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GS up and running (weird output, though)
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‎examples/fenics_grayscott/playground.py‎

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@@ -1,12 +1,12 @@
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import pySDC.core.deprecated.PFASST_blockwise_old as mp
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from examples.fenics_grayscott.HookClass import fenics_output
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from examples.fenics_grayscott.ProblemClass import fenics_grayscott
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from examples.fenics_grayscott.TransferClass import mesh_to_mesh_fenics
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from pySDC.implementations.datatype_classes.fenics_mesh import fenics_mesh
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from pySDC.implementations.sweeper_classes.generic_LU import generic_LU
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from pySDC.core import CollocationClasses as collclass
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from pySDC.core import Log
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from pySDC.implementations.datatype_classes.fenics_mesh import fenics_mesh
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from pySDC.implementations.problem_classes.ProblemClass import fenics_grayscott
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from pySDC.implementations.sweeper_classes.generic_LU import generic_LU
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if __name__ == "__main__":
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‎projects/node_failure/grayscott_example.py‎

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from pySDC.core import CollocationClasses as collclass
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from examples.fenics_grayscott.ProblemClass import fenics_grayscott
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import numpy as np
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import pySDC.core.PFASST_stepwise as mp
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import pySDC.helpers.fault_tolerance as ft
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from pySDC.core.Stats import grep_stats
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from pySDC.core.datatype_classes.fenics_mesh import fenics_mesh
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from examples.fenics_grayscott.TransferClass import mesh_to_mesh_fenics
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# from examples.fenics_grayscott.HookClass import fenics_output
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from pySDC.core.sweeper_classes.generic_LU import generic_LU
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# import pySDC.PFASST_blockwise as mp
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import pySDC.core.PFASST_stepwise as mp
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from pySDC.core import Log
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from pySDC.core.Stats import grep_stats, sort_stats
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import dolfin as df
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import numpy as np
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import pySDC.helpers.fault_tolerance as ft
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from examples.fenics_grayscott.TransferClass import mesh_to_mesh_fenics
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from pySDC.core import CollocationClasses as collclass
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from pySDC.core import Log
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from pySDC.implementations.problem_classes.ProblemClass import fenics_grayscott
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if __name__ == "__main__":

