Merge pull request #7 from rahulgayatri23/master

Parallel Solver example

Author: dilawar

parallelSolver/Fig2_v4.py

@@ -0,0 +1,229 @@
+# Generates time-series response to a Ca pulse for each of the models. No
+# diffusion involved.
+
+import sys
+import numpy as np
+import pylab
+import matplotlib.pyplot as plt
+import moose
+import abstrModelEqns2
+import rdesigneur as rd
+import time
+
+
+def singleCompt( name, params ):
+    mod = moose.copy( '/library/' + name + '/' + name, '/model' )
+    A = moose.element( mod.path + '/A' )
+    Z = moose.element( mod.path + '/Z' )
+    Z.nInit = 1
+    Ca = moose.element( mod.path + '/Ca' )
+    CaStim = moose.element( Ca.path + '/CaStim' )
+    runtime = params['preStimTime'] + params['stimWidth'] + params['postStimTime'] 
+    steptime = 100
+
+    CaStim.expr += ' + x2 * (t > ' + str( runtime ) + ' ) * ( t < ' + str( runtime + steptime ) +  ' )'
+    print CaStim.expr
+    tab = moose.Table2( '/model/' + name + '/Atab' )
+    #for i in range( 10, 19 ):
+        #moose.setClock( i, 0.01 )
+    ampl = moose.element( mod.path + '/ampl' )
+    phase = moose.element( mod.path + '/phase' )
+    moose.connect( tab, 'requestOut', A, 'getN' )
+    ampl.nInit = params['stimAmplitude'] * 1
+    phase.nInit = params['preStimTime']
+
+    ksolve = moose.Ksolve( mod.path + '/ksolve' )
+    stoich = moose.Stoich( mod.path + '/stoich' )
+    stoich.compartment = mod
+    stoich.ksolve = ksolve
+    stoich.path = mod.path + '/##'
+    runtime += 2 * steptime
+
+    moose.reinit()
+    moose.start( runtime )
+    t = np.arange( 0, runtime + 1e-9, tab.dt )
+    return name, t, tab.vector
+    #pylab.plot( t, tab.vector, label='[A] (mM)' )
+    
+    #pylab.show()
+
+def plotBoilerplate( panelTitle, plotPos, xlabel = ''):
+    ax = plt.subplot( 8,4,plotPos )
+    #ax.xaxis.set_ticks( i[1] )
+    #ax.locator_params( 
+    ax.spines['top'].set_visible( False )
+    ax.spines['right'].set_visible( False )
+    ax.tick_params( direction = 'out' )
+    if (((plotPos -1)/4) % 2) == 0:
+        ax.set_xticklabels([])
+    else:
+        ax.set_xlabel( xlabel )
+    for tick in ax.xaxis.get_major_ticks():
+        tick.tick2On = False
+    for tick in ax.yaxis.get_major_ticks():
+        tick.tick2On = False
+    
+    if (plotPos % 4) == 1:
+        plt.ylabel( 'conc', fontsize = 16 )
+        # alternate way of doing this separately.
+        #plt.yaxis.label.size_size(16)
+        #plt.title( 'B' )
+        ax.text( -0.3, 1, panelTitle, fontsize = 18, weight = 'bold',
+        transform=ax.transAxes )
+    return ax
+
+def plotPanelB():
+    panelB = []
+    panelBticks = []
+    panelB.append( singleCompt( 'fhn', abstrModelEqns2.makeFHN() ) )
+    panelB.append( singleCompt( 'bis', abstrModelEqns2.makeBis() ) )
+    panelB.append( singleCompt( 'negFB', abstrModelEqns2.makeNegFB() ) )
+    panelB.append( singleCompt( 'negFF', abstrModelEqns2.makeNegFF() ) )
+
+    panelBticks.append( np.arange( 0, 4.00001, 1 ) )
+    panelBticks.append( np.arange( 0, 4.00001, 1 ) )
