Fixed adaptivity notebook

Author: Thomas Baumann

pySDC/implementations/hooks/log_errors.py

@@ -24,7 +24,7 @@ def post_step(self, step, level_number):
             iter=step.status.iter,
             sweep=L.status.sweep,
             type='e_global',
-            value=abs(L.prob.u_exact(t=L.time + L.dt) - L.u[-1]),
+            value=abs(L.prob.u_exact(t=L.time + L.dt) - L.uend),
         )
 
 
@@ -51,5 +51,5 @@ def post_step(self, step, level_number):
             iter=step.status.iter,
             sweep=L.status.sweep,
             type='e_local',
-            value=abs(L.prob.u_exact(t=L.time + L.dt, u_init=L.u[0], t_init=L.time) - L.u[-1]),
+            value=abs(L.prob.u_exact(t=L.time + L.dt, u_init=L.u[0], t_init=L.time) - L.uend),
         )

pySDC/projects/Resilience/Adaptivity.ipynb

@@ -3,21 +3,20 @@
 from pySDC.implementations.problem_classes.AdvectionEquation_ND_FD import advectionNd
 from pySDC.implementations.sweeper_classes.generic_implicit import generic_implicit
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
-from pySDC.core.Hooks import hooks
 from pySDC.helpers.stats_helper import get_sorted
 import numpy as np
-from pySDC.projects.Resilience.hook import log_data, hook_collection
+from pySDC.projects.Resilience.hook import LogData, hook_collection
 from pySDC.projects.Resilience.fault_injection import prepare_controller_for_faults
 
 
 def plot_embedded(stats, ax):
     u = get_sorted(stats, type='u', recomputed=False)
     uold = get_sorted(stats, type='uold', recomputed=False)
-    t = [get_sorted(stats, type='u', recomputed=False)[i][0] for i in range(len(u))]
-    e_em = np.array(get_sorted(stats, type='e_embedded', recomputed=False))[:, 1]
+    t = [me[0] for me in u]
+    e_em = get_sorted(stats, type='error_embedded_estimate', recomputed=False)
     e_em_semi_glob = [abs(u[i][1] - uold[i][1]) for i in range(len(u))]
     ax.plot(t, e_em_semi_glob, label=r'$\|u^{\left(k-1\right)}-u^{\left(k\right)}\|$')
-    ax.plot(t, e_em, linestyle='--', label=r'$\epsilon$')
+    ax.plot([me[0] for me in e_em], [me[1] for me in e_em], linestyle='--', label=r'$\epsilon$')
     ax.set_xlabel(r'$t$')
     ax.legend(frameon=False)
 
@@ -26,7 +25,7 @@ def run_advection(
     custom_description=None,
     num_procs=1,
     Tend=2e-1,
-    hook_class=log_data,
+    hook_class=LogData,
     fault_stuff=None,
     custom_controller_params=None,
     custom_problem_params=None,
@@ -100,3 +99,26 @@ def run_advection(
     # call main function to get things done...
     uend, stats = controller.run(u0=uinit, t0=t0, Tend=Tend)
     return stats, controller, Tend
+
+
+if __name__ == '__main__':
+    import matplotlib.pyplot as plt
+    from pySDC.implementations.convergence_controller_classes.adaptivity import Adaptivity
+    from pySDC.projects.Resilience.hook import LogUold
+
+    adaptivity_params = dict()
+    adaptivity_params['e_tol'] = 1e-8
+
+    convergence_controllers = dict()
+    convergence_controllers[Adaptivity] = adaptivity_params
+
+    description = dict()
+    description['convergence_controllers'] = convergence_controllers
+
+    fig, axs = plt.subplots(1, 2, figsize=(12, 4), sharex=True, sharey=True)
+    plot_embedded(run_advection(description, 1, hook_class=LogUold)[0], axs[0])
+    plot_embedded(run_advection(description, 4, hook_class=LogUold)[0], axs[1])
+    axs[0].set_title('1 process')
+    axs[1].set_title('4 processes')
+    fig.tight_layout()
+    plt.show()

pySDC/projects/Resilience/advection.py

@@ -8,7 +8,7 @@
 import pySDC.helpers.plot_helper as plot_helper
 from pySDC.helpers.stats_helper import get_sorted
 
