Merge branch 'error_est'

Author: pancetta

.travis.yml

@@ -23,15 +23,12 @@ before_install:
 
 install:
   - conda install --yes -c conda-forge --file requirements.txt
-#  - conda install --yes -c conda-forge mpich-mpicc petsc4py mpi4py fenics=2018.1.0 mpi4py-fft
-#  - conda install --yes scipy matplotlib dill numba
-#  - conda install --yes pip nose pep8 coverage sphinx=1.8.5
   - conda list
-  - pip install travis-sphinx
+  - pip install travis-sphinx nose-timer
 
 script:
   - "./docs/update_apidocs.sh"
-  - nosetests -v --with-coverage --cover-erase --cover-inclusive --cover-package=pySDC/core,pySDC/implementations,pySDC/helpers,pySDC/tutorial,pySDC/projects --cover-html --cover-html-dir=doc/build/test_coverage pySDC/tests
+  - nosetests -v --with-timer --with-coverage --cover-erase --cover-inclusive --cover-package=pySDC/core,pySDC/implementations,pySDC/helpers,pySDC/tutorial,pySDC/projects --cover-html --cover-html-dir=doc/build/test_coverage pySDC/tests
   - travis-sphinx build
 
 after_success:

CHANGELOG.rst

@@ -1,6 +1,12 @@
 Changelog
 ---------
 
+- August 30, 2019: Version 3.1 adds many more examples like the nonlinear Schrödinger equation, more on Gray-Scott and in particular Allen-Cahn.
+  Those are many implemented using the parallel FFT library `mpi4pi-fft <https://bitbucket.org/mpi4py/mpi4py-fft/src/master/>`_, which can now be used with pySDC.
+  There are now 8 tutorials, where step 7 shows the usage of three external libraries with pySDC: mpi4py, FEniCS and petsc4py.
+  The MPI controller has been improved after performaning a detailed performance analysis using `Score-P <https://www.vi-hps.org/projects/score-p/>`_ and `Extrae <https://www.vi-hps.org/Tools/Extrae.html>`_.
+  Finally: first steps towards error/iteration estimators are taken, too.
+
 - February 14, 2019: Released version 3 of `pySDC`. This release is accompanied by the **ACM TOMS paper**
   `"pySDC --  Prototyping spectral deferred corrections" <https://doi.org/10.1145/3310410>`_.
   It release contains some breaking changes to the API. In detail:

README.rst

@@ -13,7 +13,7 @@ Features
 - 7 tutorials: from setting up a first collocation problem to SDC, PFASST and advanced topics
 - Projects: many documented projects with defined and tested outcomes
 - Many different examples, collocation types, data types already implemented
-- Works with `PETSc <http://www.mcs.anl.gov/petsc/>`_ through `petsc4py <https://bitbucket.org/petsc/petsc4py>`_ and `FEniCS <https://fenicsproject.org/>`_
+- Works with `PETSc <http://www.mcs.anl.gov/petsc/>`_ through `petsc4py <https://bitbucket.org/petsc/petsc4py>`_ , `FEniCS <https://fenicsproject.org/>`_ and `mpi4py-fft <https://mpi4py-fft.readthedocs.io/en/latest/>`_
 - Continuous integration via `Travis-CI <https://travis-ci.org/Parallel-in-Time/pySDC>`_
 - Fully compatible with 3.6 (or higher)
 

docs/source/index.rst

@@ -17,6 +17,7 @@ Tutorial
    tutorial/step_5.rst
    tutorial/step_6.rst
    tutorial/step_7.rst
+   tutorial/step_8.rst
 
 Playgrounds
 -----------

docs/source/tutorial/doc_step_7_A.rst

@@ -1,10 +1,7 @@
-Full code: `pySDC/tutorial/step_7/A_visualize_residuals.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/A_visualize_residuals.py>`_
+Full code: `pySDC/tutorial/step_7/A_pySDC_with_FEniCS.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/A_pySDC_with_FEniCS.py>`_
 
-.. literalinclude:: ../../../pySDC/tutorial/step_7/A_visualize_residuals.py
+.. literalinclude:: ../../../pySDC/tutorial/step_7/A_pySDC_with_FEniCS.py
 
 Results:
 
-.. literalinclude:: ../../../step_7_A_out.txt
-
-.. image:: ../../../step_7_residuals.png
-   :scale: 50 %
+.. literalinclude:: ../../../step_7_A_out.txt

docs/source/tutorial/doc_step_7_B.rst

@@ -1,13 +1,7 @@
-Full code: `pySDC/tutorial/step_7/B_multistep_SDC.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/B_multistep_SDC.py>`_
+Full code: `pySDC/tutorial/step_7/B_pySDC_with_mpi4pyfft.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/B_pySDC_with_mpi4pyfft.py>`_
 
-.. literalinclude:: ../../../pySDC/tutorial/step_7/B_multistep_SDC.py
+.. literalinclude:: ../../../pySDC/tutorial/step_7/B_pySDC_with_mpi4pyfft.py
 
 Results:
 
-.. literalinclude:: ../../../step_7_B_out.txt
-
-.. image:: ../../../step_7_residuals_mssdc_jac.png
-   :scale: 50 %
-
-.. image:: ../../../step_7_residuals_mssdc_gs.png
-   :scale: 50 %
+.. literalinclude:: ../../../step_7_B_out.txt

docs/source/tutorial/doc_step_8_A.rst

@@ -0,0 +1,10 @@
+Full code: `pySDC/tutorial/step_8/A_visualize_residuals.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_8/A_visualize_residuals.py>`_
+
+.. literalinclude:: ../../../pySDC/tutorial/step_8/A_visualize_residuals.py
+
+Results:
+
+.. literalinclude:: ../../../step_8_A_out.txt
+
+.. image:: ../../../step_8_residuals.png
+   :scale: 50 %

docs/source/tutorial/doc_step_8_B.rst

@@ -0,0 +1,13 @@
+Full code: `pySDC/tutorial/step_8/B_multistep_SDC.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_8/B_multistep_SDC.py>`_
+
+.. literalinclude:: ../../../pySDC/tutorial/step_8/B_multistep_SDC.py
+
+Results:
+
+.. literalinclude:: ../../../step_8_B_out.txt
+
+.. image:: ../../../step_8_residuals_mssdc_jac.png
+   :scale: 50 %
+
+.. image:: ../../../step_8_residuals_mssdc_gs.png
+   :scale: 50 %

docs/source/tutorial/doc_step_8_C.rst

@@ -0,0 +1,7 @@
+Full code: `pySDC/tutorial/step_8/C_iteration_estimator.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_8/C_iteration_estimator.py>`_
+
+.. literalinclude:: ../../../pySDC/tutorial/step_8/C_iteration_estimator.py
+
+Results:
+
+.. literalinclude:: ../../../step_8_C_out.txt

docs/source/tutorial/step_8.rst

@@ -0,0 +1 @@
+.. include:: /../../pySDC/tutorial/step_8/README.rst