+    panelBticks.append( np.arange( 0, 15.00001, 5 ) )
+    panelBticks.append( np.arange( 0, 6.00001, 2 ) )
+    moose.delete( '/model' )
+
+    for i in zip( panelB, panelBticks, range( len( panelB ) ) ):
+        plotPos = i[2] + 5
+        ax = plotBoilerplate( 'B', plotPos )
+        plt.plot( i[0][1], i[0][2] )
+        xmax = ax.get_xlim()[1]
+        #ax.xaxis.set_ticks( np.arange( 0, xmax, 50 ) )
+        ax.xaxis.set_ticks( np.arange( 0, 200.001, 50 ) )
+        ax.yaxis.set_ticks( i[1] )
+
+def runPanelCDEF( name, dist, seqDt, numSpine, seq, stimAmpl ):
+    preStim = 10.0
+    blanks = 20
+    rdes = rd.rdesigneur(
+        useGssa = False,
+        turnOffElec = True,
+        chemPlotDt = 0.1,
+        #diffusionLength = params['diffusionLength'],
+        diffusionLength = 1e-6,
+        cellProto = [['cell', 'soma']],
+        chemProto = [['dend', name]],
+        chemDistrib = [['dend', 'soma', 'install', '1' ]],
+        plotList = [['soma', '1', 'dend' + '/A', 'n', '# of A']],
+    )
+    rdes.buildModel()
+    #for i in range( 20 ):
+        #moose.setClock( i, 0.02 )
+    A = moose.vec( '/model/chem/dend/A' )
+    Z = moose.vec( '/model/chem/dend/Z' )
+    print moose.element( '/model/chem/dend/A/Adot' ).expr
+    print moose.element( '/model/chem/dend/B/Bdot' ).expr
+    print moose.element( '/model/chem/dend/Ca/CaStim' ).expr
+    phase = moose.vec( '/model/chem/dend/phase' )
+    ampl = moose.vec( '/model/chem/dend/ampl' )
+    vel = moose.vec( '/model/chem/dend/vel' )
+    vel.nInit = 1e-6 * seqDt
+    ampl.nInit = stimAmpl
+    stride = int( dist ) / numSpine
+    phase.nInit = 10000
+    Z.nInit = 0
+    for j in range( numSpine ):
+        k = blanks + j * stride
+        Z[k].nInit = 1
+        phase[k].nInit = preStim + seq[j] * seqDt
+    moose.reinit()
+    runtime = 50
+    snapshot = preStim + seqDt * (numSpine - 0.8)
+    print snapshot
+    #snapshot = 26
+    moose.start( snapshot )
+    avec = moose.vec( '/model/chem/dend/A' ).n
+    moose.start( runtime - snapshot )
+    tvec = []
+    for i in range( 5 ):
+        tab = moose.element( '/model/graphs/plot0[' + str( blanks + i * stride ) + ']' )
+        dt = tab.dt
+        tvec.append( tab.vector )
+    moose.delete( '/model' )
+    return dt, tvec, avec
+
+def makePassiveSoma( name, length, diameter ):
+    elecid = moose.Neuron( '/library/' + name )
+    dend = moose.Compartment( elecid.path + '/soma' )
+    dend.diameter = diameter
+    dend.length = length
+    dend.x = length
+    return elecid
+
+def plotOnePanel( tLabel, dt, tplot, numSyn, plotRange, tick ):
+    t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+    ax = plotBoilerplate( tLabel, 1 + start )
+    for i in range( 5 ):
+        plt.plot( t, tplot[i] )
+    ax.yaxis.set_ticks( np.arange( 0, plotRange, tick ) )
+
+
+def plotPanelCDEF( seq, row ):
+    makePassiveSoma( 'cell', 100e-6, 10e-6 )
+    start = (row -1) * 4
+    tLabel = chr( ord( 'A' ) + row - 1 )
+    xLabel = chr( ord( 'C' ) + row - 1 )
+    xplot = []
+    #dt, tplot, avec = runPanelCDEF( 'fhn', 15.0, 3.0, 5, seq, 0.4 )