-from pySDC.projects.Resilience.hook import hook_collection, LogUAllIter
+from pySDC.projects.Resilience.hook import hook_collection, LogUAllIter, LogData
 from pySDC.projects.Resilience.fault_injection import get_fault_injector_hook
 from pySDC.implementations.convergence_controller_classes.hotrod import HotRod
 from pySDC.implementations.convergence_controller_classes.adaptivity import Adaptivity
@@ -490,7 +490,7 @@ def generate_stats(self, strategy=None, runs=1000, reload=True, faults=True):
 
         return None
 
-    def single_run(self, strategy, run=0, faults=False, force_params=None, hook_class=hook_collection):
+    def single_run(self, strategy, run=0, faults=False, force_params=None, hook_class=None):
         '''
         Run the problem once with the specified parameters
 
@@ -505,6 +505,7 @@ def single_run(self, strategy, run=0, faults=False, force_params=None, hook_clas
             pySDC.Controller: The controller of the run
             float: The time the problem should have run to
         '''
+        hook_class = hook_collection + [LogData] if hook_class is None else hook_class
         force_params = {} if force_params is None else force_params
 
         # build the custom description
@@ -653,6 +654,7 @@ def scrutinize(self, strategy, run, faults=True):
 
         t, u = get_sorted(stats, type='u')[-1]
         k = [me[1] for me in get_sorted(stats, type='k')]
+        print(k)
 
         print(f'\nOverview for {strategy.name} strategy')
 
@@ -1089,7 +1091,10 @@ def analyse_adaptivity_single(self, run):
         t_fault = get_sorted(stats[0], type='bitflip')[0][0]
 
         # get embedded error
-        e_em = [[me[1] for me in get_sorted(stat, type='e_em', time=t_fault, sortby='iter')] for stat in stats]
+        e_em = [
+            [me[1] for me in get_sorted(stat, type='error_embedded_estimate', time=t_fault, sortby='iter')]
+            for stat in stats
+        ]
 
         # compute the global error
         u_end = [get_sorted(stat, type='u')[-1] for stat in stats]
@@ -1159,9 +1164,15 @@ def analyse_HotRod_single(self, run):
         t_fault = get_sorted(stats[0], type='bitflip')[0][0]
 
         # get embedded error
-        e_em = [[me[1] for me in get_sorted(stat, type='e_em', time=t_fault, sortby='iter')] for stat in stats]
+        e_em = [
+            [me[1] for me in get_sorted(stat, type='error_embedded_estimate', time=t_fault, sortby='iter')]
+            for stat in stats
+        ]
         # get extrapolated error
-        e_ex = [[me[1] for me in get_sorted(stat, type='e_ex', time=t_fault, sortby='iter')] for stat in stats]
+        e_ex = [
+            [me[1] for me in get_sorted(stat, type='error_extrapolation_estimate', time=t_fault, sortby='iter')]
+            for stat in stats
+        ]
 
         # compute the global error
         u_end = [get_sorted(stat, type='u')[-1] for stat in stats]

pySDC/projects/Resilience/fault_stats.py

@@ -5,15 +5,15 @@
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
 from pySDC.core.Hooks import hooks
 from pySDC.helpers.stats_helper import get_sorted
-from pySDC.projects.Resilience.hook import hook_collection, log_data
+from pySDC.projects.Resilience.hook import hook_collection, LogData
 import numpy as np
 
 
 def run_heat(
     custom_description=None,
     num_procs=1,
     Tend=2e-1,
-    hook_class=log_data,
+    hook_class=LogData,
     fault_stuff=None,
     custom_controller_params=None,
     custom_problem_params=None,

pySDC/projects/Resilience/heat.py

@@ -8,7 +8,7 @@
 hook_collection = [LogSolution, LogEmbeddedErrorEstimate, LogExtrapolationErrorEstimate, LogStepSize]
 
