven)
+# dapost/dt = -apost/tau_stdp : siemens (event-driven)
+# ''',
+# on_pre='''
+# apre += A
+# g_iKC_eKC += g_max*(tanh((g_raw - g_mid)/g_slope) + 1)/2
+# ''',
+# on_post='''
+# g_raw += apre - offset
+# ''')
+iKC_eKC = Synapses(iKC, eKC,
+ '''g_raw : siemens
+ dApre/dt = -Apre / tau_pre : siemens (event-driven)
+ dApost/dt = -Apost / tau_post : siemens (event-driven)
+ ''',
+ on_pre='''g_iKC_eKC += g_raw
+ Apre += dApre
+ g_raw = clip(g_raw + Apost, 0*siemens, g_max)
+ ''',
+ on_post='''
+ Apost += dApost
+ g_raw = clip(g_raw + Apre, 0*siemens, g_max)''',
+ )
+iKC_eKC.connect()
+# First set all synapses as "inactive", then set 20% to active
+iKC_eKC.g_raw = 'rand()*g_max/10'
+iKC_eKC.g_raw['rand() < 0.2'] = '1.25*nS + 0.25*nS*randn()'
+
+eKC_eKC = Synapses(eKC, eKC, on_pre='g_eKC_eKC += scale*w_eKC_eKC')
+eKC_eKC.connect()
+
+if use_spikemon:
+ PN_spikes = SpikeMonitor(PN)
+ iKC_spikes = SpikeMonitor(iKC)
+ eKC_spikes = SpikeMonitor(eKC)
+
+import time
+if do_run:
+ runtime = (n_patterns*n_repeats+1)*50*ms
+else:
+ runtime = 0*second
+start = time.time()
+run(runtime, report='text')
+took = (time.time()-start)
+print('took %.1fs' % took)
+neurons = N_AL + N_MB + N_LB
+synapses = len(PN_iKC) + len(iKC_eKC) + len(eKC_eKC)
+
+with open('benchmarks.txt', 'a') as f:
+ data = [neurons, synapses, device, threads, use_spikemon, do_run, took]
+ f.write('\t'.join('%s' % d for d in data) + '\n')