‎projects/node_failure/grayscott_example_new.py‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,148 @@
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import numpy as np
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import projects.node_failure.emulate_hard_faults as ft
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from projects.node_failure.allinclusive_classic_nonMPI_hard_faults import allinclusive_classic_nonMPI_hard_faults
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from pySDC.helpers.stats_helper import filter_stats, sort_stats
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from pySDC.implementations.collocation_classes.gauss_radau_right import CollGaussRadau_Right
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from pySDC.implementations.sweeper_classes.generic_LU import generic_LU
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from pySDC.implementations.datatype_classes.fenics_mesh import fenics_mesh
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from pySDC.implementations.transfer_classes.TransferFenicsMesh import mesh_to_mesh_fenics
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from pySDC.implementations.problem_classes.GrayScott_1D_FEniCS_implicit import fenics_grayscott
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# noinspection PyShadowingNames,PyShadowingBuiltins
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def main(ft_strategies):
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"""
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This routine generates the heatmaps showing the residual for node failures at different steps and iterations
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"""
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num_procs = 32
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# setup parameters "in time"
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t0 = 0
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dt = 2.0
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Tend = 1280.0
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Nsteps = int((Tend-t0)/dt)
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# initialize level parameters
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level_params = dict()
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level_params['restol'] = 1E-07
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level_params['dt'] = dt
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# initialize step parameters
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step_params = dict()
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step_params['maxiter'] = 50
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# initialize space transfer parameters
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space_transfer_params = dict()
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space_transfer_params['finter'] = True
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# initialize sweeper parameters
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sweeper_params = dict()
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sweeper_params['collocation_class'] = CollGaussRadau_Right
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sweeper_params['num_nodes'] = [3]
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sweeper_params['QI'] = 'LU'
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# initialize controller parameters
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controller_params = dict()
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controller_params['logger_level'] = 20
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# initialize problem parameters
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problem_params = dict()
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# problem_params['Du'] = 1.0
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# problem_params['Dv'] = 0.01
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# problem_params['A'] = 0.01
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# problem_params['B'] = 0.10
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# splitting pulses until steady state
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# problem_params['Du'] = 1.0
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# problem_params['Dv'] = 0.01
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# problem_params['A'] = 0.02
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# problem_params['B'] = 0.079
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# splitting pulses until steady state
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problem_params['Du'] = 1.0
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problem_params['Dv'] = 0.01
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problem_params['A'] = 0.09
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problem_params['B'] = 0.086
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problem_params['t0'] = t0 # ugly, but necessary to set up ProblemClass
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problem_params['c_nvars'] = [256]
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problem_params['family'] = 'CG'
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problem_params['order'] = [4]
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problem_params['refinements'] = [1, 0]
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# fill description dictionary for easy step instantiation
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description = dict()
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description['problem_class'] = fenics_grayscott # pass problem class
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description['problem_params'] = problem_params # pass problem parameters
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description['dtype_u'] = fenics_mesh # pass data type for u
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description['dtype_f'] = fenics_mesh # pass data type for f
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description['sweeper_class'] = generic_LU # pass sweeper (see part B)
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description['sweeper_params'] = sweeper_params # pass sweeper parameters
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description['level_params'] = level_params # pass level parameters
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description['step_params'] = step_params # pass step parameters
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description['space_transfer_class'] = mesh_to_mesh_fenics # pass spatial transfer class
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description['space_transfer_params'] = space_transfer_params # pass paramters for spatial transfer
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ft.hard_random = 0.03
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controller = allinclusive_classic_nonMPI_hard_faults(num_procs=num_procs,
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controller_params=controller_params,
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description=description)
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# get initial values on finest level
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P = controller.MS[0].levels[0].prob
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uinit = P.u_exact(t0)
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for strategy in ft_strategies:
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print('------------------------------------------ working on strategy ', strategy)
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ft.strategy = strategy
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# read in reference data from clean run, will provide reproducable locations for faults
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if strategy is not 'NOFAULT':
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reffile = np.load('data/PFASST_GRAYSCOTT_stats_hf_NOFAULT_P16.npz')
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ft.refdata = reffile['hard_stats']
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# call main function to get things done...
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uend, stats = controller.run(u0=uinit, t0=t0, Tend=Tend)
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# get residuals of the run
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extract_stats = filter_stats(stats, type='residual_post_iteration')
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# find boundaries for x-,y- and c-axis as well as arrays
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maxprocs = 0
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maxiter = 0
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minres = 0
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maxres = -99
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for k, v in extract_stats.items():
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maxprocs = max(maxprocs, getattr(k, 'process'))
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maxiter = max(maxiter, getattr(k, 'iter'))
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minres = min(minres, np.log10(v))
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maxres = max(maxres, np.log10(v))
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# grep residuals and put into array
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residual = np.zeros((maxiter, maxprocs + 1))
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residual[:] = -99
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for k, v in extract_stats.items():
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step = getattr(k, 'process')
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iter = getattr(k, 'iter')
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if iter is not -1:
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residual[iter - 1, step] = np.log10(v)
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# stats magic: get niter (probably redundant with maxiter)
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extract_stats = filter_stats(stats, level=-1, type='niter')
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sortedlist_stats = sort_stats(extract_stats, sortby='process')
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iter_count = np.zeros(Nsteps)
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for item in sortedlist_stats:
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iter_count[item[0]] = item[1]
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print(iter_count)
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np.savez('data/PFASST_GRAYSCOTT_stats_hf_' + ft.strategy + '_P' + str(num_procs), residual=residual,
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iter_count=iter_count, hard_stats=ft.hard_stats)
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if __name__ == "__main__":
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# ft_strategies = ['SPREAD', 'SPREAD_PREDICT', 'INTERP', 'INTERP_PREDICT']
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ft_strategies = ['NOFAULT']
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main(ft_strategies=ft_strategies)

‎pySDC/implementations/datatype_classes/fenics_mesh.py‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -30,12 +30,16 @@ def __init__(self, init=None, val=0.0):
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self.values = df.Function(init.V, init.values)
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self.V = init.V
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# if init is a number or a tuple of numbers, create mesh object with val as initial value
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elif isinstance(init, df.FunctionSpace):
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else:
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self.values = df.Function(init)
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self.V = init
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# (FIXME: cannot define type of functionspace)
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# elif isinstance(init, type(df.FunctionSpace)):
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# self.values = df.Function(init)
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# self.V = init
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# something is wrong, if none of the ones above hit
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else:
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raise DataError('something went wrong during %s initialization' % type(self))
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# else:
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# raise DataError('something went wrong during %s initialization' % type(init))
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def __add__(self, other):
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"""

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