 
-class log_data(hooks):
+class LogData(hooks):
     """
     Record data required for analysis of problems in the resilience project
     """
@@ -34,7 +34,7 @@ def post_step(self, step, level_number):
             process=step.status.slot,
             time=L.time,
             level=L.level_index,
-            iter=0,
+            iter=step.status.iter,
             sweep=L.status.sweep,
             type='restart',
             value=int(step.status.get('restart')),
@@ -52,6 +52,26 @@ def post_step(self, step, level_number):
             )
 
 
+class LogUold(hooks):
+    """
+    Log last iterate at the end of the step. Since the hook comes after override of uold, we need to do this in each
+    iteration. But we don't know which will be the last, so we just do `iter=-1` to override the previous value.
+    """
+
+    def post_iteration(self, step, level_number):
+        super().post_iteration(step, level_number)
+        L = step.levels[level_number]
+        self.add_to_stats(
+            process=step.status.slot,
+            time=L.time + L.dt,
+            level=L.level_index,
+            iter=-1,
+            sweep=L.status.sweep,
+            type='uold',
+            value=L.uold[-1],
+        )
+
+
 class LogUAllIter(hooks):
     """
     Log solution and errors after each iteration
@@ -68,7 +88,7 @@ def post_iteration(self, step, level_number):
             process=step.status.slot,
             time=L.time,
             level=L.level_index,
-            iter=iter,
+            iter=step.status.iter,
             sweep=L.status.sweep,
             type='u',
             value=L.uend,
@@ -77,17 +97,17 @@ def post_iteration(self, step, level_number):
             process=step.status.slot,
             time=L.time,
             level=L.level_index,
-            iter=iter,
+            iter=step.status.iter,
             sweep=L.status.sweep,
-            type='e_em',
+            type='error_embedded_estimate',
             value=L.status.get('error_embedded_estimate'),
         )
         self.add_to_stats(
             process=step.status.slot,
             time=L.time,
             level=L.level_index,
-            iter=iter,
+            iter=step.status.iter,
             sweep=L.status.sweep,
-            type='e_ex',
+            type='error_extrapolation_estimate',
             value=L.status.get('error_extrapolation_estimate'),
         )

pySDC/projects/Resilience/hook.py

@@ -7,14 +7,14 @@
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
 from pySDC.implementations.convergence_controller_classes.adaptivity import Adaptivity
 from pySDC.implementations.convergence_controller_classes.hotrod import HotRod
-from pySDC.projects.Resilience.hook import log_data, hook_collection
+from pySDC.projects.Resilience.hook import LogData, hook_collection
 
 
 def run_piline(
     custom_description=None,
     num_procs=1,
     Tend=20.0,
-    hook_class=log_data,
+    hook_class=LogData,
     fault_stuff=None,
     custom_controller_params=None,
     custom_problem_params=None,

pySDC/projects/Resilience/piline.py

@@ -8,7 +8,7 @@
 from pySDC.implementations.controller_classes.controller_nonMPI import controller_nonMPI
 from pySDC.implementations.convergence_controller_classes.adaptivity import Adaptivity
 from pySDC.core.Errors import ProblemError
-from pySDC.projects.Resilience.hook import log_data, hook_collection
+from pySDC.projects.Resilience.hook import LogData, hook_collection
 
 
 def plot_step_sizes(stats, ax):
@@ -85,7 +85,7 @@ def run_vdp(
     custom_description=None,
     num_procs=1,
     Tend=10.0,
-    hook_class=log_data,
+    hook_class=LogData,
     fault_stuff=None,
     custom_controller_params=None,
     custom_problem_params=None,

pySDC/projects/Resilience/vdp.py

@@ -162,8 +162,7 @@ def test_fault_stats():
     for strategy in vdp_stats.strategies:
         dat = vdp_stats.load(strategy, True)
         recovered = len(dat['recovered'][dat['recovered'] == True])
-        crashed = len(dat['error'][dat['error'] == np.inf])
-        print(strategy.name, dat['recovered'], dat['error'])
+        crashed = len(dat['error'][dat['error'] == np.inf])  # on some systems the last run crashes...
         assert (
             recovered >= recovered_reference[strategy.name] - crashed
         ), f'Expected {recovered_reference[strategy.name]} recovered faults, but got {recovered} recovered faults in {strategy.name} strategy!'