+    dt, tplot, avec = runPanelCDEF( 'fhn', 5.0, 0.5, 5, seq, 0.4 )
+    xplot.append( avec )
+    #plotOnePanel( dt, 'B', tplot, 5, 1.5, 0.5 )
+    t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+    #ax = plotBoilerplate( tLabel, 1 + start )
+    ax = plotBoilerplate( tLabel, 1 + start, 'Time (s)')
+    for i in range( 5 ):
+        plt.plot( t, tplot[i] )
+    yl = ax.get_ylim()[1] 
+    ax.yaxis.set_ticks( np.arange( 0, 4.0001, 1.0 ) )
+
+    #dt, tplot, avec = runPanelCDEF( 'bis', 5.0, 4.0, 5, seq, 1.0 )
+    dt, tplot, avec = runPanelCDEF( 'bis', 15.0, 2.0, 5, seq, 1.0 )
+    xplot.append( avec )
+    t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+    ax = plotBoilerplate( tLabel, 2 + start, 'Time (s)' )
+    for i in range( 5 ):
+        plt.plot( t, tplot[i] )
+    yl = ax.get_ylim()[1] 
+    ax.yaxis.set_ticks( np.arange( 0, 3.0001, 1.0 ) )
+
+    dt, tplot, avec = runPanelCDEF( 'negFB', 5.0, 2.0, 5, seq, 1.0 )
+    xplot.append( avec )
+    t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+    ax = plotBoilerplate( tLabel, 3 + start, 'Time (s)')
+    for i in range( 5 ):
+        plt.plot( t, tplot[i] )
+    ax.yaxis.set_ticks( np.arange( 0, 10.00001, 5.0 ) )
+
+    dt, tplot, avec = runPanelCDEF( 'negFF', 5.0, 4.0, 5, seq, 1.0 )
+    xplot.append( avec )
+    t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+    ax = plotBoilerplate( tLabel, 4 + start, 'Time (s)')
+    for i in range( 5 ):
+        plt.plot( t, tplot[i] )
+    ax.yaxis.set_ticks( np.arange( 0, 5.00001, 2.0 ) )
+
+    for i in zip( range(4), (4.0, 3.0, 10, 4 ), (1, 1, 5, 2) ):
+        ax = plotBoilerplate( xLabel, 9 + start + i[0], 'Position( um)' )
+        plt.plot( xplot[i[0]][:50] )
+        ax.yaxis.set_ticks( np.arange( 0, i[1] * 1.0000001, i[2] ) )
+
+##################################################################
+if __name__ == '__main__':
+    moose.Neutral( '/library' )
+    moose.Neutral( '/model' )
+
+    t1 = time.time()
+    fig = plt.figure( figsize = (10,10), facecolor='white' )
+    fig.subplots_adjust( left = 0.18 )
+    plotPanelB()
+    plotPanelCDEF( [0,1,2,3,4], 3 )
+    plotPanelCDEF( [4,1,0,3,2], 4 )
+    print ("Time taken = ", time.time() - t1)
+    plt.tight_layout()
+        
+    plt.show()
+        
+        

parallelSolver/README

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+Parallel solvers are implemented for Ksolve, Dsolve and Gsolve.
+
+Instructions to run the solvers in parallel. 
+
+1) Clone the repository from github/BhallaLab/moose-core/tree/multithreaded 
+   i.e., the multithreaded branch of the moose-core. 
+
+2) Build the code, compile and run it.
+
+3) Set the environment variable NUM_THREADS to the number of threads with which you want to execute your script. 
+
+4) The environment variable has to be set to make use of the parallelization. It runs with 1 thread by default(sequential). 
+
+3) Run your python script regularly. The framwork will pick up the number of threads set by you and parallelize the solvers using them.